Unix Software
Back Up


This Site The Web

Get your own free Search Engine

Mac Software
PC Software
Unix Software

Website Map

For Bugs or adding links,Please email me!


UNIX Software

bulletAutobodrot, an awk (UNIX term) program, explores the Ranges of dihedral angle conformations that can be explored (Updated 5/3/99).
bulletAntheprot  permits the analysis of a protein sequence and 3D structure analysis (RS6000), (Updated 4/12/99).
bulletInformation about Antheprot
bulletAQUA 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).
bulletBlast Client Software Basic Local Alignment Search Tool.  It uses amino acid and nucleic acid fragments to search for similarities (Updated 7/16/99). 
bulletBlast (stand alone version)
bulletBoxshade (Ver. 3.3.1) Pretty Printing and Shading of Multiple-Alignment files (Updated 10/03/01).
bulletDang reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each
residue or base.
bulletDomainFinder 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).
bulletFTDock, RPScore and MultiDock
bulletGarlic - Version 1.1- new.GIF (3043 bytes)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).
bulletgOpenMol 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).
bulletGROMOS (GROningen MOlecular Simulation)
bulletICM 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).
bulletKin2Dcont and kin3Dcont reads value/coordinate lists to produce contour maps in kinemage format (Updated 5/3/99).
bulletJava 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).
bulletJOY new.GIFis 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). 
bulletMage (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).
Alternatives Location Comments
Mage, Official Duke University Main site, current version 5.4
Mage, Protein
Protein Science older version 4.2
Mage, FASEB Faseb older version 4.2
Mage, PDB PDB older version 5.28
bulletMPSA is a software intended to protein sequence analysis.
bulletInformation about MPSA software
bulletpdb2pov - Molecular Raytracing. This program allows you to convert pdb formatted files to povray.
bulletprobe allows one to view and score atomic packing, either within or between molecules (Updated 5/3/99).
bulletQmol: new.GIF (3043 bytes) A lightweight molecular viewer for Windows 95/NT and X Windows (Updated 01/21/01).
bulletRasMol 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).
bulletmain homepage at UMass, Amherst
bulletRasmol 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).
bulletREDUCE   is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file.
bulletSCWRL - 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).
bulletShadyBox is a boxing and shading utility for X Windows for multiple sequence alignments (Updated 5/3/99).
bullettigr software tool collection provides a group of Java based and UNIX based programs for use in molecular biology (Updated 5/1/99).
bullet  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).
bulletNAMD (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. 
bulletXMol Homepage by Networking Computer Services: this is a program for molecular visualization on an X-windows system.