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Mol. Mod. Software
Online Protein Viewers
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Software Used in Molecular Modeling and Molecular Dynamics
 | AMBER (UNIX; proprietary) at Peter A. Kollman's research
group at the University of California San Francisco
(Updated 5/22/99).
 | Description: AMBER refers to two things: a molecular
mechanical force field for the simulation of biomolecules (which is in general use in a
variety of simulation programs); and a package of molecular simulation programs which
includes source code and demos.(Updated 5/22/99). |
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| AMMP (Unix,
Linux, and PC; Free Downloadable Software) is a modern full-featured
molecular mechanics, dynamics and modeling program. It can manipulate both small molecules
and macromolecules including proteins, nucleic acids and other polymers. This software is
found at Structural Biology at
Jefferson and the Kimmel Cancer Center (Updated 5/22/99). |
| CHARMM Homepage (UNIX; License Required) by Martin Karplus's group
at Harvard University. Charmm has been integrated
into the popular molecular modeling software package, QUANTA, of Molecular Simulations Inc.
(MSI) (Updated 5/22/99)
| CHARMM Commands |
| Description: CHARMm combines standard
minimization and dynamics capabilities with expert features including free energy
perturbation (FEP), correlation analysis and combined quantum and molecular mechanics
(QM/MM) methods. Simulations provide insight into molecular-level structure, interactions,
and energetics (Updatd 5/22/99). |
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| Chem2Pac
( Windows, Free )is intended to be
a kind of computational chemistry integrator, which has a multiple document interface, a
molecular rendering utility, and allows the manipulation of various files (Updated
7/14/99).
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| Dalton Quantum Chemistry
Program (Unix
and Windows; Free, but License Required)(represents a powerful quantum chemistry
program
for the calculation of molecular properties with SCF, MP2 or MCSCF wave
functions. The
strengths of the program are mainly in the areas of magnetic and
(frequency-dependent)
electric properties, and for studies of molecular potential energy surfaces,
both for static and
dynamical investigations (Updated 7/14/99). |
| Deep
Viewer (free
for PC and Macintosh) is an application that provides a user
friendly interface allowing to analyse several proteins at the same time.
The proteins can be superimposed in order to deduce structural alignments
and compare their active sites or any other relevant parts. Amino acid
mutations, H-bonds, angles and distances between atoms are easy to obtain
thanks to the intuitive graphic and menu interface (Updated 3/25/01).
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| DomainFinder 1.0
(Free only UNIX; Linux) is an interactive program for the determination and characterization of dynamical
domains in proteins. Its key features are
computational efficiency: even large proteins can be analyzed using a desktop computer in a
few minutes
ease of use: a state-of-the-art graphical user interface
export of results for visualization and further analysis
(VRML, PDB, and MMTK object
format) (Updated 6/14/99). |
| EGO (Unix
and PC (with GNU-c compiler); free downloadable)is a program to perform
molecular dynamics simulations on parallel as well as on sequential computers at Bayerish Acadamie of Science, Munich, Germany
(Updated 5/22/99). |
| FTDock,
RPScore and MultiDock |
| GAMESS Home Page
(Unix, VMS, MVS, VM, Mac, or PC; free downloadable Software)
for doing ab initio calculations at Ames
Laboratory/Iowa State University (Updated 5/22/99).
| Description: GAMESS can compute wavefunctions
ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections available
for some of these (Updated 5/22/99). |
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| GROMACS (Unix, and PC (in the future), free downloadable for non-commercial
users) is a useful suite of molecular modeling utilities available at
Chemistry department University of Groningen
(Updated 5/22/99). |
| GROMOS (GROningen MOlecular Simulation)
 (free
for academic usage; Unix?) is a general-purpose molecular dynamics computer simulation package for the study
of biomolecular systems. The site is maintained at ETH
(Updated 7/17/99). |
| MEPSIM distribution (Code obtainable through email; Website currently under
construction) for Molecular Electrostatic Potential SIMilarity Analysis
(Updated 5/22/99)
| Description: New features of the
program will include the possibility of performing GAMESS and GRID calculations within the
package, taking profit of the MEPSIM modules (Updated 5/22/99). |
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| MOLGEN (MSDOS; free downloadable) automatic structure
elucidation (FTP site)(Updated
5/22/99)
| Description: This software allows the user to do various
calculations (i.e. HOMO, LUMO, potential) on small molecules (Updated 5/22/99). |
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| MOLSCAT (UNIX;
free downloadble) is a code for quantum mechanical (coupled channel)
solution of the nonreactive molecular scattering problem (Updated 5/22/99). |
| MolScript (UNIX;
free for non-profit, but license required) Official Homepage by Avatar Software AB, who develops, markets and distributes
software for structural biology, protein NMR and bioinformatics (Updated 5/22/99).
