Macs in Chemistry

Insanely great science

Mac OS X Applications A-C

Aabel :- Data Analysis

Aabel is a new, and recently updated high performance data management, processing, & charting application for Mac OS X. It provides a superb visual front-end to high-performance statistical data analysis. It has over 200 data presentation styles and is capable of handling very large data sets. There is a review of Aabel 3.0 here.
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Abinit :- Density Functional Theory

Abinit is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). In addition to the main ABINIT code, different utility programs are provided

ACPC:- Virtual screening of molecules using electrostatics

 

A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening Francois Berenger, Arnout Voet, Xiao Yin Lee and Kam YJ Zhang Journal of Cheminformatics 2014, 6:23 doi

Measures of similarity for chemical molecules have been developed since the dawn of chemoinformatics. Molecular similarity has been measured by a variety of methods including molecular descriptor based similarity, common molecular fragments, graph matching and 3D methods such as shape matching. Similarity measures are widespread in practice and have proven to be useful in drug discovery. Because of our interest in electrostatics and high throughput ligand-based virtual screening, we sought to exploit the information contained in atomic coordinates and partial charges of a molecule.

I've written instructions for installing ACPC on a Mac

ADF2016 :- Density Functional Theory

ADF is an accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT). Heavy elements and transition metals are accurately modeled with ADF's reliable relativistic ZORA approach and all-electron basis sets for the whole periodic table (H-Uuo). A vast range of spectroscopic properties and comprehensive analysis tools yield invaluable insight in chemical structure and reactivity. DFT calculations are easily prepared and analyzed with our GUI. Key benefits and features of ADF: • Relativity: ZORA scalar relativistic and spin-orbit coupling • All-electron basis sets for Z=1-118: no artifacts from ECPs • Spectroscopy: NMR, UV/Vis, IR, Raman, X-ray, ESR, CD, Mössbauer, ... • Many chemical analysis tools: fragments, energy decomposition, ETS-NOCV, (P)DOS, AIM, ELF, NCI, SEDD, NBO • XC functionals: GGA, (range separated) hybrid, (hybrid)metaGGA, dispersion-corrected (D3-BJ, dDsC), model xc • Environment: solvation (COSMO, 3D-RISM, SCRF, FDE), proteins (QM/MM, QUILD), nano-particles (DIM/QM) • Modeling organic electronics: charge mobility (transfer integral, NEGF), phosphorescence lifetimes • Scripting to prepare & analyze multiple jobs, PyMD for complex MD jobs • Robust SCF and geometry optimization algorithms; excited state optimization with TDDFT • Efficiently parallelized with linear scaling techniques

Details on the latest update https://www.scm.com/support/release-notes/

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Adun:- Biomolecular Simulation

Adun is a free biomolecular simulator developed at the Computational Biophysics and Biochemistry Laboratory, a part of the Research Unit on Biomedical Informatics of the UPF. It is distributed under the GNU General Public License.

AFITT:- Fully automated ligand fitting

AFITT from OpenEye is the only software to offer a fully automatic ligand fitting process that optimizes a real-space fit to density while keeping conformational strain to a minimum. It capitalizes on a combination of core technologies that OpenEye has developed, specifically conformer generation, shape potential, high quality small molecule structure minimization, and visualization. The key step, after finding the appropriate conformers and aligning them to density, is the implementation of a refinement that combines force field and shape potentials, via a series of adiabatic optimizations [1].
The AFITT distribution includes both a GUI and a collection of command-line applications. The GUI allows users to interactively perform automatic ligand-fitting, and refinement dictionary generation. In addition, the command-line tools provide a powerful means for integration and automation, which is critical in the application of high-throughput crystallography for drug discovery.
afitt1 Pasted Graphic

[1] Wlodek, S., Skillman, A. G. and Nicholls, A., Acta Cryst. D, 2006, 62, 741.

AIMAII:- package for performing quantitative and visual QTAIM

AIMAll is a software package for performing quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems - starting from molecular wavefunction data. Two of AIMAll's components (AIMExt and AIMInt) are very heavily modified and extended derivatives of two programs (Extreme and ProaimV) from the AIMPAC package that was developed and maintained by members of Richard F.W. Bader's research group. The initial goal for AIMAll was to make a QTAIM package that was:

  • Easy to use, essentially automatic
  • Rigorous
  • Accurate
  • Reliable
  • Robust
  • Relatively fast and efficient
  • Able to calculate a rich variety of properties of interest
  • Able to produce a descriptive consolidation of all important results

Once this goal was reasonably close to being achieved, work on AIMAll accelerated, including extensive work on a visualization component (AIMStudio) and shared memory multi-processor support for AIMAll calculations.  Visualization and shared memory multi-processor support have recently been added to the AIMAll package.  These features require an AIMAll Professional license in order to be used with non-small wavefunctions. AIMAll is actively developed to address any issues which may arise, to expand upon existing features and algorithms and to implement new features and algorithms. AIMAll is available for Windows, Mac OS X and Linux.

Alchemia:- iPhone molecular weight calculator

Comprehensive molecular weight calculator
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Align-it:- Pharmacophore based alignment tool

Align-it™ is a pharmacophore-based tool to align small molecules. The tool is based on the concept of modeling pharmacophoric features by Gaussian 3D volumes instead of the more common point or sphere representations. The smooth nature of these continuous functions has a beneficent effect on the optimisation problem introduced during alignment.

ALOGPS 2.1 :- LogP and LogS prediction

The ALOGPS 2.1 Applet provides interactive on-line prediction of logP, water solubility and pKa(s) of compounds for drug design (ADME/T and HTS) and environmental chemistry studies. In addition to the ALOGPS 2.1 logP and logW it also displays values calculated with Interactive Analysis LogP and LogW, Pharma Algorithms LogP, LogW and pKa, COSMOfrag logP, Quantum Pharmaceuticals QlogP, Molinspiration logP, KOWWIN logP and XLOGP programs. The requests are sent to the corresponding servers and the results are displayed in the applet. A standalone version of ALOGPS is also available for MacOSX, Linux and Windows platforms from the Virtual Computational Chemistry Laboratory site.

AMBER :- Biomolecular force field

 

Version 16 of the Amber software suitehas been released

  • Force fields: Amber has two new fixed-charge protein force fields, ff14SB and ff14ipq, a new modular lipid force field, Lipid14, and updates to nucleic acid and carbohydrate force fields.
  • Improved options for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
  • A completely reorganized Reference Manual
  • QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available
  • More features from sander have been added to pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx GPUs.
  • Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations, and a new absolute free energy method.
  • New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

AMBERTools :- Tools to aid working with AMBER

 

Amber Tools have also been updated.

