JAMMING:- 3D Protein analysis
Although
several approaches based on physics principles (e.g.,
electrostatics) have been reported to identify
critical residues from the three dimensional
structure of proteins (3), there is a
limited accessibility to software aimed to
identify critical residues from protein
structures. Network analysis on the other hand
has been recently shown to be succesfull and
complementary to protein sequence-based
approaches, JAMMING provides a
means to identify critical residues from protein
3D structures Efficient identification of
critical residues based only on protein
structure by network analysis Cusack M, Thibert B, Bredesen DE
and del Rio G. 2007. PLoS ONE
2(5):e421
JChem :- Java chemoinformatcs toolkit
JChem
Modules:
JChem Base: adds a chemical interface to corporate databases, which can be applied for combined SQL and structural queries; imports/exports molecules, substructures, or reactions in standard formats (Molfile, SD file, RD file, SMILES, SMARTS, etc.).
JChem Cartridge: adds chemical knowledge to the Oracle platform giving automatic access to Oracle's security, scalability, and replication features.
Standardier: structure canonicalization tool converting molecules from different formats into standard representation.
Screen: screening based on pharmacophore or chemical fingerprints or other descriptors.
Reactor: generating reaction products from reaction equations and reactants.
Fragmenter: generating building blocks based on Recap rules from molecule libraries.
Serial Molecule Generator: transforming molecules by a sequence of user-defined transformations.
Chemical Term Evaluator: evaluating chemical expressions.
JKlustor: clustering and diversity calculations based on molecular fingerprints or other properties
Also a review of Instant JChem
JChem 3.2.1 has been released.
For the list of changes please see:
http://www.chemaxon.com/jchem/changes.html
JChem Base: adds a chemical interface to corporate databases, which can be applied for combined SQL and structural queries; imports/exports molecules, substructures, or reactions in standard formats (Molfile, SD file, RD file, SMILES, SMARTS, etc.).
JChem Cartridge: adds chemical knowledge to the Oracle platform giving automatic access to Oracle's security, scalability, and replication features.
Standardier: structure canonicalization tool converting molecules from different formats into standard representation.
Screen: screening based on pharmacophore or chemical fingerprints or other descriptors.
Reactor: generating reaction products from reaction equations and reactants.
Fragmenter: generating building blocks based on Recap rules from molecule libraries.
Serial Molecule Generator: transforming molecules by a sequence of user-defined transformations.
Chemical Term Evaluator: evaluating chemical expressions.
JKlustor: clustering and diversity calculations based on molecular fingerprints or other properties
Also a review of Instant JChem
JChem 3.2.1 has been released.
For the list of changes please see:
http://www.chemaxon.com/jchem/changes.html
Jmol :-Molecule viewer
Jmol is a
Java molecular viewer for three-dimensional
chemical structures. Features include reading a
variety of file types and output from quantum
chemistry programs, and animation of multi-frame
files and computed normal modes from quantum
programs. Also available as an applet. Jmol is a
fully compatible replacement for rasmol/chime in
that it will use rasmol/chime scripts
jVisualizer :- NMR analysis
Kinemage :-Protein structure analysis
Kinemage have a variety of very useful
bits of software for investigating protein
structure Mage
a 3D display
program, KiNG, Rduce, Probe, Dang
KnowledgeMiner :- A self-organising data mining tool
KnowledgeMiner
A
self-organising data mining tool
Ligand Scout:-
LigandScout
is a software tool
that allows to rapidly and transparently derive
3D pharmacophores from structural data of
macromolecule/ligand complexes in a fully
automated and convenient way.
LiBMCS:- Clusters based on maximum common substructure
LibraryMCS clusters a set
of chemical structures on a structural basis.
Structures that share a common substructure are
clustered together. The common substructure is
identified by the clustering program, and it is
always the largest one among all substructures
found in the structure set. Such substructure is
called the Maximum Common Substructure (MCS). No
predefined fragments are applied in finding the
MCS.
