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UNIX Software
 | Autobodrot,
an awk (UNIX term) program, explores the Ranges of dihedral angle conformations that can
be explored (Updated 5/3/99). |
| Antheprot permits the
analysis of a protein sequence and 3D structure analysis (RS6000), (Updated 4/12/99).
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| AQUA
is a suite of programs for Analyzing the QUAlity of
biomolecular structures that were determined via NMR spectroscopy. AQUA was
initially developed by Ton Rullmann and Jurgen Doreleijers in the NMR
Spectroscopy Department, Bijvoet Center for Biomolecular Research, Utrecht,
The Netherlands. It is currently maintained and expanded by Jurgen
Doreleijers at the BioMagResBank,
University of Wisconsin-Madison, USA (Updated 3/25/01). |
| Blast Client Software Basic Local Alignment Search Tool. It uses amino acid and nucleic
acid fragments to search for similarities (Updated 7/16/99). |
| Blast (stand
alone version) |
| Boxshade
(Ver. 3.3.1) Pretty Printing and
Shading of Multiple-Alignment files (Updated 10/03/01). |
| Dang
reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a
table of several useful geometric measurements for each
residue or base. |
| 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). |
| FTDock,
RPScore and MultiDock |
| Garlic - Version
1.1-  free
molecular visualization program, protein structure, DNA structure, PDB,
molecular rendering, biological macromolecule, unix, linux, free software
download, open source software, Damir Zucic (Updated 3/24/01). |
| gOpenMol graphics
interface to the OpenMol and cand be used for the analysis and display of molecular
dynamics trajectories and the display of molecular orbitals, electron densities and
electrostatic potentials (4/14/99). |
| GROMOS (GROningen MOlecular Simulation)
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| ICM lite
(registration required)
provides both a command line and graphical interface, allowing the user to
take advantage of whichever medium suits their needs best (Updated 8/20/00).
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| Kin2Dcont
and kin3Dcont reads value/coordinate lists to produce contour maps in kinemage format
(Updated 5/3/99). |
| Java based Molecular
Biologist's Workbench is a group of Java based tools that have varying levels of
usefulness at EMBL-Heidelberg (Updated
4/6/99). |
| JOY
 is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and help understand the conservation of amino acids in their specific local environments. For instance, it has been recognised that a sidechain hydrogen-bonded to a main-chain amide plays an important role in stabilizing the 3D structure and is generally well conserved during
evolution. You can
access the main page by clicking here (Updated 10/03/01). |
| Mage
(Version 5.4) Three dimensional viewing of molecules. It is
rather primitive by current standards, but it is a good educational tool. This is the
official site of kinemage and it is found at Duke
University (Updated 5/3/99). |
| MPSA is a software intended to
protein sequence analysis.
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| pdb2pov -
Molecular Raytracing. This program allows you to convert pdb formatted files to povray. |
| probe
allows one to view and score atomic packing, either within or between molecules (Updated
5/3/99). |
| Qmol:
A lightweight molecular viewer for Windows 95/NT and X Windows
(Updated 01/21/01). |
| RAMP
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| RasMol is the
universal molecular modeling program. I would suggest that everyone should have this
program because it allows visualization of molecules and it does not require too much
memory. It does require, however, that you know its commands (Updated 5/3/99).
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| Rasmol
2.7.1 Rasmol
2.7.1 (Latest Version) RasMol version 2.7.0 combined Roger Sayle's version 2.6.4 with Herbert Bernstein's CIF modified version 2.6_CIF(Rev 2)
and with Arne Mueller's version 2.6x1. This site is maintained by Bernstein
and Sons (Updated 6/15/99). |
| REDUCE
is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure
file. |
| SCWRL - Sidechain placement With a Rotamer Library
( free for academic users ) is a program for adding sidechains to a protein backbone based on the
backbone-dependent rotamer library. (Updated 9/23/99). |
| ShadyBox is a boxing and
shading utility for X Windows for multiple sequence alignments (Updated 5/3/99). |
| tigr software tool collection provides
a group of Java based and UNIX based programs for use in molecular biology (Updated
5/1/99). |
| Viewmol 2.2.1
is a graphical front end for some quantum chemical as well as for some molecular modelling
programmes (Updated 6/17/99).
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| VMD
 | NAMD
(Unix)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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| XMol Homepage by Networking Computer Services: this is a program for
molecular visualization on an X-windows system. |
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