Among the new features in AmberTools16:

  • The sander module, our workhorse simulation program, is now a part of AmberTools;
  • Greatly expanded and improved cpptraj program for analyzing trajectories;
  • new documentation and tools for inspecting and modifying Amber parameter files;
  • Improved workflow for setting up and analyzing simulations;
  • new capability for semi-empirical Born-Oppenheimer molecular dynamics;
  • EMIL: a new absolute free energy method using TI;
  • New Free Energy Workflow (FEW) tool automates free energy calculations (LIE, TI, and MM/PBSA-type calculations);
  • Completely reorganized Reference Manual

AMBIT :-Chemoinformatics system

AmbitDiscovery is part of the AMBIT project, a software for chemoinformatic data management, is an outcome of the LRI project: ‘Building blocks for a future (Q)SAR ((Quantitative) Structure Activity Relationship) decision support system. Since the software goal is to support decisions, including chemical grouping and QSAR applicability domain appraisal, the name AMBIT was chosen meaning ‘an area in which something acts or operates or has power or control’. The AMBIT software is available online and as a stand-alone application for beta testing. AmbitDiscovery is an user-friendly stand alone open source Java application, which estimates applicability domain of QSAR models by various methods, it uses the CDK for structure visualisation and seems to function fine under Mac OS X.

The full AMBIT data management system has a modular structure and is implemented in two versions: stand-alone and web-based (http://ambit.acad.bg ). It is written in Java to be platform independent and its cheminformatics functionality relies on the open source Java library – The Chemistry Development Kit. The database uses the MySQLdatabase, an open source relational database for speed and convenient access to disparate data sources. The chemical structures are stored in Chemical Markup Language (CML) the acknowledged method of encoding chemical data in XML. The choice of CML as the internal format makes the database independent of the software that is able to access it. Whilst it has not been tested on Mac OS X the developers would be very keen to hear about peoples experiences and seem very responsive.

AMMOS:- Minimisation of protein ligand complexes

AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening) [1] employs an automatic procedure for energy minimization of protein-ligands complexes (package AMMOS_ProtLig) or of small chemical compounds present in a library (package AMMOS_SmallMol). As such, the software offers valuable solutions to assist structure-based in silico screening experiments or ligand-based projects. The package makes use of molecular mechanics concepts and is based on the program AMMP [2-3], available under GNU license (http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html). AMMOS has been developed in the INSERM – University Paris Diderot, lab. Bioinformatics-MTI (http://www.vls3d.com/). The package AMMOS is written in C and Python and is available for Linux and Mac OS X systems under the GNU General Public license.


References

1. Pencheva T., D. Lagorce, I. Pajeva, B.O. Villoutreix, M.A. Miteva. AMMOS: Automated
Molecular Mechanics Optimization tool for in silico Screening.
2. Harrison R., C. Reed, I. Weber. Analysis of Comparative Modeling Predictions for
CASP2 Targets 1, 3, 9, and 17. Proteins: Structure, Function, and Genetics, 1997, Suppl.
1, 68-73
3. Weber I., R. Harrison. Molecular Mechanics Calculations on Protein–Ligand Complexes.
Perspectives in Drug Discovery and Design, 1998, 9/10/11, 115-127
4. Sperandio O., M.A. Miteva, F. Delfaud, B.O. Villoutreix. Receptor-Based Computational
Screening of Compound Databases: The Main Docking-Scoring Engine. Current Protein
and Peptide Science, 2006, 7, 369-393
5. Miteva M.A., W.H. Lee, M.O. Montes, B.O. Villoutreix. Fast Structure-Based Virtual
Ligand Screening Combining FRED, DOCK, and Surflex. Journal of Medicinal
Chemistry, 2005, 48, 6012-6022
6. Sauton N., D. Lagorce, B.O. Villoutreix, M.A. Miteva. MS-DOCK: Accurate multiple
conformation generator and rigid docking protocol for multi-step virtual ligand screening.
BMC Bioinformatics, 2008, 9:184
7. Bagossi P., G. Zahuczky, J. Tözsér, I. Weber, R. Harrison. Improved Parameters for
Generating Partial Charges: Correlation with Observed Dipole Moments, Journal of
Molecular Modeling, 1999, 5, 143-152

APBS :- Calculate Electrostatics

Adaptive Poisson-Boltzmann Solver (APBS) -- Software for evaluating the electrostatic properties of nanoscale biomolecular systems
APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:
  • simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics,
  • implicit solvent molecular dynamics of biomolecules,
  • solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design,
  • and biomolecular titration studies

ARChem:- Synthetic route design

ARChem is a web-based tool for the design of synthetic routes

• Automated extraction of chemical reaction rules from on-line chemical reaction databases (such as MOS and ChemInform from Accelrys, Reaxys from Elsevier,  etc.)
• Easy integration with electronic notebooks, i.e. capability to extract rules from documented inhouse synthetic expertise.
• Easy plug-in of any starting material database with catalog numbers (e.g. Aldrich, Acros, Alfa Aesar etc.), as well as updated on a regular basis when the suppliers release a new version of their catalogues
• Exhaustive and systematic retrosynthetic search from a target compound to readily available starting materials.
• Capability to identify published synthetic routes for novel drug-like compounds
• Routes sorted according to a merit ranking
• Every step on the route is illustrated with examples from the literature according to the reactions suggested.
• User  friendly,  web-based front end, example using "Zatosetron" drug molecule as the target:

ARP/wARP:- software project for automated protein model building

ARP/wARP is a software project for automated protein model building and structure refinement. It is based on a unified approach to the structure solution process. It combines electron density interpretation using the concept of the hybrid model, pattern recognition in an electron density map and maximum likelihood model parameter refinement with REFMAC.

AstexViewer :- Java molecule viewer

AstexViewer A Java molecular graphics program that assists in structure based drug design for viewing small molecules and macromolecules such as PDB files. It can be used as an Applet in a web page with web page controls and as a desktop application.

The following pages from the Astex websiteshow examples of the use of AstexViewer™ for displaying protein/ligand complexes.

  • An applet using the internal Java graphical user interface.

  • An applet using HTML and Javascript controls.

  • An example that displays multiple structures.

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Aten:- Molecular editor for building periodic systems

Aten is a tool for computational chemists, molecular dynamicists, or other poor souls who find themselves wondering if there is an easier way to create and edit the suitable atomic configurations they need, be it for the purposes of their research. More so, Aten was created for those who wonder if there is tool that can handle periodic systems well. At the time of Aten's inception the answer was, in my opinion, 'No'. Aten attempts to at least partially fill this void.

