QuantumBio :- QuantumMechanics

QuantumBio provides Pharmaceutical and Biotech companies with patent pending fast Quantum Mechanical (QM) solutions for Lead Optimization!
The pressure is on: optimize lead compounds faster and at less cost. Whether you are discovering leads through Virtual Screening (VS), High Through Screening (HTS) or combining VS & HTS, Lead Optimization involves complex, and expensive multi-step process of refining the chemical structure of a compound to improve its drug characteristics with the goal of producing a preclinical drug candidate. Researchers focus on a number of considerations in optimizing a drug candidate, some of those characteristics are Potency, Toxicity, Metabolism and Formulation. QuantumBio offers the following
lead optimization capabilities for your drug discovery investment:
  • 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.

Q-Chem :- Ab Initio

Q-Chem the latest version of a modern ab initio electronic structure program, is capable of performing first principles calculations on both the ground and excited states of molecules.
Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from the highest performance DFT/HF calculations to high level post-HF correlation methods. Q-Chem tackles a wide range of problems in commercial, academic and government laboratories, including:
  • Molecular Structures
  • Chemical Reactions
  • Molecular Vibrations
  • Electronic Spectra
  • NMR Spectra
  • Solvation Effects
Q-Chem provides users with some distinct advantages:
  • 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

QMForge:- program used to analyze the results of quantum chemistry (DFT) calculations.

QMForge is a program used to analyze the results of quantum chemistry (DFT) calculations. Gaussian 98/03, ADF, GAMESS (US), GAMESS (UK), PC-GAMESS, Jaguar, and ORCA files are supported (see below). The following analyses are available:
  • Mulliken Population Analysis (MPA)

  • C-squared Population Analysis (SCPA)

  • Overlap Population Analysis (OPA)

  • Mayer's Bond Orders

  • Charge Decomposition Analysis (CDA)

  • Fragment Analysis

QuteMol:- Molecule Viewer

  • 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
  • Quick installers for Win and Mac OS X (intel)
  • Support as a plugins of the NanoEngineer-1 the modeling and simulation program for nano-compositesTN_par_med_2c

Rasmol :-Molecule viewer

Rasmol A 3D molecule viewer ported to Mac OS X

RASMOL UCB enhanced :- Molecule Viewer

UCB enhanced RASMOL
How has MultiCHEM enhanced the program?
  • 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.

Raster 3D :- Molecule images

Raster3D - is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.

RAVE:-single and multiple crystal real-space electron-density averaging

RAVE is a suite of programs for single and multiple domain, single and multiple crystal real-space electron-density averaging. It also contains tools for the detection of secondary structure elements in macromolecular electron-density maps. The package succeeds the previous A suite.

Reaxys:- Chemical Reaction and substance searching

Reaxys is designed for reaction, substance and citation data searching, combined with synthesis planning. Users can search for reactions, methods, compounds, properties and literature queries (authors, journals etc.). Reaxys provides a seamless access to the Scopus abstract and citation database, ScienceDirect online collection of published scientific research—and Beilstein reaction information database.
Reaxys requires Mac OS 10, Safari 3.0 or higher, JRE 5.0 or higher and Javascript and cookies need to be enabled and currently supports the following editors:
  • 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. )

RED:- RESP ESP charge Derive

R.E.D. allows computational biologists involved in AMBER/GAFF, CHARMM, GLYCAM & OPLS force field based biological studies to automatically derive highly effective and reproducible charge values, and to build force field libraries for new molecules and molecular fragments.

RDKit:- Cheminformatics toolkit

RDKit: A software suite for cheminformatics, computational chemistry, and predictive modeling written in C++ and Python

Ribbons :- Molecule viewer

Ribbons A popular molecular graphics program.

ROCS :- Molecular shape comparison

ROCS is a shape comparison program, based on the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity. ROCS uses a smooth Gaussian function to represent the molecular volume, so it is possible to routinely minimize to the best global match. ROCS is capable of processing 600-800 comparisons each second, making it is possible to search multi-conformer representations of corporate collections in a day on a single processor to find compounds with similar shape to a lead compound.

SARchitect :- Explore structure activity relationships

SARchitect is a tool for analysing structure activity relationships and ADME/T modeling.

