Computational & Web Resources
Protein Structural Prediction
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[Osford Molecular] This is a molecular simulation program.
[European Molecular Biology Lab.] A program for the refinement of protein structures that interactivelly combines the reciprocal space structure factor refinement with updating of the model in real space.
B Molecular Modeling
[Scripps Institute] Formerly called Biomer, this Java applet builds molecular models to order. Designate components like DNA bases and amino acids to assemble into one molecule. The program also offers functions for energy minimization and molecular dynamics.
[Molecular Mechanics] This is a program for building 3D molecular structures, analyzing molecular geometry and reaction energetics, and for exploring molecular mechanics. These are fully functional 60 day trial versions of ChemPen and ChemPen3D.
[Univ. of Massachusetts, Department of Microbiology] This program is used to view molecular structures on Netscape.
[NCBI] This 3D molecular structure viewer for data entries from Entrez, allows the rotation of structures.
Cornell Theory Center
[Advance Cluster Computing Consortium] A high-performance computing and interdisciplinary research center. This site provides information about the center, resources like software and training, and research information.
DDL - Drug Design Laboratory
[Milan University, Italy] This site presents downloadable programs for drug design, including molecular dynamics for solvated molecules, program Predator to predict secondary structure of proteins, and molecular orbital calculations.
[UCSF] DOCK addresses the problem of "docking" molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together.
[Kabsch & Sander] This program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format.
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[Univ. du Maine-France] A special purpose Reverse Monte Carlo code for ab initio crystal structure determination.
[Sealy Center for Structural Biology, Univ. of Texas] Calculates low-energy conformations of polypeptides and proteins, compatible with distance and dihedral angle constraints obtained typically from NMR experiments.
[Imperial Cancer Research Tech.] A program that performs rigid-body docking on two biomolecules in order to predict their correct binding geometry.
[Columbia University] This tool is designed to facilitate the study of macromolecular function by mapping a number of structural, chemical, and biological properties onto various representations of molecular structure (molecular surfaces, wire frame, CPK spheres, or backbone tracing ribbons).
[University of Groningen] (Herman J.C. Berendsen) A molecular dynamics program for multiprocessor machines. The program is a fully automated topology builder for proteins, can conduct various simulations, as well as electrostatic and non-equilibrium molecular dynamics. It is free for non-commercial users.
[Univ. of Groningen] This is a general-purpose molecular dynamics simulation package.
[MDL Information Systems] A 2-D molecular structure visualization program.
[D. Richardson, Duke Univ.] A package of 2 programs, Prekins and Mage, that enables the user to create a 3-D image from a PDB-format coordinate file, which then can be modified.
[Univ. College London] A program for automatically plotting protein-ligand interactions. The interactions shown are those mediated by hydrogen bonds and hydrophobic contacts.
[Indiana University] This is a tool for drawing RNA secondary structures.
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[Molecular Ventures, Inc.] Molecular visualization programs designed for students/teachers in chemistry, biology, biochemistry, and related fields.
[University of Montreal] This program determines 3D protein and RNA structures.
[UCSF Computer Graphics Lab] An advanced molecular modeling system that can display and manipulate macromolecules such as proteins and nucleic acids.
[University College, London] A graphical user interface for MODELLER that replaces the the Modeller control language.
[Rockefeller Univ.] A program for homology protein structure modelling by satisfaction of spatial restraints.
[The State University of New York] (Carlos Simmerling) This program may be used to view and analyze molecular structures and dynamics.
[CMBI] (G.Schaftenaar) A package for the visualization of molecular and electronic structure.
A package of 3 programs, Psearch, Molw and Showcase, designed for searching, viewing, analyzing, and imaging macromolecular structures from PDB files.
This is a program for the analysis and display of molecules.
This completely interactive program can read different types of coordinate files and show various displays such as ribbon, CPK, stick, ball&stick, and surface figures.
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[Stockholm Univ. & Uppsala Univ.] MOVIEMOL visualizes and animates molecular structures.
[The Scripps Research Institute] MSMS allows users to compute triangulations of Solvent Excluded Surfaces very efficiently. This program is written in C programming language and can be used as a stand alone program or as an AVS (Advanced Visualization System) module. Binary versions of MSMS are available for SGI, Dec Alpha, HP9000, and Sun workstations.
[The Scripps Research Institute] MSV is an OpenGL based viewer for molecular surfaces computed with MSMS.
NAB: Nucleic Acid Builder
[Scripps Research Institute] A computer language for modelling nucleic acids, which allows description in a heirarchial fashion.
[Theorectical Biophysics Group] This program is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. The software is available via anonymous ftp.
NAMOT2: Nucleic Acid MOdeling Tool
[LANL] A graphic tool to build and manipulate nucleic acid structures.