Aten can:
  • Edit molecules and multi-molecule configurations, or build them from scratch
  • Handle periodic configurations such as crystals and condensed phases such as liquids
  • Handle several crystal formats, and can replicate and scale unit cells
  • Render other primitive object types, as well as surface/gridded data
  • Be fully scripted / automated
  • Import/export coordinates in the format of your choice with its Filters system
  • Run on Linux, Mac, and Windows
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Atomic Dashboard

The Atomic Dashboard features an interactive periodic table that lets you explore the chemical elements -- their properties, periodic trends, history, and relevance to society. And more exciting, with its new 3D Molecule Library and its physics-based, 3D models of atomic orbitals, molecules, compounds, gases, and crystals, you can explore the relationships between the behavior of atoms and molecules and their 3D structure.
atomDash

Atom in a Box :- Visualise atomic orbitals

Atom in a box a scientific and educational program that aids in visualizing the Hydrogenic atomic orbitals, a prime and otherwise unwieldy example of quantum mechanics.
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Atomic Mac :- Periodic table

Atomic Mac A periodic table of elements. In addition to the usual information found in such programs, The Atomic Mac also contains a wealth of nuclear information on each isotope, including half life, decay mode, and daughter products.
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AtVol :-Atomic vol calculation

AtVol performs atomic volume calculations by separating each atom from neighboring atoms where their van der Waals spheres join and performing Monte Carlo integration to estimate the volume

AutoDock :- Docking tool

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Updated to version 4 August 2007.
AutoDock actually consists of three separate programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid pre-calculates these grids; and AutoTors sets up which bonds will treated as rotatable in the ligand. This now includes the graphical front-end of AutoDock and AutoGrid, called AutoDockTools (ADT) for Mac OS X.
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AutoDock Vina:- Docking

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott, Arthur J. Olson


Department of Molecular Biology, The Scripps Research Institute, La Jolla, California

Abstract
AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user

The software can be downloaded from here.
AutoDock Vina

Avogadro:- Advanced molecule editor

Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Windows, Linux and Mac OS X. The source code source is available under the GNU GPLv2.

This release highlights a great deal of new features, including a built-in crystal library, crystallographic editing, building slabs / surfaces with arbitrary Miller planes, support for Abinit (and soon Quantum Espresso), searching for IUPAC names in PubChem, custom atomic colors and radii, and much more.

See the Release Notes: http://avogadro.openmolecules.net/wiki/Avogadro_1.1.0

What does Avogadro do?

  • We've tried to make the best, most intuitive "builder," including common fragments, downloading directly from PDB or PubChem, and peptide sequences
  • Innovative "auto-optimize" tool which allows you to continue to build and modify, during molecular mechanics optimization
  • Interfaces to many common computational packages
  • Designed to help both educational users and advanced research
  • Plugins that allow Avogadro to be extended and customized
  • Well defined public API, library and Python bindings for development
  • Embedded Python interpreter
  • Translations available in 19+ languages

For more information: http://avogadro.openmolecules.net/wiki/

Balloon :- 3D structure generation

Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm. The input can be SMILES, SDF or MOL2 format. Output is SDF or MOL2. Flexibility of aliphatic rings and stereochemistry about double bonds and tetrahedral chiral atoms is handled.
Mikko J. Vainio and Mark S. Johnson (2007) Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm.
Journal of Chemical Information and Modeling, 47, 2462 - 2474.

Biscu-it:- Python wrapper for RDKit

Biscu-it™ is a collection of - hopefully - useful Python tools and functions that have been built on top of the RDKit chemoinformatics toolkit and that have been wrapped in a single Python package called Biscu-it™.

Bingo:- Cartridge for Oracle database

  • Bingo: Cartridge for Oracle database supporting a wide range of searches in organic chemistry databases. Absolute portability, great scalability, plus unique features like:

    • Resonance substructure search

    • Tautomer substructure search with user-defined rules

    • Canonical (absolute) SMILES computation

    • Fast table update with no need to rebuild the index

    • Multi-threaded table indexing

Bioclipse :- Chemoinformatics platform

Bioclipse 2.4

Bioclipse is a free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc. The major features are:


  • Import and export in various file formats

  • Visual editing of molecular 2D-structures

  • 3D-visualization of molecules and proteins

  • Editing and visualization of sequences and features (DNA, RNA, proteins etc)

  • Graphing and editing of various types of spectra, e. g. NMR, MS

  • Retrieval of resources (sequences, proteins, etc) from public data repositories

  • Scripting of 3D-visualizations with syntax highlighting and content assistance

  • PDB-editor with syntax highlighting for working with PDB files

  • CMLRSS-viewer for downloading chemical content published on the web using RSS-feeds

  • Chemtree for displaying a hierarchical view of molecular and macromolecular substructures

  • Visualization of syandard chemical properties

  • Powerful scripting language based on Mozilla Rhino for automating tasks

  • Integrated, searchable help-system

  • Connection with external programs, e. g. PyMol

Bioclipse is a rich client, which means it is run on your local computer but also gives the possibility to communicate with servers for data retrieval and computational services. The powerful plugin architecture is based on Eclipse, and results in a responsive, integrated user interface designed for simple and intuitive operations that at the same time is easy to extend with custom functionality.

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biOpen :-Sequence analysis and visualisation

biOpen is a new and unique sequence analysis and structure visualization software based on dynamic integration of analysis tools.

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BioX :- Bioinformatics tool

BioX takes advantage of the Unix underpinnings of Mac OS X by using command line sequence analysis tools from the ebiotools package (which contains software from the EMBOSS project, among others). By presenting these Unix tools in the form of a Mac application, BioX leverages the best of both worlds.

BKChem:- Chemical Drawing Package

BKChem is a free chemical drawing package written in Python.

Drawing
  • bond-by-bond drawing
  • bond lenght and angle restrictions to assist with the drawing
  • ready to use templates of common rings
  • ability to expand common groups from abbreviated to structural form
  • Support for linear formulas (such as -CH2CH(COOCH3)2)
  • radicals, charges...
  • arrows (several types - normal, retro, equilibrium, etc.)
  • rich text
  • color support
  • simple vector graphics (rectangles, circles, polygons etc.)
Editing
  • unlimited undo and redo capabilities
  • aligning
  • scaling
  • rotation (2D, 3D)
  • aligning of molecules so that particular bond is horizontal/vertical
  • rotation of molecular fragments around bonds (conformation changes)
  • definition of personal preferred drawing style (bond lenghts, widths, colors...)
Export
  • full export to SVG (native data are transparently embedded into SVG file)
  • full export to OpenOffice Draw format
  • full export to ODF (OpenOffice 2.0) format
  • full export to Encapsulated PostScript
  • full export to PDF
  • full export to PNG (if pycairo is installed, available in Windows binary build)
  • basic support for both CML1 and CML2
  • Molfiles
  • generation of SMILES
Import
  • basic support for both CML1 and CML2
  • Molfiles
  • SMILES (subset)
  • INChI (subset)
Other features
  • localization support (currently English, French, Czech, Polish, German and Traditional Chinese translations are available)
  • native format is XML based
  • validity checking of drawn structures
  • support for user written plugins
  • support for user written batch scripts
  • searching for BKChem files containing specified molecules or molecule fragment

BLAST from Apple :- Sequence analysis

BLAST This version has been optimised by Apple to afford a considerable speed improvement

BLAST from WU :- Sequence analysis

Washington University BLAST (WU BLAST) version 2.0 is a powerful software package for gene and protein identification, using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases. The feature list for WU BLAST 2.0 is long and continues to expand. Much of this is outlined here. A complete suite of search programs (blastp, blastn, blastx, tblastn and tblastx) is included in the package, along with database management and support programs that include nrdb, patdb, xdformat, xdget, seg, dust and xnu.
WU BLAST is neither a re-hashed nor “Mac-ified” version of NCBI BLAST, although WU BLAST is in many ways easier to use. WU BLAST shares essentially no code with NCBI BLAST, except for some portions that both packages copied from the public domain ungapped BLAST 1.4 (W. Gish, unpublished).

