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

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/

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.

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.

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.

• 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.

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

• 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

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.

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.

• 

• 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
• 

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/

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 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

• 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.

• 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
• 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...)

• 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

• basic support for both CML1 and CML2
• Molfiles
• 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

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.

• 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)

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) 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.

• 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.

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

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

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.

"Convenient interactive Mendeleev's Periodic table. Tap a chemical element in the table to find more information about it.

The calculator of molar masses. Enter a chemical compound correctly and it will show molar masses and percentages of elements.

The table of solubility of substances is added in the app as well as Acid strength chart. Now your textbooks become waste!

All these tables and charts are available in the app for free: * Periodic table * Offline access to information about chemical elements * Solubility table * Molar mass calculator * Electronegativity of elements * Molecular weights of organic substances * Reactivity series * Acid strengths chart"

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

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 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.

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.

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 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

• 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)

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.

• Vapour-Liquid binary phase diagrams
• Activity coefficients
• Excess properties
• Isomeric effects
• Temperature dependency

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 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

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.