[Biomolecular Structure Modelling Group] A program that generates schematic diagrams from 3-D coordinates found in a given PDB file. The program works for single and double stranded proteins, DNA, DNA-ligand, and protein-RNA complexes.
The O Files
[University of Aarhus] A general purpose macromolecular modelling program aimed at the field of protein crystallography. It enables the scientist to model, build, and display macromolecules.
[ORNL] A thermal ellipsoid plot program for crystal structure illustrations.
[National Univ. of Ireland, Galaway] A software system for solving, refining, and examining small molecule crystal structures.
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[University of Aarhus] A package of computer programs designed to compute phase angles for diffraction data from macromolecular crystals. The package contains programs for merging and scaling of native and derivative data sets, analyzing difference statistics, computing Patterson and electron density maps, and various isomorphous replacement routines.
[Paul Thiessen] PovChem takes 3-D chemical information in the PDB format, constructs a model, and outputs a plain-text file that contains that model in the POV-Ray format.
[Imperial Cancer Research Fund] This program produces molecular representations of proteins and nucleic acids, as well providing information on secondary structure.
Protein Modelling Software
[National University of Singapore] Well-annotated links to software for protein modelling programs and their online manuals.
[SciTech Software] A program for generating space-filling models from PDB files. Is is capable of generating worms and ball-and-stick models, as well as using preprocessing filters.
[EMBL Heidelberg] A program to detect contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.
[Univ. of Massachusetts, Department of Microbiology] RasMol is intended for visualization of proteins, nucleic acids, and small molecules.
RasMol 2.7.1 and 2.7.2
[Bernstein+Sons] New versions of RasMol, for molecular display and manipulation, with new manual, languages other than English.
[Stanford Univ.] Rayshade is an extensible system for creating ray-traced images. Its main function is to read a multiple-line ASCII file describing a scene to be rendered and produce a file containing the ray traced image.
[Gosper, Brunel Univ.] This program is a 4-D chemical viewer/analyzer, which is capable of 3-D molecular display, animation, and geometrical analysis.
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[CMC, Univ. of Alabama at Birmingham] (Mike Carson) This program is used for general molecular modeling and error analysis in protein crystallography.
[CABIOS] An application that uses RNA optimal structure, basepair-probability matrix, and heat curve calculation to predict RNA structure.
SIgMA: Simulations of Macromolecules
[Univ. of North Carolina] A program for conducting energy minimization, free molecular dynamics, constrained and restrained molecular dynamics, and molecular dynamics with free-energy methods.
[W. Wriggers, Univ. of California San Diego] A program package for the docking of protein crystal structures to single-molecule, low-resolution maps from electron microscopy, or small angle X-ray scattering.
[York Univ., Dept. of Chemistry] SQUID is a program to display, analyze, and validate molecular structures; carry out MD analysis; draw 2D, 3D, and 4D graphical representation of data; do data processing; and also has a macro language.
[Columbia Univ.] A tool for the simultaneous display of information about macromolecular structure (in STING's Graphics Frame) and sequence (in STING's Sequence Frame). Special attention is given to MacroMolecular INTERFACE analysis.
[Roman A. Laskowski] Generates surface and void regions between surfaces from coordinate data supplied in a PDB file. It can compute: van der Waals surfaces; gaps between molecules; clefts, cavities, and binding sites; 3D denisty distributions and sidechain interactions; and planes, paraboloids, and boxes.
[ExPASy] Application that provides an interface to analyze several proteins at the same time. Amino acid mutations, H-bonds, angles, and distances between atoms are easily obtained using the graphical user interface.
[ExPASy] Provides an interface allowing analysis of several proteins at the same time by superimposing them in order to deduce structural alignments and compare their active sites or any other relevant parts.
[Washington Univ. School of Medicine] This site includes McLachlan ASP and MacroModel GB/SA solvation; our own truncated Newton (TNCG) local optimizer; surface areas and volumes with derivatives; a simple free energy perturbation facility; normal mode analysis; minimization in Cartesian, torsional, or rigid body space; a new spherical energy cutoff method; reaction field treatment of long range electrostatics; and much more.
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[Dept. Biochemistry & Molecular Biology, Univ. College London] Generates protein topology cartoons. Places circles and triangles depicting alpha-helices and beta-strands respectively, giving a pictoral summary of any protein structure.
[Molecular Simulations Inc.] Combines desktop computing, validated computational chemistry methods, and the communications infrastructure offered by the World Wide Web.
[CMBI] This protein structure analysis program can be used for molecular graphics and structure verification.
[The Scripps Research Institute] The construction of x-ray crystal structures by the fitting of molecular models into an electron density map.