LigBuilder: Build ligands for protein active sites
I
recently came across a program called LigBuilder
developed at the Molecular Design
Laboratory, it is a
multiple-purposed program written for
structure-based drug design procedure. Based on
the three-dimensional structure of the target
protein, it can automatically build ligand
molecules within the binding pocket and
subsequently screen them.
To quote from the website:-
"(1) The program analyzes the binding pocket of the target protein and derives the key interaction sites. A pharmacophore model is suggested and it could be applied to 3D database searching.
(2) User can choose either growing strategy or linking strategy to develop ligand molecules.
(3) Molecules are constructed by using fragments as building blocks. Various kinds of structural manipulation are provided, such as growing, linking, and mutation. On-the-fly minimization of conformation is performed during the building-up procedure. While the target protein is kept rigid, flexibility of the ligand molecules is considered.
(4) Molecules are evolved by Genetic Algorithm. The fitness score of a molecule is evaluated by considering its chemical viability as well as binding affinity.
(5) Chemical rules for judging "drug-likeness" are applied to screen the resultant molecules. Chemical stability, synthesis feasibility, and toxicity can also be taken into account by defining "forbidden structure" libraries.
(6) All the input and output molecules are in popular format, i.e. protein in PDB format and ligand in Sybyl Mol2 format. The program is very easy to use and maintain."
LigBuilder is written in ANSI C++ language and has been tested on UNIX and LINUX but not MacOSX, I've downloaded the siource and with minor modificartions got it to run under MacOSX.
For more detailed description of LigBuilder, please refer to: Wang, R.; Gao, Y.; Lai, L. "LigBuilder: A Multiple-Purpose Program for Structure-Based Drug Design", J.Mol.Model., 2000, 6, 498-516.
Instructions for running LigBuilder under MacOSX.
Download LigBuilder
A folder called LigBuilderv1.2 will be created in 'Downloads' in that folder you should find
bin/ default working directory
pocket/ source codes of POCKET module
grow/ source codes of GROW module
link/ source codes of LINK module
process/ source codes of PROCESS module
parameter/ necessary parameters
example/ test examples
manual/ user manual in HTML
fragment.mdb/ building-block fragment library
forbidden.mdb/ forbidden substructure library
toxicity.mdb/ toxic substructure library
LigBuilder has four main modules, i.e. POCKET, GROW, LINK, and PROCESS. You need to compile them respectively. You can do this by simply entering each subdirectory, i.e. "pocket/", "grow/", "link/", and "process/", and typing "make" to run the Makefile scripts. The scripts will compile the source codes automatically and generate the executable codes. The default C++ compiler assigned in the Makefile script is SGI "CC" compiler. To compile under MacOSX you should open the "MakeFile" in a text editor (i used BBEdit) and modify the first line in the "Makefile" scripts as "CC = g++" before compiling. You need to do this in each of the POCKET, GROW, LINK, and PROCESS folders.
Now open a terminal window and cd to the LigBuilderv1.2 folder
>cd /Downloads/LigBuilderv1.2/
Now cd to each of the POCKET, GROW, LINK, and PROCESS folders in turn and run make and then copy the resulting executable to usr/local/bin, you will need the admin password.
>cd pocket/
>make
g++ -c -o main.o main.c
g++ -c -o parameter.o parameter.c
g++ -c -o protein.o protein.c
g++ -c -o ligand.o ligand.c
g++ -c -o pocket.o pocket.c
g++ -c -o misc.o misc.c
g++ main.o parameter.o protein.o ligand.o pocket.o misc.o -o pocket -lm
>sudo cp pocket /usr/local/bin/pocket
Password:
>cd ..
>cd grow/
>make
g++ -c -o main_grow.o main_grow.c
g++ -c -o basic.o basic.c
g++ -c -o parameter.o parameter.c
g++ -c -o forcefield.o forcefield.c
g++ -c -o fraglib.o fraglib.c
g++ -c -o pocket.o pocket.c
g++ -c -o check.o check.c
g++ -c -o misc.o misc.c
g++ -c -o ligand.o ligand.c
g++ -c -o logp.o logp.c
g++ -c -o grow.o grow.c
g++ -c -o mutate.o mutate.c
g++ -c -o score.o score.c
g++ -c -o search.o search.c
g++ -c -o ga_grow.o ga_grow.c
g++ main_grow.o basic.o parameter.o forcefield.o fraglib.o pocket.o check.o misc.o ligand.o logp.o grow.o mutate.o score.o search.o ga_grow.o -o grow -lm
>sudo cp grow /usr/local/bin/grow
>cd ..
