Mac OS X Applications A-C
Aabel :- Data Analysis
Abinit :- Density Functional Theory
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/
Adun:- Biomolecular Simulation
AFITT:- Fully automated ligand fitting
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.
 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
- 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
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.
AlvaDesc:- calculation of a wide range of molecular descriptors and a number of molecular fingerprints.
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
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
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.
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
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
• 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
The following pages from the Astex websiteshow examples of the use of AstexViewer™ for displaying protein/ligand complexes.
Aten:- Molecular editor for building periodic systems
- 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
Atom in a Box :- Visualise atomic orbitals
Atomic Mac :- Periodic table
AtVol :-Atomic vol calculation
AutoDock :- Docking tool
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.
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|
|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|
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
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
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 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.
biOpen :-Sequence analysis and visualisation
BioX :- Bioinformatics tool
BKChem:- Chemical Drawing Package
- 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.)
- unlimited undo and redo capabilities
- 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...)
- 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
- generation of SMILES
- basic support for both CML1 and CML2
- SMILES (subset)
- INChI (subset)
- 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 from WU :- Sequence analysis
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
BndLst :- List interatomic interactions
Buffers:- iPhone app for designing buffer solutions for pH control
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
CaGe :- Graph theory for molecules
CAMEO :- Evaluation of reactions
CATVS :- Chemoinformatics
CCP4 :- Crystallography programs
CDK :- Chemistry Development Kit
CDK Descriptor Calculator:- GUI to calculate CDK descriptors and fingerprints.
- 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
CellDesigner:- A modeling tool of biochemical networks
Major Features of CellDesigner
- 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
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
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 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.
ChemBioDraw :- Chemical Drawing Package
chemCal:- iPhone app concentration and dilutions calculator
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.
Chemdoodle :- Chemical Drawing Package
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.
- 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
Chemjuice:- iPhone Chemical drawing
ChemKey :- Chemistry reference
Chemkit:- open-source C++ library for molecular modelling
Chemkit is an open-source C++ library for molecular modelling, cheminformatics, and molecular visualization.
ChemLab :- Lab Expt simulation
ChemMobi:- iPhone application to access online chemical info
Chenomx :- NMR analysis
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
ChemTree :- Recursive partioning
Chemical Thesaurus :- Chemical Information
ChemVector: Chemical Drawing rendering
ChemWriter:- Chemical Drawing
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.
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 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:
• 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
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 ⁴ 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
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.
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
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
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
CNS:- Crystallography & NMR System
CoLocalizer Pro:- quantitative colocalization analysis software.
COLUMBUS :- Ab Initio calculations
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
CONFLEX :- Conformation searching
Coot :- Crystallographic Object Oriented Toolkit
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
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
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:
- Vapour-Liquid binary phase diagrams
- Activity coefficients
- Excess properties
- Isomeric effects
- Temperature dependency
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
- 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:
Examples of graphical animations of vibrational modes are shown here
Crystal Explorer :- Crystal structure analysis
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)
CrystalMaker :- Crystal structure analysis
Cylview:- Molecule viewer
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.