BLAST from NCBI :- Sequence analysis

This is the NCBI version of BLAST

BndLst :- List interatomic interactions

Bndlst reads a PDB format file and for each atom prints a list of covalent and H-bonded neighboring atoms, along with several atomic properties. It is useful in building scripts which process atomic structures

Buffers:- iPhone app for designing buffer solutions for pH control

Buffers is a scientific tool for designing buffer solutions for pH control. Buffers is useful both as a handy reference of available buffering agents and as an accurate, portable buffer calculator for chemical, biochemical and biological research.

Brood:- Generates analogues of lead structure

BROOD is a software application designed to help project teams in drug discovery explore chemical and property space around their hit or lead molecule. BROOD generates analogs of the lead by replacing selected fragments in the molecule with fragments that have similar shape and electrostatics, yet with selectively modified molecular properties. BROOD fragment searching has multiple applications, including lead-hopping, side-chain enumeration, patent breaking, fragment merging, property manipulation, and patent protection by SAR expansion.

CAChe :- Molecular Modelling

CAChe is molecular modelling software that aids researchers in studying and modeling structures and reactions. CAChe allows visualization of molecules in 3D, searching for conformations, analyzing chemical reactivity and predicting properties of compounds on desktop computer.
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CaGe :- Graph theory for molecules

CaGe is an Open Source software package, implemented in C and Java. CaGe's task is to generate mathematical graphs of different types -- often types that relate to interesting chemical molecules -- and allow the user to view selected graphs in various ways or save them in several formats. If you have a normal, fairly modern UNIX system with Java, you can probably run CaGe.

CAMEO :- Evaluation of reactions

Computer Assisted Mechanistic Evaluation of Organic reactions CAMEO

CATVS :- Chemoinformatics

The Cactvs Chemoinformatics Toolkit for Mac OS X is being developed.

CCP4 :- Crystallography programs

CCP4 The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography. They have been collected and developed under the auspices of the Collaborative Computing Project Number 4, in Protein Crystallography, supported by the UK Science and Engineering Research Council (serc) since 1979 and currently the Biotechnology and Biological Sciences Research Council (bbsrc), and coordinated at Daresbury Laboratory. An excellent description of how to install together with a great selection of crystallography tools is available from the W.G.Scott research group here .

CDK :- Chemistry Development Kit

The Chemistry Development Kit (CDK) is a Java library for structural chemo- and bioinformatics. It is now developed by more than 50 developers all over the world and used in more than 10 different academic as well as industrial projects world wide.

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CDK Descriptor Calculator:- GUI to calculate CDK descriptors and fingerprints.

CDKdesc is a tool for calculating molecular descriptors.

  • Automatically detects descriptor classes defined in the CDK QSAR descriptor dictionary
  • Groups of descriptors and individual descriptors can be selected for evaluation
  • Input can be SDF or SMI formats
  • Output can be a variety of delimited text formats, annotated SDF or ARFF
  • Can evaluate fingerprints (hashed, MACCS, EState)

A nightly listing of the descriptors available is kept
here.

But as of 26 Feb 2010 the following were available.

Title ALogP ALogp2 AMR BCUTw-1l BCUTw-1h BCUTc-1l BCUTc-1h BCUTp-1l BCUTp-1h PPSA-1 PPSA-2 PPSA-3 PNSA-1 PNSA-2 PNSA-3 DPSA-1 DPSA-2 DPSA-3 FPSA-1 FPSA-2 FPSA-3 FNSA-1 FNSA-2 FNSA-3 WPSA-1 WPSA-2 WPSA-3 WNSA-1 WNSA-2 WNSA-3 RPCG RNCG RPCS RNCS THSA TPSA RHSA RPSA fragC Wlambda1.unity Wlambda2.unity Wlambda3.unity Wnu1.unity Wnu2.unity Wgamma1.unity Wgamma2.unity Wgamma3.unity Weta1.unity Weta2.unity Weta3.unity WT.unity WA.unity WV.unity WK.unity WG.unity WD.unity nA nR nN nD nC nF nQ nE nG nH nI nP nL nK nM nS nT nY nV nW apol naAromAtom nAromBond nAtom ATSc1 ATSc2 ATSc3 ATSc4 ATSc5 ATSm1 ATSm2 ATSm3 ATSm4 ATSm5 ATSp1 ATSp2 ATSp3 ATSp4 ATSp5 nB bpol C1SP1 C2SP1 C1SP2 C2SP2 C3SP2 C1SP3 C2SP3 C3SP3 C4SP3 SCH-3 SCH-4 SCH-5 SCH-6 SCH-7 VCH-3 VCH-4 VCH-5 VCH-6 VCH-7 SC-3 SC-4 SC-5 SC-6 VC-3 VC-4 VC-5 VC-6 SP-0 SP-1 SP-2 SP-3 SP-4 SP-5 SP-6 SP-7 VP-0 VP-1 VP-2 VP-3 VP-4 VP-5 VP-6 VP-7 SPC-4 SPC-5 SPC-6 VPC-4 VPC-5 VPC-6 ECCEN GRAV-1 GRAV-2 GRAV-3 GRAVH-1 GRAVH-2 GRAVH-3 GRAV-4 GRAV-5 GRAV-6 nHBDon nHBAcc khs.sLi khs.ssBe khs.ssssBe khs.ssBH khs.sssB khs.ssssB khs.sCH3 khs.dCH2 khs.ssCH2 khs.tCH khs.dsCH khs.aaCH khs.sssCH khs.ddC khs.tsC khs.dssC khs.aasC khs.aaaC khs.ssssC khs.sNH3 khs.sNH2 khs.ssNH2 khs.dNH khs.ssNH khs.aaNH khs.tN khs.sssNH khs.dsN khs.aaN khs.sssN khs.ddsN khs.aasN khs.ssssN khs.sOH khs.dO khs.ssO khs.aaO khs.sF khs.sSiH3 khs.ssSiH2 khs.sssSiH khs.ssssSi khs.sPH2 khs.ssPH khs.sssP khs.dsssP khs.sssssP khs.sSH khs.dS khs.ssS khs.aaS khs.dssS khs.ddssS khs.sCl khs.sGeH3 khs.ssGeH2 khs.sssGeH khs.ssssGe khs.sAsH2 khs.ssAsH khs.sssAs khs.sssdAs khs.sssssAs khs.sSeH khs.dSe khs.ssSe khs.aaSe khs.dssSe khs.ddssSe khs.sBr khs.sSnH3 khs.ssSnH2 khs.sssSnH khs.ssssSn khs.sI khs.sPbH3 khs.ssPbH2 khs.sssPbH khs.ssssPb Kier1 Kier2 Kier3 nAtomLC nAtomP LOBMAX LOBMIN LipinskiFailures nAtomLAC MDEC-11 MDEC-12 MDEC-13 MDEC-14 MDEC-22 MDEC-23 MDEC-24 MDEC-33 MDEC-34 MDEC-44 MDEO-11 MDEO-12 MDEO-22 MDEN-11 MDEN-12 MDEN-13 MDEN-22 MDEN-23 MDEN-33 MOMI-X MOMI-Y MOMI-Z MOMI-XY MOMI-XZ MOMI-YZ MOMI-R PetitjeanNumber topoShape geomShape nRotB TopoPSA VAdjMat MW WTPT-1 WTPT-2 WTPT-3 WTPT-4 WTPT-5 WPATH WPOL XLogP Zagreb