>cd link
>make
g++ -c -o main_link.o main_link.c
g++ -c -o basic.o basic.c
g++ -c -o parameter.o parameter.c
g++ -c -o forcefield.o forcefield.c
g++ -c -o fraglib.o fraglib.c
g++ -c -o pocket.o pocket.c
g++ -c -o check.o check.c
g++ -c -o misc.o misc.c
g++ -c -o ligand.o ligand.c
g++ -c -o logp.o logp.c
g++ -c -o link.o link.c
g++ -c -o mutate.o mutate.c
g++ -c -o score.o score.c
g++ -c -o search.o search.c
g++ -c -o ga_link.o ga_link.c
g++ main_link.o basic.o parameter.o forcefield.o fraglib.o pocket.o check.o misc.o ligand.o logp.o link.o mutate.o score.o search.o ga_link.o -o link -lm
>sudo cp link /usr/local/bin/link
>cd ..
>cd process
>make
g++ -c -o main_process.o main_process.c
g++ -c -o parameter.o parameter.c
g++ -c -o basic.o basic.c
g++ -c -o ligand.o ligand.c
g++ -c -o population.o population.c
g++ -c -o check.o check.c
g++ -c -o misc.o misc.c
g++ main_process.o parameter.o basic.o ligand.o population.o check.o misc.o -o process -lm
>sudo cp process /usr/local/bin/process
To quote from the website:-
"(1) The program analyzes the binding pocket of the target protein and derives the key interaction sites. A pharmacophore model is suggested and it could be applied to 3D database searching.
(2) User can choose either growing strategy or linking strategy to develop ligand molecules.
(3) Molecules are constructed by using fragments as building blocks. Various kinds of structural manipulation are provided, such as growing, linking, and mutation. On-the-fly minimization of conformation is performed during the building-up procedure. While the target protein is kept rigid, flexibility of the ligand molecules is considered.
(4) Molecules are evolved by Genetic Algorithm. The fitness score of a molecule is evaluated by considering its chemical viability as well as binding affinity.
(5) Chemical rules for judging "drug-likeness" are applied to screen the resultant molecules. Chemical stability, synthesis feasibility, and toxicity can also be taken into account by defining "forbidden structure" libraries.
(6) All the input and output molecules are in popular format, i.e. protein in PDB format and ligand in Sybyl Mol2 format. The program is very easy to use and maintain."
LigBuilder is written in ANSI C++ language and has been tested on UNIX and LINUX but not MacOSX, I've downloaded the siource and with minor modificartions got it to run under MacOSX.
For more detailed description of LigBuilder, please refer to: Wang, R.; Gao, Y.; Lai, L. "LigBuilder: A Multiple-Purpose Program for Structure-Based Drug Design", J.Mol.Model., 2000, 6, 498-516.
Instructions for running LigBuilder under MacOSX.
Download LigBuilder
A folder called LigBuilderv1.2 will be created in 'Downloads' in that folder you should find
bin/ default working directory
pocket/ source codes of POCKET module
grow/ source codes of GROW module
link/ source codes of LINK module
process/ source codes of PROCESS module
parameter/ necessary parameters
example/ test examples
manual/ user manual in HTML
fragment.mdb/ building-block fragment library
forbidden.mdb/ forbidden substructure library
toxicity.mdb/ toxic substructure library
LigBuilder has four main modules, i.e. POCKET, GROW, LINK, and PROCESS. You need to compile them respectively. You can do this by simply entering each subdirectory, i.e. "pocket/", "grow/", "link/", and "process/", and typing "make" to run the Makefile scripts. The scripts will compile the source codes automatically and generate the executable codes. The default C++ compiler assigned in the Makefile script is SGI "CC" compiler. To compile under MacOSX you should open the "MakeFile" in a text editor (i used BBEdit) and modify the first line in the "Makefile" scripts as "CC = g++" before compiling. You need to do this in each of the POCKET, GROW, LINK, and PROCESS folders.
