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List of Software for Modeling Biopolymers
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AbM - an integrated suite of programs for antibody structure modeling. It combines the benefits of knowledge databases with ab initio methods, permitting you to model the tertiary structure of an antibody starting with its primary sequence. The program was marketed by Oxford Molecular Group, but is no longer available.
ASP is a fast, automatic similarity assessment program which calculates molecular similarity based on electrostatic, steric, lipophilic or refractive properties. It is available from Accelrys
Biomer, an on-line molecular modeling program is located athttp://www.scripps.edu/~nwhite/Biomer/index.html. The program features biopolymer model builders ( nucleic acids, proteins, and polysaccharides ), AMBER force-field based geometry optimization, an interactive molecule editor, and simulated annealing with molecular dynamics. It should run on all platforms that support java and/or have a current java-enabled web browser.
- Neill K. White
- The Scripps Research Institiute
- 10550 North Torrey Pines Rd.
- La Jolla, CA 92037
- (619) 784-9620
BioModel was a biomolecular structure display and analysis program for Windows95 and Windows NT developed by Microsimulations. The program is no longer available.
BioPad was a Windows95 and Windows NT drawing tool for protein sequences developed by Microsimulations. The program is no longer available.
BIOPROP is a generalized, programmable neural network simulator for predicting protein structures. Designed for use on mainframe and supercomputers, however, the Fortran 77 code can be modified for use on personal computers. Contact: Office of Technology Licensing, 2150 Shattuck Avenue, STE 510, Berkeley, CA 94704 USA, Tel: +1-510-643-7201, Fax: +1-510-642-4566, E-mail: firstname.lastname@example.org
BRAGI is the tool for the interactive modeling unknown proteins from the structure of a known one. The current version has a number of features necessary and helpful for planning site-directed mutagenesis or for designing proteins with new properties. The program package is written in such a way that it can be used almost instantly by the average scientist who is not a computer specialist. BRAGI is fully menu driven, using many well known features of OSF-MOTIF, a window like user interface. 3-D representation includes features like wireframe display of structures, chicken wire surface colored by electrostatics, ball and stick display, solids to show secondary structure and generation of ray traced images. Contact:
- Joachim Reichelt
Gesellschaft fur Biotechnologische Forschung
Mascheroder Weg 1
Braunschweig, DW 38124
Cerius2 is a software environment designed to facilitate the chemical computing needs of R&D organizations. With Cerius2, scientists are able to apply the predictive power of computational chemistry to the critical issues in their research. WIth Cerius2 users can visualize structures, predict the properties and behavior of chemical systems, refine structural models, and integrate in-house computational codes in a commercial software environment. The Cerius2 environment integrates builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences. Biopolmer modeling components include:
- C2*Protein Active Site Viewer helps you visualize the
key elements of protein structure and protein-ligand interactions.
A "Hit-List-Browser" is included to review an active site, enabling
you to visualize the results of a database search in the context of
the protein active site.
- C2*Receptor helps you prioritize lead candidates for drug development by investigating their interaction with a protein receptor site, represented as a 3D surface. You can develop predictive QSAR models or rank the results of a database search by volumetric similarity.
The program is available fromAccelrys
Composer is a set of routines which assists in the construction of three dimensional homology models for proteins. The program is available fromTripos, Inc.
CONGEN (CONformation GENerator) is a noninteractive molecular modeling program that uses systematic conformational search to explore the energy surface of proteins (see Bruccoleri, Molecular Simulation,10, 151-174 (1993)). It can be used on either small peptides or segments (loops) within proteins. In addition, it can perform molecular mechanics and analysis operations. CONGEN is licensed only for research or educational usage, and the license is free of charge. This program is unsupported, but full source code, a 278-page manual, and additional tools (including graphical display) are provided. Contact:
Center for Advanced Biotechnology
679 Hoes Lane
Tel: (732) 235-5796
Consensus builds a 3D model of a protein from its amino acid sequence and the known structures of related proteins using distance constraints derived from the reference proteins. The program is available fromAccelrys
CREATOR is an integrated molecular modeling package for nucleic acids, protein engineering and drug design. The system couples molecular modeling, sequence analysis and structural analysis. The knowledge based query and modeling system is used to identify comparative structure-activity relationships for pharmacophore design. Contact: Thomas Kieber-Emmons, Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 USA, 215-898-2479, 215-898-3995 (F)
CURVES, by Richard Lavery and Heinz Sklenar is a very useful nucleic acid helical analysis program. The current version is CURVES 4.1 and its available free directly from the author. Contact: Richard Lavery, Laboratoire de Biochimie Theorique, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, 75005 Paris, France. Tel: +33 1 43 25 26 09; Fax: +33 1 43 29 56 45;Email: email@example.com
DRAGON is a protein modelling tool using Distance Geometry. DRAGON attempts to predict the tertiary structure of small water-soluble proteins, given a sequence, the secondary structure and possibly a set of distance restraints obtained from experimental sources or from sequence-structure alignments (comparative modelling or threading). Platforms supported: SGI, PC/Linux, Sun/Solaris. Multiprocessor and PVM support. Executables are available via anonymous ftp free of charge. The contact & download site is located athttp://www.nimr.mrc.ac.uk/~mathbio/a-aszodi/dragon.html
Escher Next Generation (NG) is an enhanced version of the original ESCHER protein-protein automatic docking system developed in 1997 by Gabriele Ausiello, Gianni Cesareni and Manuela Helmer Citterich. The new release, with a reengineered code, includes some new features:
- Protein-protein and DNA-protein docking capability.