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CellDesigner:- A modeling tool of biochemical networks

Major Features of CellDesigner

Major Features:

  • Biochemical Gene Regulatory Networks Modeling with GUI
  • Visual Representation of Biochemical Semantics
  • Comprehensive Graphical Notation: SBGN Process Diagram
  • SBML Compliant
  • Direct integration with SBML ODE Solver and Copasi
  • Smooth linkage to SBW-powered simulation module
  • Database Connections
  • Export image to image files including PDF and SVG format

CFOUR:- Coupled-Cluster techniques for Computational Chemistry

CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Møller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. Studies of excited electronic states and other "multireference" problems are possible using the equation-of-motion (EOM) coupled-cluster techniques. These techniques which are closely related to (and in some cases identical to) so-called Fock space multireference coupled-cluster theory, offer a powerful means to study open-shell systems and decided advantages when configuration mixing is important. At present, these include the EOMEE approach for singlet and triplet excited states, and the EOMIP and EOMEA methods that are best applied to low-spin doublet states. Analytic derivatives are available for these methods. A number of methodological developments have been added to the program in the last two decades. These include: analytic second derivatives for all coupled-cluster approaches up to full CCSDT; the calculation of NMR chemical shifts at MP and CC levels of theory; the calculation of anharmonic force fields (via numerical differentation of analytic derivatives); relativistic corrections; corrections to the Born-Oppenheimer approximation at the CC level; nonadiabatic coupling within the EOM framework, and several others.

Ch :- Programming

Ch is a superset of C/C++ interpreter for cross platform numerical computing and 2D/3D plotting. Ch supports ISO C standard (C90), major new features in C99, classes in C++, POSIX, X/Motif, Windows, OpenGL, ODBC, GTK+, C LAPACK, CGI, XML, 2D/3D graphical plotting, advanced numerical computing, and shell programming. Moreover, Ch has many salient features from other languages and software packages.
C is for low-level system programming and embedded systems; C++ for large-scale projects; Ch for platform-independent script computing. C/Ch/C++ allow users to use one language, anywhere and everywhere, for any programming tasks

Chargemol:- Determine DDEC net atomic charges, atomic spin moments, and effective bond orders

 

Chargemol program performs atomic population analysis to determine DDEC net atomic charges, atomic spin moments, and effective bond orders. Because the DDEC net atomic charges are simultaneously optimized to reproduce atomic chemical states and the electrostatic potential surrounding a material, they are well-suited for constructing force-fields used in atomistic simulations (e.g., classical molecular dynamics or monte carlo simulations) and for quantifying electron transfer between atoms in complex materials and during chemical reactions

Checkmol/Matchmol :- Molecular functional group analysis

Checkmol is a command-line utility program which reads molecular structure files in different formats and analyzes the input molecule for the presence of various functional groups and structural elements. At present, approx. 200 different functional groups are recognized. Output can be either clear text (English or German), a bitstring or its ASCII representation, or a set of special 8-character codes. This output can be easily placed into a database table, permitting the creation of chemical databases with a functional group search option.

Another output option of checkmol is a set of statistical values derived from a given molecule, which can also be used for quick retrieval from a database. These values include: the number of atoms, bonds, and rings, the number of differently hybridized carbon, oxgen, and nitrogen atoms, the number of C=O double bonds, the number of rings of different sizes, the number of rings containing nitrogen, oxygen, sulfur, the number of aromatic rings, the number of heterocyclic rings, etc. The combination of all of these values for a given molecule represents some kind of "fingerprint" which is useful for rapid pre-selection in a database structure/substructure search prior to a full atom-by-atom match (see below).

Matchmol complements the capabilities of checkmol. It compares two (or more) molecular structures and determines whether one of them is a substructure of the other one. This is done by a full atom-by-atom comparison of the input structures. Thus, matchmol can be used as a back-end program for structure/substructure search operations in chemical database.

Note: if you are running MacOS X, use the following command:
fpc checkmol.pas -S2 -Tdarwin

Chem4-D :- Drawing Package

Chemistry 4-D Draw is a chemistry program written in Java combining the most advanced technologies in structure drawing.
Chemistry 4-D Draw Modules
NamExpert that understands IUPAC nomenclature rules. If you enter an IUPAC chemical name, it creates the corresponding structure
  • Nomenclator automatically assigns systematic names to organic structures according to IUPAC nomenclature rules
  • Chem4D Database manages databases of molecular structures, graphics and information associated with the data. It helps you to search and reuse graphics you have created.
Chem4D Graph module that creates multi-line graphs of different styles. It supports non-linear and linear curve fitting, response curve fitting and data analysis. The program allows you to create high-quality structures simply by entering molecular names. It assigns systematic names to structures. It includes a full set of tools for drawing, text and structure editing, and labeling.

ChemBioDraw :- Chemical Drawing Package

ChemBiodraw 11.0 The best chemistry drawing package is now available for MacOSX available from Cambridgesoft. They also supply browser plugins that allow almost all the desktop functionality to be accessed from within a web browser. Here is a review I wrote describing the latest version.

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chemCal:- iPhone app concentration and dilutions calculator

chemCal is a basic chemistry concentration (molarity, moles per liter) and dilutions calculator for students of chemistry, biology, biochemistry, and biomedical sciences at school, college or university

ChemCore:- Java-based Chemiformatics foundation

ChemCore is the chemiformatics foundation of all of the Metamolecular products and services. Written in Java and cross-compilable to a number of target runtimes and platforms, ChemCore is both fast and flexible.