Now open a terminal window and cd to the LigBuilderv1.2 folder
>cd /Downloads/LigBuilderv1.2/
Now cd to each of the POCKET, GROW, LINK, and PROCESS folders in turn and run make and then copy the resulting executable to usr/local/bin, you will need the admin password.
>cd pocket/
>make
g++ -c -o main.o main.c
g++ -c -o parameter.o parameter.c
g++ -c -o protein.o protein.c
g++ -c -o ligand.o ligand.c
g++ -c -o pocket.o pocket.c
g++ -c -o misc.o misc.c
g++ main.o parameter.o protein.o ligand.o pocket.o misc.o -o pocket -lm
>sudo cp pocket /usr/local/bin/pocket
Password:
>cd ..
>cd grow/
>make
g++ -c -o main_grow.o main_grow.c
g++ -c -o basic.o basic.c
g++ -c -o parameter.o parameter.c
g++ -c -o forcefield.o forcefield.c
g++ -c -o fraglib.o fraglib.c
g++ -c -o pocket.o pocket.c
g++ -c -o check.o check.c
g++ -c -o misc.o misc.c
g++ -c -o ligand.o ligand.c
g++ -c -o logp.o logp.c
g++ -c -o grow.o grow.c
g++ -c -o mutate.o mutate.c
g++ -c -o score.o score.c
g++ -c -o search.o search.c
g++ -c -o ga_grow.o ga_grow.c
g++ main_grow.o basic.o parameter.o forcefield.o fraglib.o pocket.o check.o misc.o ligand.o logp.o grow.o mutate.o score.o search.o ga_grow.o -o grow -lm
>sudo cp grow /usr/local/bin/grow
>cd ..
>cd link
>make
g++ -c -o main_link.o main_link.c
g++ -c -o basic.o basic.c
g++ -c -o parameter.o parameter.c
g++ -c -o forcefield.o forcefield.c
g++ -c -o fraglib.o fraglib.c
g++ -c -o pocket.o pocket.c
g++ -c -o check.o check.c
g++ -c -o misc.o misc.c
g++ -c -o ligand.o ligand.c
g++ -c -o logp.o logp.c
g++ -c -o link.o link.c
g++ -c -o mutate.o mutate.c
g++ -c -o score.o score.c
g++ -c -o search.o search.c
g++ -c -o ga_link.o ga_link.c
g++ main_link.o basic.o parameter.o forcefield.o fraglib.o pocket.o check.o misc.o ligand.o logp.o link.o mutate.o score.o search.o ga_link.o -o link -lm
>sudo cp link /usr/local/bin/link
>cd ..
>cd process
>make
g++ -c -o main_process.o main_process.c
g++ -c -o parameter.o parameter.c
g++ -c -o basic.o basic.c
g++ -c -o ligand.o ligand.c
g++ -c -o population.o population.c
g++ -c -o check.o check.c
g++ -c -o misc.o misc.c
g++ main_process.o parameter.o basic.o ligand.o population.o check.o misc.o -o process -lm
>sudo cp process /usr/local/bin/process
MacChess :-Crystallography
MacChess A
Macromolecular crystallographic facility
MacMolPlt :-GAMESS viewer
MacMolPlt an excellent tool for viewing
GAMESS results.
A modern graphics program for plotting 3-D molecular structures and normal modes (vibrations). Modern means: Mouse driven interface for real-time rotation and translation. Copy and paste functionality for interfacing to other programs such as word processors or other graphics programs (like ChemDraw). Simple printing to color or black and white printers (publication quality).
A modern graphics program for plotting 3-D molecular structures and normal modes (vibrations). Modern means: Mouse driven interface for real-time rotation and translation. Copy and paste functionality for interfacing to other programs such as word processors or other graphics programs (like ChemDraw). Simple printing to color or black and white printers (publication quality).
