• Use QM based Scoring Function to predict protein-ligand binding affinities on a daily basis.
• Build computational expensive QM descriptors for QSAR & ADME/Tox Models.
• Study protein-ligand complexes containing metals.
• Predict ligand-induced NMR (Nuclear Magnetic Resonance) Chemical Shift Perturbation on protein.
• Study large biomolecules of 500 or 15,000 atoms with QM.
• Understand the Pair-Wise Energy Decomposition of protein-ligand complex interaction.
• Improve QSAR (Quantitative Structure-Activity Relationships) understanding with Quantum Chemistry Molecular Field Analysis (MFA).
• Leverage the accuracy and speed of divide & conquer linear-scaling QM.

• Molecular Structures

• Chemical Reactions

• Molecular Vibrations

• Electronic Spectra

• NMR Spectra

• Solvation Effects

• Fast DFT calculations with accurate linear scaling algorithms
• A wide range of post-HF correlation methods that are efficient and unique
• Quantum calculations extended with QM/MM and molecular dynamics

• Mulliken Population Analysis (MPA)

• C-squared Population Analysis (SCPA)

• Overlap Population Analysis (OPA)

• Mayer's Bond Orders

• Charge Decomposition Analysis (CDA)

• Fragment Analysis

QUACPAC provides pKa and tautomer enumeration in order to get correct protonation states. It also offers multiple partial charge models (including MMFF94 [1], AM1-BCC [2], and AMBER [3]) that cover a range of speed and quality in order to allow appropriate charging for every end use. QUACPAC's approach to tautomeric enumeration is to provide multiple tautomeric states rather than one "correct" tautomer. Subsequent downstream processes are then used to identify the appropriate tautomeric form.

Quantum Expresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

Details of the packages is available in the documentation

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins. * Real Time Ambient Occlusion * Depth Aware Silhouette Enhancement * Ball and Sticks, Space-Fill and Liquorice visualization modes * High resolution antialiased snapshots for creating publication quality renderings * Automatic generation of animated gifs of rotating molecules for web pages animations * Real-time rendering of large molecules and protein (>100k atoms) * Standard PDB input

• Multiple Molecules: Up to five molecules can be viewed in the same canvas window.
• Molecules Window: New window displays molecules currently loaded, allows selection of active molecule.
• Toolbar: Commonly used commands are easily accessed from a graphical toolbar.
• World Rotation: Individual molecules can be rotated about their individual centers of gravity, or the entire world can be rotated around the center of the screen.
• Bond Rotation: Part of a molecule can be rotated about a bond.
• Distance Command: Find distance between two atoms
• Angle Command: Find angle between 3 atoms
• Dihedral Angle Command: Find dihedral angle of 4 atoms
• Distance/Angle Labels: Distances, angles and dihedral angles are labeled directly on the molecule.

• ChemAxon's Marvin Sketch
• Symyx ISIS/Draw (version 2.5 or higher; connection software included in Reaxys Structure Editor plugin)
• Symyx Draw (version 3.0 or higher; connection software included in Reaxys Structure Editor plugin)
• CrossFire Structure Editor (version 7.0 or higher; connection software included in Reaxys Structure Editor plugin)
• CambridgeSoft ChemDraw (version 11 or higher; connection software NOT included in plugin.)
• InfoChem ICEdit (version 1.8 or higher; connection software NOT included in plugin. )

The REFMAC program can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where "missing data" have been restored.

• Statistical Tests & Correlation
• Forward/Backward Selection
• GA Wrappers

• K-Means
• Hierarchical
• SOM
• Random Walk

Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It enables generation of and navigation in a scaffold tree hierarchy annotated with various data.

Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering.

A recent publication describes it in detail. Mining Chemical Libraries with "Screening Assistant 2, Vincent Le Guilloux, Alban Arrault, Lionel Colliandre, Stéphane Bourg, Philippe Vayer and Luc Morin-Allory. DOI

• sdf2tinkerxyz

• tinkerxyz2sdf

Sdfchecker is a free inspection and manipulation program for SDFiles (.sdf). Summary of functions: - Indicate number of structure records - Indicate number of blank structure records - Display list of Data Field names - Remove blank structure records - Split large files into smaller multiple files, a single random sized file, or containing a specified range of records - Convert into individual MOL files - Inspect for duplicate Data Field names within each record

Shape-it™ is a shape-based alignment tool by representing molecules as a set of atomic Gaussians. The software is based on the method described by Grant and Pickup (J. Phys. Chem. 1995, 99, 3503).

Smina is a fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.

SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will help us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure).

Strip-it™ is a tool to extract molecular scaffolds according predefined rules. These rules are based on the definitions of scaffolds as described by Murcko (J. Med. Chem. 1996, 39, 2887), Pollock (J. Chem. Inf. Model. 2008, 48, 1304) and Schuffenhauer (J. Chem. Inf. Model. 2007, 47, 47).

SugarMagnolia, a freeware program to use as an aid when interpreting mass spectrometric data from carbohydrates. It can calulate the molecular weight of carbohydrates, calculate fragment ions (B-, C-, Y-, and Z-type ions), modify the complete molecule or, modify individual residues, save and print sequences.

• SYBYL-X from Tripos is a high end molecular modeling package that provides tools for almost every aspect of molecular modeling.

• Small molecule and macromolecule modelling

• 3D QSAR:  use the power of industry leading CoMFA in a new way to generate novel ideas for R-groups — predict the level of biological activity or potency based on structure-activity data, not just yes/no activity predictions
• Ligand-based virtual screening:  search millions of compounds overnight — don’t miss hits because you only screened subsetted portions of your database
• Cheminformatics:  produce highly focused queries that avoid false positives using rich set of 3D queries; on-the- fly conformational searching means you only store a single conformation of your molecules, keeping database size small and very transportable
• Docking:  custom tailor and fine-tune docking to a particular receptor site using information like SAR or known poses to improve rank ordering of ligands

SZYBKI optimizes molecular structures with the Merck Molecular Force Field, either with or without solvent effect, to yield quality 3D molecular structures for use as input to other programs. Since the chemistry of molecular interactions is a matter of shape and electrostatics, it is impossible to consider either without reasonable 3D molecular structures. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.

SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding. The newly released tool GAMEPLAN, suggests ways to modify ligand chemistry based on this understanding of water structure in the immediate environment of the ligand.