Features * Fast subgraph matching * Powerful graph query capabilities * Flexible, efficient graph traversals * Fast file input/output * A complete system of atomic weights and elemental properties * Sensible handling of implicit hydrogens * Molecule validation and correctness-checking * Molecule transformations, including canonicalization and salt-stripping * 100% Java cross-compilable to JavaScript and other target runtimes and platforms * Extensively tested and documented

Chemdoodle :- Chemical Drawing Package

ChemDoodle is an innovative Java-based 2D chemical drawing application developed by iChemLabs. Created by computational chemists, ChemDoodle is an intuitive tool for drawing chemical structures and figures.
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I've written a review of ChemDoodle 3.0 here.
3D ChemDoodle Web Components

WebGL has been quickly progressing, and we have been hard at work building our 3D ChemDoodle Web Components. The release of ChemDoodle Web Components 3.0, contains the alpha development versions of the 3D ChemDoodle Web Components.

ChemEquate:- Chemical equation balancer

ChemEquate automatically formats and balances chemical equations. Copy with one click for use in word processing applications. Molecular weights are also conveniently provided.

FEATURES:

  • Create clear and professional looking chemical equations
  • Powerful tool for balancing chemical equations instantly
  • Export beautifully formatted equations to other applications
  • Quickly calculate the molecular weight of any compound
  • Save equations to Favorites list for future use

Chemfp :- fingerprint generation and high-performance similarity search

With chemfp, you get command-line programs for fingerprint generation and high-performance similarity search. The tools support the FPS fingerprint file format, so if you want something beyond the OEChem, Open Babel and RDKit fingerprinters then you can write your own FPS files and still use the fast Tanimoto search tool. The programs are writen in Python, with a C extension for better performance. The core Python module is documented, which means you can write your own programs on top of the core API.


ChemiCal:- iPhone molecular weight calculator

ChemiCal is a simple chemistry application that takes a given chemical formula and returns the mass of one mole of that chemical.

Chemjuice:- iPhone Chemical drawing

ChemJuice lets your finger draw chemical structures.
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ChemKey :- Chemistry reference

ChemKey is a desktop chemistry refererence database containing over 90,000 records collected over 40 years covering all aspects of chemistry.

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Chemkit:- open-source C++ library for molecular modelling

Chemkit is an open-source C++ library for molecular modelling, cheminformatics, and molecular visualization.

Chemkit-builder1

ChemLab :- Lab Expt simulation

Model ChemLab is a unique product incorporating both an interactive simulation and a lab notebook workspace with separate areas for theory, procedures and student observations. Commonly used lab equipment and procedures are used to simulate the steps involved in performing an experiment. Users step-through the actual lab procedure while interacting with animated equipment in a way that is similar to the real lab experience.
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ChemMobi:- iPhone application to access online chemical info

ChemMobi uses Symyx, ChemSpider and Discoverygate webservices to access online chemical information.
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Chenomx :- NMR analysis

Chenomx Chenomx provides a set of powerful software applications that allow you to quickly identify and quantify metabolites in NMR spectra based on validated compound signatures. The products include Chenomx NMR suite, Chenomx Profiler and Chenomx Signature Builder.

ChemNomParse:- Chemical Nomenclature Parser

 

The ChemNomParse project is an open source Java project to create a chemical nomenclature parser. The project aims to build molecules from an IUPAC chemical name and comes in two parts: • The ChemNomParse library - which contains the core of the project and is now part of the CDK • Nomen - A complete program which demonstrates the library's abilities.

ChemPencil:- Chemical Drawing App

 

ChemPencil is an inexpensive chemical drawing application

ChemPencil tools and features include:

  • Draw bonds and molecules in ACS standardized style.
  • Label heteroatoms directly in the drawing without losing sight of your document.
  • Add common abbreviations to atom’s labels.
  • Heteroatom’s labels rearrange conveniently when rotating the molecule.
  • Represent bond stereochemistry with hashed and bold bond type.
  • Ring building tools to draw aromatic and aliphatic rings.
  • Add text to the document for example for naming a molecules or naming a reaction scheme.
  • Export or email your document as a PDF.
  • Select and copy molecules in ChemPencil and paste them directly in your Keynote document.
  • Calculation and plot of isotopic distribution graph

However it does not currently support round-trip editing, structures are pasted into documents as images and can not be then copy and pasted into ChemPencil for further editing.

ChemSpotlight :- Chemistry aware spotlight plugin

ChemSpotlight is a Spotlight metadata importer plugin for Mac OS X 10.4 Tiger written by Geoff Hutchison, which reads common chemical file formats (MDL .mol, .mdl, .sd, .sdf, Tripos .mol2, Protein Data Bank .pdb, Chemical Markup Language .cml, and XYZ) using the Open Babel chemistry library. It is provided as a Universal Binary for PowerPC and Intel, for optimized performance on both. ChemSpotlight indexes chemistry files, adds molecular formulas (complete with subscripts in the Finder), molecular weight, and a variety of other information for Spotlight searches and "Get Info" windows. iBabel can be used to search this information.
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ChemTree :- Recursive partioning

ChemTree is now available for MacOSX, it is a statistical analysis software based on recursive partitioning, that facilitates intelligent, target specific compound selection for High Throughput Screening (HTS). The software takes the compound structures and results from a screen, generates a model that predicts the results based on molecular features, and applies that model to untested compounds.
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Chemical Thesaurus :- Chemical Information

The Chemical Thesaurus from meta-synthesis is a great collection of free chemical information, slides and gadgets

ChemVector: Chemical Drawing rendering

ChemVector™ offers a modern solution to the chemical structure imaging problem. Features 100% JavaScript. No browser plugins are necessary. Runs with all commonly-used browsers on Windows, Linux, Mac, and iPad. This includes Internet Explorer 6-9 in addition to Firefox, Google Chrome, and Safari. Renders structures directly from individual molfiles on a server, or as inline content. Renders chemical structure content directly from ChemDraw™ binary files (.cdx). Declarative syntax replaces <img> tags with analogous <object> tags, making it easy for both developers and designers to work with the resulting markup. Non-blocking implementation makes it possible to render dozens of structures on a single page while maintaining UI responsiveness. Structures can be magnified pre- or post-rendering with no pixelation.

ChemWriter:- Chemical Drawing

ChemWriter from Metamolecular is a javascript based chemical drawing package.
ChemWriter is supported on all major desktop browsers: Internet Explorer 6+; Firefox 3+; Chrome 9+; Safari 4+; and Opera 11+.
Supported on iPad/Mobile Safari, allowing easy access to emerging mobile computing platforms.
Requires no browser plugins, reducing customer support issues.
Written entirely in JavaScript, ensuring excellent page integration.
Ergonomic Editor component is deployable with a single line of JavaScript, and works in lightboxes and underneath menus.
Painter component eliminates the need for server-side structure image rendering and easily enable in-place editing effects.
Editor and painter appearance can be controlled through CSS. Behavior can be customized through API or startup parameters.