Marvin :-Structure drawing/viewing
Marvin is a java
application/applet recently updated, for
displaying and editing chemical structures, it
can be used to render different structure
formats including SMILES/SMARTS and MOL files,
it can also be used as a drawing package to
generate a variety of file formats. There is a
more detailed review here.
Mathematica :- Numerical analysis
Mathematica 6
Now
available for MacOSX. Also check out
gridMathematica and Mathematica for students.
Now gridMathematica 2 delivers a parallel
Mathematica environment that’s optimized for
modern multiprocessor
machines and
computational
clusters.
"Authoring with Mathematica and the new Publish for Player web service couldn't be simpler: educators, researchers, and others upload their Mathematica 6 notebooks to the Publish for Player website and instantly get back Player-compatible files. That means that people can now share dynamic content across classrooms and workgroups and publish their work without any software barriers. Mere documents become robust applications--virtually free-standing and cross-platform--in seconds."
The free Mathematica Player software and more information about the notebook conversion process are available online.
"Authoring with Mathematica and the new Publish for Player web service couldn't be simpler: educators, researchers, and others upload their Mathematica 6 notebooks to the Publish for Player website and instantly get back Player-compatible files. That means that people can now share dynamic content across classrooms and workgroups and publish their work without any software barriers. Mere documents become robust applications--virtually free-standing and cross-platform--in seconds."
The free Mathematica Player software and more information about the notebook conversion process are available online.
Mercury :- Crystal structure viewer
Mercury updated to
version 2.0 (Jan 2008) is now available for
MacOSX from CCDC. Mercury offers a comprehensive
range of tools for structure visualisation and
the exploration of crystal packing.
Its features include:
Input of hit-lists from ConQuest, or other format files such as CIF, PDB, MOL2 and MOLfile. A full range of structure display styles, including displacement ellipsoids (please note that displacement ellipsoids can be displayed for CIFs or SHELX res files which contain Uequiv or Uij values only). The ability to measure and display distances, angles and torsion angles involving atoms, centroids and planes. The ability to create and display centroids, least-squares mean planes and Miller planes. The ability to display unit cell axes, the contents of any number of unit cells in any direction, or a slice through a crystal in any direction. Location and display of intermolecular and/or intramolecular hydrogen bonds, short nonbonded contacts, and user-specified types of contacts. The ability to build and visualise a network of intermolecular contacts. The ability to show extra information about the structure on display, such as the chemical diagram (if available) and the atomic coordinates. The ability to calculate, display and save the powder diffraction pattern for the structure on view. The ability to save displays
Its features include:
Input of hit-lists from ConQuest, or other format files such as CIF, PDB, MOL2 and MOLfile. A full range of structure display styles, including displacement ellipsoids (please note that displacement ellipsoids can be displayed for CIFs or SHELX res files which contain Uequiv or Uij values only). The ability to measure and display distances, angles and torsion angles involving atoms, centroids and planes. The ability to create and display centroids, least-squares mean planes and Miller planes. The ability to display unit cell axes, the contents of any number of unit cells in any direction, or a slice through a crystal in any direction. Location and display of intermolecular and/or intramolecular hydrogen bonds, short nonbonded contacts, and user-specified types of contacts. The ability to build and visualise a network of intermolecular contacts. The ability to show extra information about the structure on display, such as the chemical diagram (if available) and the atomic coordinates. The ability to calculate, display and save the powder diffraction pattern for the structure on view. The ability to save displays
MestReNova NMR processing software
MestReNova is the
natural evolution of the popular application MestReC.
In addition to all the functionality available in
MestReC 4.9.9.6, MestReNova incorporates a
wealth of additional features:
- Full WYSIWYG with different Zoom in/out levels
- Powerful Undo/Redo mechanism
- Powerful drawing tools with advanced text editing capabilities.
