QuantumBio :- QuantumMechanics
QuantumBio provides Pharmaceutical and
Biotech companies with fast Quantum Mechanical
(QM) solutions for Lead Optimization
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
Rasmol :-Molecule viewer
Rasmol A 3D molecule
viewer ported to Mac OS X
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.
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.
Ribbons :- Molecule viewer
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:
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
- K-Means
- Hierarchical
- SOM
- Random Walk
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!
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.
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.
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.
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).
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)
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.
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
carbonised version is available in alpha
form