Chenomx NMR Suite :- Integrated suite of NMR tools

Chenomx NMR suite is an integrated suite of tools that allow you to easily identify and quantify metabolites in NMR spectra.
Chenomx Profiler offers you a broad range of tools to assist in identifying and quantifying compound concentrations based on data in an NMR spectrum.
Chenomx Signature Builder was developed to address a recurring customer request: the capability to add custom compounds to a Compound Library. Signature builder allows a user to create a signature that models the compound of interest.
Chenomx Spin Simulator is a simple yet powerful tool for creating simulations of NMR spectra, based on user-defined spin systems, coupling relationships and reference spectra. You can use these simulations as starting points for creating your own compound signatures based on fundamentals of NMR theory.
Chenomx Library Manager allows you to create and manage Compound Sets for use in Profiler. Compound Sets can contain any compound signatures in your library, including those from the Chenomx library as well as those that you create with Compound Builder.
Chenomx Processor allows a variety of native spectrum formats to be converted into the Chenomx file format. These include:
• Varian
• Bruker
• JCAMP (Version 5.0 and above)
In addition, Processor allows users to identify or manually override the automatically determined parameters for the Chemical Shift Indicator. Processor can also be used to determine and set a variety of properties for the spectrum, such as pH.

CHil2 :- Molecular modelling

The Chil² platform offers a complete molecular modeling environment. It consists of numerous competitive components used for molecular modeling and screening. The main focus is on structural- and ligand based docking. Chil² utilizes graph theoretical methods to gain more insight on molecules and their interaction. All services and applications are embedded in a flexible Ruby environment.

GlamDock, is a docking tool, has recently been validated on two benchmark datasets
(see publications). On the smaller benchmark, on which data for other docking tools is available, GlamDock was shown to perform better than the best established docking tools (62% scoring accuracy compared to 57% for the best contender Gold, Glide 55%). GlamDock is based on a Monte-Carlo with minimization (basin hopping) search in a hybrid interaction matching / internal coordinate search space. GlamDock is highly efficient, taking from 5 seconds (fast virtual screening settings) to ~20 seconds (high quality docking settings) on average on standard 2.8GHz Intel Xeon CPUs. Newest developments include an improved scoring function for pose recognition and virtual screening, and the introduction of protein flexibility into GlamDock. In cooperation with our partners GlamDock has been integrated in a de novo molecular design strategy.
Graph based Molecular Alignment (GMA) is a combined 2D/3D approach for the fast superposition of flexible chemical structures, which is based on recent progress in the efficient identification of common subgraphs and a gradient-based torsion space optimization algorithm. The simplicity of the approach is reflected in its generality and computational efficiency. The approach neither requires precalculated conformations of the molecules nor does it make simplifying assumptions on the topology of the molecules being compared. Graph-based molecular alignment produces alignments that are consistent with the chemistry of the molecules as well as their general structure, as it depends on both the local connectivities between atoms and the overall topology of the molecules. Results from extensive evaluation suggest that, for most practical purposes, graph-based molecular alignment is a viable alternative to molecular field alignment with respect to structural superposition and leads to structures of comparable quality in a fraction of the time, taking on average less than 0.1 sec per molecule pair. GMA can claim to be the fastest available explicitly flexible molecular alignment method.

HomDock
is a combination of the ligand based GMA molecular alignment tool and the docking tool GlamDock. It is used to improve docking accuracy and efficiency in cases where a complex structure of a ligand with the target protein is known. The approach can be extended to cases where a known ligand exists, however the complex structure is unknown, so only the identity of an active molecule is needed to improve efficiency of docking. HomDock docks in less than 0.5 seconds on average on a standard PC, and shows significantly higher accuracy than normal docking in cross docking benchmarks .
Fuzzee allows the identification of functionally similar molecules, based upon functional and structural groups or fragments. The softening of the similarity definition of molecules allows scaffold hopping without additional effort. The algorithm can be used for the identification of topologically different molecules that share similar physico-chemical features. Compared to competing reduced graph or tree based approaches it has the advantage that it allows a weighted matching on the one hand and does not make assumptions on the topology of the molecules on the hand. Fuzzee is highly efficient, allowing more than 1.000 comparisons per second.

Chimera :- Molecular viewer

UCSF Chimera is a highly extensible, interactive molecular graphics program is available for MacOSX, both X-windows and native versions are available.
They also have a huge collection of images and movies
available

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Citrin :- Interactive scientific graphing and curve fitting

Citrin 1.0: A low-cost ($120), high-performance Mac OS X universal application for interactive scientific graphing and curve fitting, providing commonly-used charts, such as scatter and line series, bar, column, area, 3-D (column, pyramid, prism, area and band), ternary scatter, pie, polar, box and whisker, histograms, probability charts, etc.; curve fitting with built-in functions, as well as a module for user-defined, non-linear curve fitting with an interactive graphical interface; flexible capabilities for applying error bars; full Unicode support, diverse graphic export formats; support for drag-and-drop; native worksheets that can import and store large data sets from diverse data formats.

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CLC Chemistry Workbench

CLC Drug Discovery Workbench is a virtual lab bench. It gives you access to atomic level insights in protein-ligand interaction, and allows new ideas for improved binders to be quickly tested and visualized, it includes.

Molecule Structure Visualization

Molecule 3D structure import: Mol2, SDF, PDB Direct download of PDB structures from NCBI Quick-style options including ball-n-sticks and molecular surfaces Custom visualization applied to selected atoms Save molecule visualizations on data Molecule tables with 2D depiction of molecules

Chemical Awareness

Generate molecule 3D structure from SMILES or 2D representation* Automatic assignment of missing atom and bond properties Automatic binding site setup Chemical consistency checker Lipinski’s rule of five check

Structure Based Drug Discovery

Binding pocket finder Easy, graphical docking target setup Fast track molecular docking Optimize ligand interactions in binding site Virtual screening Ligand binding inspection Calculate molecular properties Protein structure and binding site alignment

Sequence analysis tools

Search for sequences at UniProt BLAST Sequence alignment Phylogenetic trees Motif and Pfam domain search

CLiDE:- Chemical Literature Data Extraction

CLiDE is a chemistry intelligent equivalent of Optical Character Recognition (OCR) software. Just as an OCR can recognize characters from a scanned images of printed text, CLiDE can recognize structures, reactions and text from scanned images of printed chemistry literature.
The software saves users hours of redrawing structures from printed material, as it transforms the 'images' into a 'real structures' that can then be input into databases.

CN3D :- Molecule viewer

Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service together with sequence data.
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CNS:- Crystallography & NMR System

Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.

CoLocalizer Pro:- quantitative colocalization analysis software.