- Fast surface calculation based on the NSC algorithm. No external software are required.
- Only two PDB files are required as input.
- Language localization.
- Parallel code.
ESCHER NG is one of the first docking software that take full advantages of the multiprocessor hardware. Tested on two processor systems, ESCHER runs about 1.8 time faster than an equivalent single processor workstations (same CPU and same clock). These performances can be increased optimizing the code that was not originally developed to the parallel execution. ESCHER NG can run also on single processor systems in sequential mode. The Win32 version is included in the latest VEGA OpenGL package and in the full package we can find the source code and the executables for Win32, Irix6.2, Linux, AmigaOS. Escher NG 1.0 is freely downloadable athttp://www.ddl.unimi.it
EuGene and SAm is a menus based DNA and protein sequence analysis package. The program efficiently manages data during DNA sequencing projects. The system can simulate genetic engineering experiments, search databases of DNA and protein sequences, compare multiple sequences for similarities and provide detailed structural information of sequences. Runs on Sun workstations. Contact: Christine B. Powaser, Lark Sequencing Technologies, 9545 Katy Freeway, Ste 200, Houston, TX 77024 USA, 713-464-7488, 713-464-7492 (F)
FANTOM The main purpose of the program FANTOM (Fast Newton - Raphson Torsion Angle Minimizer) is the calculation of conformations of linear and cyclic polypeptides and proteins with low conformational energies including distance and dihedral angle constraints from nuclear magnetic resonance experiments or for modeling purposes. The user can run energy minimizations and/or Monte Carlo simulations of an empirical energy function. Protein-solvent interaction is included with a fast routine for the calculation of accessible surface areas of individual atoms and their gradients. FANTOM is also suited for the exploration of low energy conformations of cyclic peptides or flexible loops in proteins.
FANTOM is available from the Sealy Center for Structural Biology, University of Texas Medical Branch. Program home page:http://www.scsb.utmb.edu/fantom/fm_home.html
Contact: prof. Werner Braun, (E-mail: firstname.lastname@example.org; phone: (409) 747-6810).
FlexX (http://www.biosolveit.de/FlexX/) is an extremely fast, robust, and highly configurable (FlexX-able) computer program for predicting protein-ligand interactions. It is capable of binding mode prediction, affinity estimation and virtual screening
FlexS (http://www.biosolveit.de/FlexS/) predicts the conformation and orientation of two ligands as assumed when they bind to a protein. It simultaneously assesses their similarity and this way facilitates ligand-based virtual screening
FTrees (http://www.biosolveit.de/FTrees/) is a highly efficient software tool for fuzzy similarity searching facilitating virtual HTS. Its ability to detect novel molecular scaffolds is one of several features that characterizes FTrees capabilities
GERM (Genetically Evolved Receptor Models) is used to develop three-dimensional atom-based models of previously uncharacterized receptor sites starting from a small structure-activity model of active and inactive compounds.
getpdb a ksh script which automates incremental mirroring of the Protein Data Bank.
GOLD is a program for calculating the docking modes of small molecules into protein-binding sites. It features a genetic algorithm for protein-ligand docking, full ligand and partial protein flexibility, choice of scoring functions, and a number of constraints to allow greater control over the output solutions. The software is available for Windows and UNIX. ContactCambridge Crystallographic Data Centre at http://www.ccdc.cam.ac.uk.