- Anti-aliasing for improved drawing quality
- Cutting tool to exclude non-interesting regions from the spectrum
- Automatic processing capabilities
- Powerful scripting engine
- Molecular viewer
- Peak to atom assignment module
- Prediction of 1H and 13C NMR from chemical structure
- Simulation of spin systems with any number of spin particles
- Automatic fitting of experimental to predicted spectrum
mMass :- Open Source Mass Spectrometry Tool
mMass is an open
source and multi-platfrom package of many tools
for mass spectrometric data analysis, mainly in
proteomics.
MOE :-Molecular modelling
Chemical Computing
Group have
released MOE for MacOSX. The
Molecular Operating Enviroment is a
comprehensive piece of software providing
extensible tools for molecualr modelling,
bioinformatics, computer aided molecular design
all built using Scientific Vector Language
(SVL). This programming language allows the
rapid construction of novel tools many examples
of which are available via SVL exchange.
Read a review of MOE I wrote for MacResearch here
Read a review of MOE I wrote for MacResearch here
MODELLER :-Protein modelling
MODELLER is used for
homology or comparative modeling of protein
three-dimensional structures. The user provides
an alignment of a sequence to be modeled with
known related structures and MODELLER
automatically calculates a model containing all
non-hydrogen atoms. MODELLER implements
comparative protein structure modeling by
satisfaction of spatial restraints and can
perform many additional tasks, including de novo
modeling of oligopeptides, optimization of
various models of protein structure with respect
to a flexibly defined objective function,
multiple alignment of protein sequences and/or
structures, clustering, searching of sequence
databases, comparison of protein structures,
etc.
MoFa :-Chemoinformatics
MoFa is a program
for finding frequent, discriminative molecular
substructures in a set of molecules. The name
MoFa is an acronym for Molecular Fragment
Miner
MOLCAS :-Quantum chemistry
MOLCAS is a quantum
chemistry software developed by scientists to be
used by scientists. It is not primarily a
commercial product and it is not sold in order
to produce a fortune for its owner (the Lund
University). The authors have tried in MOLCAS to
assemble their collected experience and
knowledge in computational quantum chemistry.
MOLCAS is a research product and it is used as a
platform by the Lund quantum chemistry group in
their work to develop new and better
computational tools in quantum chemistry
Molconn :-QSAR
Molconn is the standard
program for generation of Molecular
Connectivity, Shape, and Information Indices for
Quantitative Structure Activity Relationship
(QSAR) Analyses.
MOLDEN :-Molecular density display
MOLDEN is a package
for displaying molecular density. It is
tuned to the Ab Initio packages GAMESS* and
GAUSSIAN
Molecula Numerica:- Molecular Dynamics
Molecula Numerica
is a software
categorized in Molecular Dynamics Simulator. The
software is produced to give priority to the
visualization of the atoms/molecules. You can
see what happened in the atomic world in a
REAL-TIME sense. Of course the actual time scale
of the phenomena in atomic world is pretty
small, we mean you can see the computation
results in REAL-TIME.
The software simulates not only translating motions but also rotational motions of atoms/molecules. Multi-atom molecules are dealt as a rigid body. So the software has a limitation coming from which High frequency vibration of the bonding is neglected. But the time integration is effectively fast by the simple model. To solve the rotational motion the simulator adopts quaternion based rotational equation. As for the scheme for time stepping, a Leap-Frog is adopted.
The software simulates not only translating motions but also rotational motions of atoms/molecules. Multi-atom molecules are dealt as a rigid body. So the software has a limitation coming from which High frequency vibration of the bonding is neglected. But the time integration is effectively fast by the simple model. To solve the rotational motion the simulator adopts quaternion based rotational equation. As for the scheme for time stepping, a Leap-Frog is adopted.
Molecule :- Molecular editor
Molegro Data Modeller :- Chemoinformatics data analysis
Molegro
Data Modeller offers a high-quality modelling tool
based on state-of-the-art data mining techniques.