| Documentation |
| Description: MolScript is a program for creating
schematic or detailed molecular graphics images from molecular 3D coordinates, usually,
but not exclusively, protein structures (Updated 5/22/99). |
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| Molecular Structure
Editor
with the complete
source code in
C and x86 assembler language and can rotate a molecule
of 5000
atoms drawn with nice realistically looking balls and sticks on a lowly 80386/16MHz and can be configured to read output files generated by almost
any popular
quantum-chemical application (Updated 6/14/99). |
| MMTK (UNIX
(Requires Python); free downloadable) Molecular Modelling Toolkit (MMTK)
is a program library for molecular modelling applications at Theoretical biophysics at the CBM (Updated
5/22/99).
| Description: MMTK provides researchers, especially those
working on the development of new simulation and modelling methods, with a code basis that
can be easily extended and modified to deal with standard and non-standard problems in
molecular modelling (Updated 5/22/99). |
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| MOE
(UNIX and Windows, proprietary)
the Molecular Operating Environment is the next generation of chemical
computing software. MOE is an integrated Applications Environment and
Methodology Development Platform. MOE integrates visualization, simulation
and application development in one package (Updated 5/13/01). |
| NAMD Home Page
(UNIX; free downloadable, but registration required )
is a parallel, object-oriented molecular dynamics code designed for high- performance
simulation of large biomolecular systems at the Theoretical
Biophysics Group of University of Illinois at Urbana. (Updated 5/22/99) |
| SCWRL - Sidechain placement With a Rotamer Library
( Unix; free
for academic users ) is a program for adding sidechains to a protein backbone based on the
backbone-dependent rotamer library. The library provides lists of
chi1-chi2-chi3-chi4 values and their relative probabilities for residues at
given phi-psi values, and explores these conformations to minimize sidechain-backbone clashes and sidechain-sidechain
clashes (Updated 9/23/99). |
| Swiss PDB
Viewer (free
for PC and Macintosh) is an application that provides a user
friendly interface allowing to analyze several proteins at the same time.
The proteins can be superimposed in order to deduce structural alignments
and compare their active sites or any other relevant parts. Amino acid
mutations, H-bonds, angles and distances between atoms are easy to obtain
thanks to the intuitive graphic and menu interface (Updated 3/25/01).
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| TINKER Molecular Modeling Package,
(PC; free downloadable) it is a program that
accepts a variety of different parameter files from a variety of different molecular
dynamics packages, including AMBER, and CHARMM (Note: Trouble connecting to server
5/22/99, Updated 5/22/99).
| Molda is a
Graphics interface for Tinker. Note: the Tinker server is sometimes down, so in the
near future I will try to make copies available to this site. (Updated 5/22/99) |
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| Viewmol
(Unix; free downloadable) is a graphical
front end for computational chemistry programs. It is able to
graphically aid in the generation of molecular structures for computations
and to visualize their results. The program has many features.
(Updated 7/15/99) |
| VMD
| NAMD
(Unix and Free)is a parallel, object-oriented molecular
dynamics code designed for high-performance simulation of large biomolecular
systems. NAMD is distributed free of charge and includes source code. |
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| WHAT IF (UNIX
and PC; proprietary) is a versatile protein structure analysis program
that can be used for mutant prediction, structure verification, molecular graphics, etc.
at the EMBL Heidelberg Germany,
BIOcomputing unit, 3D modeling, protein structure analysis. (Updated 5/22/99) |
| WHAT IF
(web interface) (platform independent; Free)
provides nearly 2000 options in fields as diverse as
homology modeling, drug docking, electrostatics calculations, structure
validation and visualisation (Updated 6/9/99). |
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