Gon+predss / Gon+predss+MULT: The Eisenberg Group's protein threading program which is a part of the UCLA-DOE frsvr server. Includes Fischer threading approach, considers predicted secondary structure in addition to fold recognition. Reference is D. Fischer and D. Eisenberg, "Fold recognition using sequence-derived predictions" in Protein Science 5: 947-955 (1996). Available athttp://www.mbi.ucla.edu/people/frsvr/frsvr.html
H3P2: The Rice threading approach (also a part of the UCLA-DOE frsvr server), which considers predicted secondary structure. Reference is D. Rice and D. Eisenberg, "A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence" J. Mol. Biol. (1996). Available athttp://www.mbi.ucla.edu/people/frsvr/frsvr.html
Hingefind is a new algorithm to determine and visualize protein domain movements by comparing two structures.
HINT (Hydrophobic INTeractions) a program for calculating and visualizing hydrophobic and hydrophobic interactions of biomolecular species is available from eduSoft.
Homology builds a 3D model of a protein from its amino acid sequence and the known structures of related proteins. Tools for assigning structurally conserved regions and building loops are built into the program. Homology is available fromAccelrys.
Insight II is a 3D graphical environment for molecular modeling. Its powerful user interface enables the seamless flow of data between a wide range of scientific applications. The Insight II environment integrates builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences.
- Biopolymer constructs models of peptides, proteins,
carbohydrates, and nucleic acids for visualizing complex
macromolecular structures and for use in further simulation
- DelPhi calculates electrostatic potentials and solvation
energies of both large and small molecules, including nucleic
acids. You can use DelPhi to rigorously examine the effects of
charge distribution, ionic strength, and the dielectric constant on
the electrostatic potentials of macromolecules.
- Modeler quickly and automatically generates a refined homology model of a protein, given only the sequence alignment to a known 3D protein structure. You are able to generate excellent structural models given as little as 30% homology to known structures.
The program is available fromAccelrys
INTERCHEM is a molecular modeling system designed for use on Silicon Graphics workstations. It includes facilities for handling and display of small molecules and large bio-molecules. Building new structures is made easy by a library of 380 pre-optimized (MOPAC) fragments. It incorporates a molecular mechanics program PIFF (written by Armin Widmer, Sandoz A.G.), which provides rapid optimization of structures. Structure files may be read into the program in SYBYL, BIOSYM, Cambridge Crystallographic Database XR and native INTERCHEM formats. The Proteins Package provides selective editing, display and highlighting of special features, investigation of homology, prediction of protein secondary structure, prediction of important sites, etc. The Crystal Structure package allows reading of files in Cambridge XR format, display of unit cells, the replication of the asymmetric unit necessary to fill a 3X3X3 nest of unit cells. Contact: Peter Bladon, Dept of Pure and Applied Chemistry, The University of Strathclyde, Glasgow G1 1X1, Scotland UK, 41-552-4400, 41-552-5664 (Fax), email@example.com@nsf-relay-ac.uk (e-mail)
Look was a program developed by Molecular Applications Group comprising a set of informatics tools which allowed the researcher to seamlessly access and manage protein sequences, structures, literature and experimental data. It is no longer available.
Match-Box Web Server: for protein threading is available at http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html
MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model.
Molegro Virtual Docker is an integrated platform for predicting protein - ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity. Highlights of Molegro Virtual Docker:
- Automated preparation of molecular structures
- Active site prediction
- Constraints to reward/penalize docked solutions
- Reranking score and estimation of binding energy
- Visual inspection and clustering of docked solutions
- Macro system to customize menus and program commands
- GUI wizards and online help
- Cross platform: Windows, Linux, and Mac OS X is supported
For more information, or to download a trial version, please visit our company website at:http://www.molegro.com
MPSRCH: is a program which permits rapid searches of DNA and protein sequence data banks using the full Smith-Waterman algorithm for the most rigorous searching available. The program is available fromEdinburgh Biocomputing Systems Limited. The authors recently have ported MPSRCH to general purpose hardware. It can be accessed free of charge atthe company's website.
MS calculates coordinates of points on the solvent-accessible surface of a molecule. These points can be used to display a variety of properties. Written by Michael Connolly and available fromQCPE
Molecular Surface Package is made up of two computer programs, MSRoll and MSDraw. The programs are written in ANSI C. Since neither currently does interactive graphics, they will run on any computer with an ANSI C compiler. MSP computes molecular surfaces, areas and volumes. Five programs provide robust, highly accurate areas and volumes and identify internal cavities. The programs are written in machine independent C. Source code is included with the license.
