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Molecular Modeling

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  Protein Structural Prediction
2nd Window Opens resource in a 2nd browser window.

2nd Window AMBER
[Osford Molecular] This is a molecular simulation program.
[more info][11290]

2nd Window ARP/wARP
[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.
[more info][11291]

2nd Window 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.
[more info][13639]

2nd Window ChemPen3D
[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.
[more info][11292]

2nd Window Chime
[Univ. of Massachusetts, Department of Microbiology] This program is used to view molecular structures on Netscape.
[more info][11293]

2nd Window Cn3D
[NCBI] This 3D molecular structure viewer for data entries from Entrez, allows the rotation of structures.
[more info][11294]

2nd Window 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.
[more info][12491]

2nd Window 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.
[more info][13641]

2nd Window DOCK
[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.
[more info][11295]

2nd Window DSSP
[Kabsch & Sander] This program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format.
[more info][11297]


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2nd Window Espoir
[Univ. du Maine-France] A special purpose Reverse Monte Carlo code for ab initio crystal structure determination.
[more info][11298]

2nd Window Fantom
[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.
[more info][11299]

2nd Window FTDOCK
[Imperial Cancer Research Tech.] A program that performs rigid-body docking on two biomolecules in order to predict their correct binding geometry.
[more info][11300]

2nd Window GRASS
[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).
[more info][11301]

2nd Window GROMACS
[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.
[more info][11302]

2nd Window GROMOS96
[Univ. of Groningen] This is a general-purpose molecular dynamics simulation package.
[more info][11303]

2nd Window ISIS/Draw
[MDL Information Systems] A 2-D molecular structure visualization program.
[more info][11304]

2nd Window Kinemage
[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.
[more info][11305]

2nd Window LIGPLOT
[Univ. College London] A program for automatically plotting protein-ligand interactions. The interactions shown are those mediated by hydrogen bonds and hydrophobic contacts.
[more info][11306]

2nd Window loopDloop
[Indiana University] This is a tool for drawing RNA secondary structures.
[more info][11307]


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2nd Window MacMolecule2
[Molecular Ventures, Inc.] Molecular visualization programs designed for students/teachers in chemistry, biology, biochemistry, and related fields.
[more info][11308]

2nd Window MC-SYM
[University of Montreal] This program determines 3D protein and RNA structures.
[more info][11223]

2nd Window MidasPlus
[UCSF Computer Graphics Lab] An advanced molecular modeling system that can display and manipulate macromolecules such as proteins and nucleic acids.
[more info][11310]

2nd Window MINT
[University College, London] A graphical user interface for MODELLER that replaces the the Modeller control language.
[more info][11311]

2nd Window MODELLER
[Rockefeller Univ.] A program for homology protein structure modelling by satisfaction of spatial restraints.
[more info][11224]

2nd Window MOIL-View
[The State University of New York] (Carlos Simmerling) This program may be used to view and analyze molecular structures and dynamics.
[more info][11312]

2nd Window MOLDEN
[CMBI] (G.Schaftenaar) A package for the visualization of molecular and electronic structure.
[more info][11313]

2nd Window Molecular Images
A package of 3 programs, Psearch, Molw and Showcase, designed for searching, viewing, analyzing, and imaging macromolecular structures from PDB files.
[more info][11314]

2nd Window MOLMOL 2.4
This is a program for the analysis and display of molecules.
[more info][11315]

2nd Window MolView
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.
[more info][11317]


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2nd Window MOVIEMOL
[Stockholm Univ. & Uppsala Univ.] MOVIEMOL visualizes and animates molecular structures.
[more info][11318]

2nd Window MSMS
[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.
[more info][11319]

2nd Window MSV
[The Scripps Research Institute] MSV is an OpenGL based viewer for molecular surfaces computed with MSMS.
[more info][11320]

2nd Window NAB: Nucleic Acid Builder
[Scripps Research Institute] A computer language for modelling nucleic acids, which allows description in a heirarchial fashion.
[more info][11321]

2nd Window NAMD2.0
[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.
[more info][11322]

2nd Window NAMOT2: Nucleic Acid MOdeling Tool
[LANL] A graphic tool to build and manipulate nucleic acid structures.
[more info][11323]

2nd Window NUCPLOT
[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.
[more info][11324]

2nd Window 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.
[more info][11325]

2nd Window ORTEP-III
[ORNL] A thermal ellipsoid plot program for crystal structure illustrations.
[more info][11326]

2nd Window Oscail
[National Univ. of Ireland, Galaway] A software system for solving, refining, and examining small molecule crystal structures.
[more info][11327]


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2nd Window Phases
[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.
[more info][11328]

2nd Window PovChem
[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.
[more info][11330]

2nd Window PREPI v0.9
[Imperial Cancer Research Fund] This program produces molecular representations of proteins and nucleic acids, as well providing information on secondary structure.
[more info][11331]

2nd Window Protein Modelling Software
[National University of Singapore] Well-annotated links to software for protein modelling programs and their online manuals.
[more info][12311]

2nd Window QTree
[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.
[more info][11333]

2nd Window QUILT
[EMBL Heidelberg] A program to detect contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.
[more info][11334]

2nd Window RasMol
[Univ. of Massachusetts, Department of Microbiology] RasMol is intended for visualization of proteins, nucleic acids, and small molecules.
[more info][11335]

2nd Window 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.
[more info][13614]

2nd Window Rayshade
[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.
[more info][11336]

2nd Window ReView
[Gosper, Brunel Univ.] This program is a 4-D chemical viewer/analyzer, which is capable of 3-D molecular display, animation, and geometrical analysis.
[more info][11338]


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2nd Window Ribbons
[CMC, Univ. of Alabama at Birmingham] (Mike Carson) This program is used for general molecular modeling and error analysis in protein crystallography.
[more info][11339]

2nd Window RNAdraw
[CABIOS] An application that uses RNA optimal structure, basepair-probability matrix, and heat curve calculation to predict RNA structure.
[more info][11173]

2nd Window 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.
[more info][11341]

2nd Window Situs
[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.
[more info][11342]

2nd Window SQUID
[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.
[more info][11344]

2nd Window STING
[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.
[more info][11345]

2nd Window SURFNET v.1.4
[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.
[more info][11346]

2nd Window Swiss-PdbViewer
[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.
[more info][11347]

2nd Window Swiss-PdbViewer
[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.
[more info][12341]

2nd Window TINKER
[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.
[more info][11348]


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2nd Window TOPS
[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.
[more info][11349]

2nd Window WebLab
[Molecular Simulations Inc.] Combines desktop computing, validated computational chemistry methods, and the communications infrastructure offered by the World Wide Web.
[more info][11351]

2nd Window WHAT IF
[CMBI] This protein structure analysis program can be used for molecular graphics and structure verification.
[more info][11352]

2nd Window XtalView
[The Scripps Research Institute] The construction of x-ray crystal structures by the fitting of molecular models into an electron density map.
[more info][11355]

 

 
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