Highlights of Molegro Data Modeller: - Regression: Multiple Linear Regression, Support Vector Machines, and Neural Networks - Feature selection and cross-validation is simple to set up and use (using the built-in wizards) - Principal Component Analysis (PCA) - Visualization: Histograms, 2D scatter plots, and 3D plots - Clustering: K-means clustering and density-based clustering - Built-in algebraic data transformation tool - Outlier Detection - Sophisticated subset creation: create diverse subsets by sampling from n-dimensional grids
Highlights of Molegro Data Modeller: - Regression: Multiple Linear Regression, Support Vector Machines, and Neural Networks - Feature selection and cross-validation is simple to set up and use (using the built-in wizards) - Principal Component Analysis (PCA) - Visualization: Histograms, 2D scatter plots, and 3D plots - Clustering: K-means clustering and density-based clustering - Built-in algebraic data transformation tool - Outlier Detection - Sophisticated subset creation: create diverse subsets by sampling from n-dimensional grids
Molegro Virtual Docker :- Protein ligand docking
Molegro Virtual Docker
is
an integrated platform for predicting protein -
ligand interactions. Molegro Virtual Docker
handles all aspects of the docking process from
preparation of the molecules to determination of
the potential binding sites of the target
protein, and prediction of the binding modes of
the ligands.
Molecules:- A molecular viewer for the iPhone and iPod Touch
Molecules is an
application from Sunset Lake Software for the
iPhone and iPod Touch that allows you to view
three-dimensional renderings of molecules and
manipulate them using your fingers. The
molecules can be downloaded from the Protein
Data Bank (http://www.rcsb.org/pdb).
You can rotate the molecules by moving your finger
across the display, zoom in or out by using
two-finger pinch gestures, or pan the molecule by
moving two fingers across the screen at once.
Molecules is free and its source code is available
under the BSD license.
Molekel :- Molecular visualiser
Molekel is a
multiplatform molecular visualization program
being developed at the Swiss National Supercomputing
Centre (CSCS).
Molekel was developed at the University of Geneva and CSCS/ETH Zurich in the early nineties, and is currently being rewritten under an open source GPL license.
Current version is only alpha release, source code is available here
Molekel was developed at the University of Geneva and CSCS/ETH Zurich in the early nineties, and is currently being rewritten under an open source GPL license.
Current version is only alpha release, source code is available here
Molinspiration :-Chemoinformatics
Molinspiration
Molinspiration
specializes in the development of
cheminformatics software in Java. Molinspiration
tools are therefore platform independent and may
be run on any PC, Mac, UNIX or LINUX machine.
The software is distributed in a form of
toolkits, which may be used as stand-alone
computational engines, used to power web-based
tools, or easily incorporated into larger
in-house Java applications
MOLMOL :-Molecule viewer
MOLMOL A molecule
viewer ported to Darwin
Moloc :- Molecular Design Software Suite
Moloc a
Molecular Design Software Suite, includes
Small Molecule Modeling
Matching Utilities
Conformational analysis
Peptide and Protein Modeling
Pharmacophore Modeling
Similarity Concepts and Database Mining
Diversity Analysis and Similarity Models
Dynamics: trajectory generation and evaluation
X-ray Facilities
Display Features
Small Molecule Modeling
Matching Utilities
Conformational analysis
Peptide and Protein Modeling
Pharmacophore Modeling
Similarity Concepts and Database Mining
Diversity Analysis and Similarity Models
Dynamics: trajectory generation and evaluation
X-ray Facilities
Display Features
MolView X :- Molecule viewer
MolView X is the OSX
version of MolView
MolWorks :-Chemoinformatics
MOLWORKS a platform for
chemical information software written in
Java
MOSFLM :- CCD analysis
MPQC :-Parallel quantum chemistry
MPQC is the
Massively Parallel Quantum Chemistry Program. It
computes properties of atoms and molecules from
first principles using the time independent
Schrödinger equation. It runs on a wide range of
architectures ranging from individual
workstations to symmetric multiprocessors to
massively parallel computers. Its design is
object oriented, using the C++ programming
language and has been ported to
G5/MacOSX.
MultiSEq 2.0:- A unified bioinformatics analysis environment
MultiSeq is a unified
bioinformatics analysis environment that allows
one to organize, display, and analyze both
sequence and structure data for proteins and
nucleic acids. Special emphasis is placed on
analyzing the data within the framework of
evolutionary biology. MultiSeq is included with
VMD