NAB - We have developed an approach to the modeling of nucleic acids that is implemented as a computer language called NAB. The method was primarily designed to construct models of helical and non-helical nucleic acids from a few dozen to a few hundred nucleotides in size, and uses a combination of rigid body transformations and distance geometry to create candidate structures that match input criteria. The language is designed to provide a flexible way to described nucleic acid structures at several levels of resolution, and contains built-in implementation of the AMBER force field, a generalized Born model for solvation effects, and a link to the AVS visualization system.
NAB is a computer language (specified through lex and yacc) that allows nucleic acid structures to be described in a hierarchical fashion, using a language similar to C or awk, but designed especially for the manipulation of molecular structures. We have applied NAB to duplex- and triplex- and tetraplex DNA, to RNA hairpins and pseudo-knots, to closed-circular DNA, and to models of the small subunit of the ribosome and of recombination sites.
NAB contains connections to the Amber and YAMMP modeling programs and force fields. This means that NAB programs can run analysis (including minimization and molecular dynamics simulations) using either the all-atom force fields from Amber or the reduced representation nucleic acids models from YAMMP. The generalized Born solvent model is also included.
This language may also be useful for other molecular modelling tasks, and a protein library is included in the distribution. NAB can also be used as a general-purpose language for writing programs that deal with three- dimensional molecular structures.
NAB is distributed as source code via anonymous ftp. It runs on many flavors of UNIX (IRIX, Linux, Solaris, HP-UX, Digital UNIX) and on Windows 95/98/NT. Details at:http://www.scripps.edu/case. FTP site:ftp://ftp.scripps.edu/pub/macke/nab-4.0.tar.gz
The 123D protein threading server is located athttp://www-lmmb.ncifcrf.gov/~nicka/run123D.html
The 123D TopLign: threading tool based on secondary structure prediction and residue-residue contact potential (part of the GMD-SCAI server), is available from the Zimmer group athttp://cartan.gmd.de/123D-test.html
PAP is a suite of programs to analyze protein structures. Modules are available to compute and display as a function of sequence Ramachandran and linear phi-psi plots, distance diagonal plots and temperature factors. Modules are also available to compute and plot RMS structure differences for two proteins. Proteins with sequence insertions or deletions can be handled. Priestle's RIBBON program has been converted to run as an interactive stand-alone program of SGI 4D series workstations. All programs accept Brookhaven PDB format for input and all programs have options to generate HP and PostScript output files. The programs run on Silicon Graphics 4D GT, GTX, Personal Iris and Indigo workstations. The programs were developed by T. Callahan, W.B. Gleason and T.P. Lybrand. It is available as program number 594 fromQCPE
ProFIT - Protein Fold Identification Tool conducts
threading based on an empirical "energy" function. For information,
The program is available at the ftp siteftp://gundi.came.sbg.ac.at.
The PSCAN threading server page is located athttp://www.biokemi.su.se/~threader_server/pscan/
Profiles-3D, a patented technology exclusively licensed to MSI, uses "environmental classification" of protein residues to assess whether a primary sequence is compatible with the current 3D structural model. Profiles-3D is used to search a structural-motif database with a new sequence, looking for compatibility; search a sequence database with an example structure, seeking similarity; or verify the agreement between the sequence and current model of a protein sequence/structure under study. The program is available fromAccelrys
Protein Adviser is a visualization, analysis and drawing program for biomolecular structures
PS - A Macintosh based graphics program for molecular analysis and modeling. It is designed to display, analyze, manipulate and redesign protein structures. It is applicable to proteins, DNA, RNA and small molecules. Contact: Office of Technology Licensing, 2150 Shattuck Avenue, STE 510, Berkeley, CA 94704 USA, Tel: +1-510-643-7201, Fax: +1-510-642-4566, E-mail: firstname.lastname@example.org
QUANTA is a 3D graphical environment for molecular modeling. Its powerful user interface enables the seamless flow of data between a wide range of scientific applications. The QUANTA environment integrates builder modules, simulation and visualization tools with tools specifically developed for protein design, NMR structure determination and X-ray structure analysis. Bioploymer-related modules include:
- Modeler automatically generates a refined homology model
of a protein, given only the sequence alignment to a known 3D
protein structure. You are able to generate excellent structural
models given as little as 30% homology to known structures.