CoLocalizer Pro is a quantitative colocalization analysis software. It calculates specialized coefficients to characterize colocalization of fluorescence markers objectively. The software works with images produced by all major manufacturers of fluorescence confocal microscopes and is highly cost efficient

COLUMBUS :- Ab Initio calculations

COLUMBUS is a collection of programs for high-level ab initio molecular electronic structure calculations. The programs are designed primarily for extended multi-reference (MR) calculations on electronic ground and excited states of atoms and molecules. A variety of methods, including
  • MCSCF (multiconfiguration self-consistent field)

  • MR-CISD (multireference configuration interaction with all single and double excitations),

  • MR-ACPF (multireference averaged coupled-pair-functional) and

  • MR-AQCC (multi-reference average quadratic coupled-cluster)

Compounds- iPhone to calculate stoichiometry

Stoichiometry or "grams-to-moles" calculations can be some of the most tedious chemistry problems. Mistakes are easily made as you look up atomic information and type them in your calculator.

CONFLEX :- Conformation searching

CONFLEX Corporation develops and licenses the CONFLEX5™ and PARALLEL CONFLEX software packages for fast, accurate molecular conformational analysis and searching

Coot :- Crystallographic Object Oriented Toolkit

Coot is for model building, model completion and validation.
Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots etc.
For more information visit the website
here
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CORINA:- 3D structure generation

CORINA is a fast and powerful 3D structure generator for small and medium sized, typically drug-like molecules. Its robustness, comprehensiveness, speed and performance makes CORINA a perfect application to convert large chemical datasets or databases.

COSMOtherm:- calculation of solvation mixture thermodynamics

Thermodynamic Property Prediction
COSMOtherm predicts a wide range of properties for mixtures and pure compounds, such as boiling points, vapor pressures, solubilities, ADME properties, viscosities, partition coefficients, phase equilibria, phase diagrams, azeotropes, heat of mixing, reaction thermodynamics, activity coefficients, sigma profiles, pKa and much more.

COSMOtherm: Application Examples
The following examples demonstrate some of COSMOtherm's capacities in chemical and engineering thermodynamics:

As a new feature, COSMOtherm now is able to generate VRML files for the visualization of the screening charge density s on the molecular surface. This gives a very vivid picture of the molecules, showing the local positions of strongly interacting sites. Even details like lone-pairs are well resolved. Note, that s is a much more local and detailed property compared to electrostatic potential (ESP).

CPMD:- :-Parallelized plane wave / pseudopotential implementation of Density Functional Theory

The CPMD code is a plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. The first version  was developed by Jurg Hutter at IBM Zurich Research Laboratory starting from the original Car-Parrinello codes. During the years many people from diverse organizations contributed to the development of the code and of its pseudopotential library:

Full installation instructions for Mac OSX are available http://cpmd.org/documentation/cpmd-html-manual

CPMD capabilities

  • Works with norm conserving or ultrasoft pseudopotentials
  • LDA, LSD and the most popular gradient correction schemes; free energy density functional implementation
  • Isolated systems and system with periodic boundary conditions; k-points
  • Molecular and crystal symmetry
  • Wavefunction optimization: direct minimization and diagonalization
  • Geometry optimization: local optimization and simulated annealing
  • Molecular dynamics: constant energy, constant temperature and constant pressure
  • Path integral MD
  • Response functions
  • Excited states
  • Many electronic properties
  • Time-dependent DFT (excitations, molecular dynamics in excited states)
  • Coarse-grained non-Markovian metadynamics

CPMD is free for non-profit organisations.

CRYSTAL:- Computes the electronic structure of periodic systems

CRYSTAL is a general-purpose program for the study of crystalline solids, and the first which has been distributed publicly. The first version was released in 1988 and then five next versions have followed: CRYSTAL92, CRYSTAL95, CRYSTAL98, CRYSTAL03 and CRYSTAL06 and now CRYSTAL09..
The CRYSTAL program computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid approximations. The Bloch functions of the periodic systems are expanded as linear combinations of atom centred Gaussian functions. Powerful screening techniques are used to exploit real space locality. Restricted (Closed Shell) and Unrestricted (Spin-polarized) calculations can be performed with all-electron and valence-only basis sets with effective core pseudo-potentials.
The program can automatically handle space symmetry (230 space groups, 80 two-sided plane groups, 99 rod groups, 45 point groups are available ). Point symmetries compatible with translation symmetry are provided for molecules. Helical symmetry is now available (up to order 48). Input tools allow the generation of a slab (2D system), or a cluster (0D system), from a 3D crystalline structure, or the creation of a supercell with a defect, or nanotubes (1D system) from a single-layer slab model (2D system).
The code may be used to perform consistent studies of the physical and chemical properties of molecules, polymers, surfaces and crystalline solids:

  • Structural features

  • Vibrational properties

    • Examples of graphical animations of vibrational modes are shown here

  • Electronic structure

  • Magnetic properties

  • Dielectric properties

  • Elastic properties

Crystal Explorer :- Crystal structure analysis

CrystalExplorer is a program designed principally to calculate, display and colour the Hirshfeld surface for a chosen molecule, or cluster or atoms, within a crystal.

What can CrystalExplorer do for you?

CrystalExplorer can display a two dimensional representation of the Hirshfeld surface, which is referred to as a "fingerprint" of the crystal. This can help uniquely classify a crystal, even polymorphic crystals.

The Hirshfeld surfaces in CrystalExplorer give a novel alternative view of the crystal, which may enable you to see trends that are not apparent otherwise.

CrystalExplorer enables you to view a CIF containing multiple crystal structures, and measure distances and angles within the crystal. All molecules and surfaces are displayed in three dimensions; with rotation, translation and zooming of the viewpoint.

CrystalExplorer is interfaced to the free software
Tonto. As a result, it can calculate SCF energies of and obtain molecular orbitals for any fragments of the crystal. Once molecular orbitals are obtained, they can be used to generate quantum mechanical isosurfaces which are then displayed.

Crystallographic and NMR System (CNS)

CNS A crystallographic and NMR system. An excellent description of how to install is available here. Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.

CrystalMaker :- Crystal structure analysis

CrystalDiffract X and CrystalMaker and Single Crystal for fully-interactive visualization and analysis of crystal and molecular structures and simulation x-ray & neutron patterns from CrystalMaker files.

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Recent update adds much improved 3D graphics and an improved interface
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Cylview:- Molecule viewer

Cylview is a molecular viewer written in Python.

There are a couple of
nice examples on the website showing it in action.

Cytoscape:- Data analysis in molecular biology

 

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.

Cytoscape supports many use cases in molecular and systems biology, genomics, and proteomics: * Load molecular and genetic interaction data sets in many standards formats * Project and integrate global datasets and functional annotations * Establish powerful visual mappings across these data * Perform advanced analysis and modeling using Cytoscape Apps * Visualize and analyze human-curated pathway datasets such as WikiPathways, Reactome, and KEGG.