Sarchitect has a wide range of graphical visualizations to enable visual analysis. The viewing options include: 2D/3D Chemical Structure viewer, 2D/3D Scatter Plots, Profile Plot, Heat Maps, Box-whisker Plots, Histograms, Matrix Plots, Bar Charts and Chemical Space views.
All views in Sarchitect are dynamically linked selections in one view get highlighted all other open views.
Similarly, a range of powerful algorithms enable launching algorithmic inquiry.
For feature selection:
  • Statistical Tests & Correlation
  • Forward/Backward Selection
  • GA Wrappers
For clustering:
  • K-Means
  • Hierarchical
  • SOM
  • Random Walk
Principal Component Analysis

SciFinder :- Scientific literature search

SciFinder is now MacOSX native!! it is an easy to use desktop research tool that allows you to explore research topics, browse scientific journals, and stay up to date on today's most recent scientific developments. With SciFinder, no special training is needed. You simply point and click to access more than 19 million abstracts and 35 million substances.

Scilab :- Numerical analysis

Scilab Scilab is a scientific software package for numerical computations in a user-friendly environment

SciPy :- Numerical analysis

ScilPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python. The core library is NumPy which provides convenient and fast N-dimensional array manipulation. The SciPy library is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization. Together, they run on all popular operating systems, are quick to install, and are free of charge. NumPy and SciPy are easy to use, but powerful enough to be depended upon by some of the world's leading scientists and engineers. If you need to manipulate numbers on a computer and display or publish the results, give SciPy a try!

SDF2XYZ2SDF:- Cheminformatics link to TINKER

sdf2xyz2sdf is an open-source software aimed at converting SDF files into TINKER XYZ files (and viceversa) while performing automatic assignment of MMFF94 atom types, bond types and charges.
The sdf2xyz2sdf package consists of two programs:

sdf2xyz2sdf depends on
OpenBabel for MMFF atom type and charge assignment. Since input to sdf2tinkerxyz is entered through standard input, and output from tinkerxyz2sdf is printed on standard output, it is possible to pipe output from OpenBabel into sdf2tinkerxyz, or to pipe tinkerxyz2sdf output into OpenBabel, so that virtually any format conversion from/to TINKER XYZ may be accomplished.
Interestingly, also ionic heteroaromatic rings which could not be assigned proper charges by the original TINKER-MMFF code are correctly accounted for by sdf2xyz2sdf.

J Mol Model

SemiChem :-QSAR

SemiChem report that the semiempirical quantum mechanical program Ampac and advanced, fully featured quantitative structure/activity relationship (QSAR) program Codessa are available for MacOSX

ShaEP :- Molecular overlayer

ShaEP aligns (superimposes) two rigid 3D molecular structure models and computes a similarity index for the overlay. It can be used for the virtual screening of libraries of chemical structures against a known active molecule, or as a preparative step for 3D QSAR methods.
Mikko J. Vainio, J. Santeri Puranen and Mark S. Johnson (2009) ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential. J. Chem. Inf. Model. Article ASAP.

Siesta :-ab initio simulation of solids

Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

Silicos Tools:- Cheminfomatics tols

Open source software

SieveFiltering out molecules with unwanted properties.
PharaoGeneration and alignment of pharmacophores.
PiramidShape-based alignment of molecules.
StripperExtraction of scaffolds from molecules according to different rule sets.
Spectrophores™Silicos' Spectrophores™ technology is incorporated in Open Babel.

To install the software you will first need to download and install CMake a cross-platform, open-source build system.

The following instructions describe compiling and installing sieve but a similar approach is used for all installations.
Open a Terminal window, and decompress the downloaded file with following command:
> tar -xvf sieve-3.0.6.tar.gz
This will create a folder called 'sieve-3.0.6'.
(You may find it have already been decompressed in your default downloads location)

You now need to configure and compile SIEVE. Run the following commands in a Terminal, one after the other:

> cd sieve-3.0.6
> cmake CMakeLists.txt
> make
To install for everyone to use.
> sudo make install
you will be asked for your admin password.

You should find the application has been installed in /usr/local/bin

If you now type
> sieve -h
SIEVE v3.0.6 | Mar 15 2011 13:24:09

-> GCC: 4.2.1 (Apple Inc. build 5664)
-> Open Babel: 2.3.0

Copyright (C) 2005-2010 by Silicos NV

This file is part of the Open Babel project.
For more information, see

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
GNU General Public License for more details.


Sieve is a tool to filter out molecules according user-defined criteria.


Specifies the file containing the input molecules. The format of the
file is specified by the file extension. Gzipped files are also read.

Specifies the file to which the molecules are written that pass the filtering.
The format of the file is specified by the file extension. Gzipped
files are also read.

Specifies the file in which the filter criteria have been defined.


Specifies the file to which the molecules are written which do not
pass the filter criteria. The format of the file is specified
by the file extension. Gzipped files are also read.

This flag directs the program to keep all separate fragments instead of
stripping away all but the largest fragments before the filtering takes
place. By specifying this option, this stripping is not performed and
ensures that all salt counterions are taken into account in the filtering

This flag directs the program to rename the title of each molecules
into a increasing digit reflecting the sequence of the molecule in
the input file. Existing titles are overwritten.

This flag directs the program to calculate all properties listed in
the filter definition file without applying any filtering. This option
can be used for database characterisation. The calculated parameters
are written to standard output.

This flag specifies whether verbose logging should be switched off. If not
specified, then for each molecule a message is written to standard error
whether the molecule passes or fails the filter criteria. This behaviour
can be switched off with this command line option. However, even
when this option is specified, information is still written to standard error,
but reduced to a large extend.

-h --help

-v --version

SIMPSON:- General Simulation Program for Solid-State NMR

SIMPSON a General Simulation Program for Solid-State NMR. It features multi-pulse 1D/2D experiments on large spin-systems with input-files implemented using a simple scripting language. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, rf irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition.

SIMREF:-structure refinement program for the simultaneous evaluation of several powder diffraction data sets

SIMREF a structure refinement program for the simultaneous evaluation of several powder diffraction data sets and multiple phases per data set. With a structural model all calculated diffraction profiles are fitted to the corresponding observed diffraction profile by the method of least squares. This procedure is called Rietveld method (Rietveld, 1969 ). By the simultaneous refinement of several data sets new evaluation techniques are possible

Situs:- modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering

Situs is an award-winning program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering. The software supports both rigid-body and flexible docking using a variety of fitting strategies. Situs is developed by Willy Wriggers and coworkers: biomachina.org.

SIR2008:- Direct Method program for the resolution and refinement of crystal structures using single crystal data

SIR2008 Direct Method program for the resolution and refinement of crystal structures using single crystal data), SIR2002 (Direct Method program for the resolution of proteins using single crystal data; can be used also for resolution and refinement of small and medium size crystal structures) and SIR2004 (automatic solution of crystal structures by Direct and Patterson Methods; it can be used both for resolution and refinement of small/medium size crystal structures and for macromolecules with data up to 1.4-1.5 Ang.)

SketchEl:- Molecular drawing

SketchEl is an interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. The feature set provided by the molecular sketcher is largely limited to the minimum features required to conveniently edit diagram representations of small molecule structures. Toolbars, templates, mouse gestures, keyboard shortcuts, utility commands and several view modes are offered in order to make this as convenient as possible. Molecules can be easily interconverted with the ubiquitous MDL MOL file format, though not not necessarily without information loss. Molecule diagrams are rendered interactively in high quality, and can also be exported as SVG graphics.

SMARTCyp:- Predict CYP mediated metabolism

SMARTCyp is a method for prediction of which sites in a molecule that are labile for metabolism by Cytochromes P450 isoform 3A4. It is also a reactivity model which is applicable to all P450 isoforms. The implementation is in the form of a java program using the CDK and JChemPaint java libraries. The program has been tested on Linux, MacOS X and Windows XP, but it should work on any platform.
The new version includes a specific CYP2D6 model and improved reactivity for benzothiophene sulfurs.
A paper describing the CYP2D6 model has also been published in ACS Medicinal Chemistry Letters.

Smell-o-mints :- Periodic table

Smell-o-mints is a Periodic table of the elements for the Macintosh. It's not as full-featured as a lot of other Periodic tables out there, but it's free and looks very nice.

smi23D:- Convert SMILES to 3D structures

smi23d consists of two programs that can be used to convert one or more SMILES strings to 3D. The first step uses a program called smisdf which generates a set of rough 3D coordinates using an iterative refinement procedure. These coordinates are then optimized with a MMFF94 force field by mengine to generate a reasonable 3D structure. In addition to generating an optimized structure, the code can optinally calculate some molecular properties such as XlogP, dipole moment and vibrational properties. By default these are not calculated. The resultant coordinates are written in SD format.

The source code for the programs can be obtained from the CICC-Grid Sourceforge SVN repository and binary builds are available for Intel Mac OS X.

SMSD: Calculate MCS

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).

SnB:- Crystal structure determination

SnB is a computer program based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data. This program has been used in a routine fashion to solve difficult structures, containing as many as 1000 unique non-H atoms, that could not be solved by traditional reciprocal-space routines based on the tangent formula alone.

Solutions:- iPhone app for calculating concs of buffers

Solutions, Whether you are a chemist, biologist or student, no one likes the calculations
needed before making chemical solutions.

Solver:- Linear programming for Excel

Solver for Microsoft Excel 2008 on Macintosh is available here.  You can download it here.

SOMA:- Web-based molecular modelling

SOMA2 is a web-based molecular modelling environment.

Open Source Molecular Modelling Workflow Environment
SOMA2 is a versatile modelling environment for computational drug discovery and molecular modelling. SOMA2 is operated through WWW-browser. The SOMA2 environment offers a full scale modelling environment from inputting molecular data to visualisation and analysis of the results.
Kinnunen, T., Nyrönen, T., Lehtovuori, P., SOMA2 - Open Source Framework for Molecular Modelling Workflows, Chemistry Central Journal, 2(Suppl 1):P4 (2008)

Sparky :-NMR analysis

Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. For more information about what Sparky does look at the introduction in the manual.

Spartan :- Molecular modelling

Spartan 04 is the most sophisticated version offered. The latest Spartan release offers all features and methods included in the Spartan Essential Edition, and in collaboration with Q-Chem, provides a full range of post-Hartree-Fock methods including Density Functional, Moller Plesset (new RI-MP2), Thermochemistry recipes (including the new T1 procedure), and an assortment of Advanced Correlated approaches.

SQLGrinder :- SQL tool

SQLGrinder If you need a tool to access any database that has a JDBC driver (Oracle, Sybase, mySQL, postgresql etc) I highly reccomend this tool, it is a native Cocoa application that has applescript support.

Stardrop:- Platform for supporting drug discovery

StarDrop provides a comprehensive range of features to support design and prioritisation of high quality compounds, including:

ADME QSAR models – predict a full range of ADME properties
P450 metabolism models – guide your chemistry to resolve metabolic liabilities
'Chemical space' visualisation and compound selection tools – explore the full chemical space of your chemistry
‘Probabilistic’ scoring – estimate each compound's likelihood of success using data on many properties simultaneously
Glowing Molecule visualisation - Interactively redesign compounds
Auto-Modeler - develop and deploy models of your own data


Sugarmagnolia :- Carbohydrate Mass Spec

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.

Sweet J :- Calculator for the Karplus Equation

Sweet J calculates the 3J coupling constant from the dihedral angle and the electronegativity of the substituents using either the Altona equation or a generalized Karplus equation.

Swiss-Pdb Viewer :-Molecule viewer

Swiss-PdbViewer a universal binary is now available.

SYBYL-X:- Molecular modelling

  • 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
SYBYL-X requires Mac OS X 10.6.x (Snow Leopard) they are already working on Lion support and aim to have it ready when the next Mac OS X update is released. For 3D graphics you might be better having a NVidia graphics card, ATI/AMD work as well, but there are currently some minor driver based issues.  So rather than having Hardware 3D on by default for ATI based cards, on detection, hardware stereo will be disabled only for ATI based chipsets.  You can however override this using a commandline switch. They also provide KNIME nodes for those who would like to include it in workflows. There are a number of licensing options and they are aware that users with multi-core machines would want to be able to take advantage of all cores.