- Protein Design is where protein modelers can find all
the tools they need to build, mutate, and design proteins. These
include multiple-sequence-alignment, homology construction (both
manual and automated, using Modeler), loop searching, secondary
structure analysis and prediction, domain analysis.
- Protein Health is a large collection of tools to analyze protein structure. Graphically oriented, this easy-to-use and easy-to-understand module enables scientists to review whether the current protein model has: hydrophobic residues on the surface, hydrophillic residues in the interior, backbone phi/psi angles outside standard Ramachandran areas, or buried cavities.
The programs are available fromAccelrys
RDP is a threading approach developed by the Lengauer group which uses recursive dynamic programming (part of the GMD-SCAI server). Reference is R. Thiele, R. Zimmer and T. Lengauer, "Recursive dynamic programming for adaptive sequence and structure alignment" Ismb 3: 384-92 (1995).
The server is located athttp://cartan.gmd.de
Swiss-Model protein threading server is located athttp://expasy.hcuge.ch/swissmod/SWISS-MODEL.html
Threader 2 protein threading program is available for downloading athttp://globin.bio.warwick.ac.uk/~jones/threader.html
Threading by Recursive Dynamic Programming [RDP] and Easy ToPLign Fold Prediction servers are available athttp://cartan.gmd.de/ToPLign.html. See N.N. Alexandrov, R. Nussinov and R.M. Zimmer, "Fast protein fold recognition via sequence to structure alignment and contact capacity potentials" Pacific Symposium on Biocomputing '96, Lawrence Hunter & Teri E. Klein, Eds, World Scientific Publishing Co., Singapore, pp. 53-72
TOPITS also called PHDthreader as part of the PredictProtein server is a protein threading program by Burkhard Rost based on secondary structure prediction and solvent accessibility prediction. Reference is B. Rost, "TOPITS: threading one-dimensional predictions into three-dimensional structures" Ismb 3: 314-321 (1995). The program is located athttp://www.embl-heidelberg.de/predictprotein/
VMD is a new package for the graphical display and visualization of biomolecular systems
VOID (Volume Overlap, Isotopy and Docking) is a program for computing the packing defects and the tunnels that connect them in protein molecules and for attempting to predict protein-protein associations. The program examines structures from the perspective of solid geometry rather than physical chemistry. It is available as program number 617 fromQCPE
WHAT IF is an extensive protein modeling, protein structure analysis, database handler, molecular graphics package. It is available for all Evans & Sutherland equipment and Silicon Graphics machines. The program is supplied with source code, databases and documentation.
- G. Vriend
The program is also available from Suhaib M. Siddiqi (email@example.com) for Windows at the Inspire Pharmaceuticals Web page athttp://www.inspirepharm.com/whatif
WINMGM, is a software package for visualization, manipulation and analysis of biomolecules ( Proteins, Nucleic Acids, Lipids,...). Visualization capabilities include real-time manipulation of high-grade graphics (CPK, ribbons,...), manipulation in relative or absolute coordinates of several molecules, rendering tools providing complex representations of " workstation quality ". Construction and optimization tools for peptides and proteins include systematic search using stereo-alphabet combinatorial methods, Monte Carlo calculations, side chain optimization. Analysis tools include.properties calculation such as hydrophobic/ hydrophilic or electrostatic potentials, interdistance maps, Ramachandran maps, solvent accessible surfaces... Available on PC under MS-Windows 3.1, NT and 95
Demo version available at http://www.fsagx.ac.be/info_faculte/info_dep/info_bp/mehdi/winmgm/winmgmen.htm
Product commercialized by: Ab Initio Technology , 1 place de l'Etoile F-67210 Obernai, France phone : +33 188.8.131.52 (after October 18/1996 : +33 03.88.95.68.52) Fax : +33 88.95.07.92 (after October 18/1996 : +33 03.88.95.07.92) email : firstname.lastname@example.org
Yeti and Yak molecular mechanics and display programs for receptor modeling with special treatment of h-bonding. The paper describing the program isYETI: An Interactive Molecular Mechanics Program for Small-Molecule Protein Complexes,Journal of Computational Chemistry, Vol. 9, No. 3, 269-280 (1988). The Yak reference is Vedani, A.; Zbinden, P.; Snyder, J.P. Pseudoreceptor modeling: A New Concept for the Three-dimensional Construction of Receptor Binding Sites,J. Receptor Res., 1993, 13, 163-177. An application of Yak is described in Snyder, J.P.; Rao, S.N.; Koehler, K.F.; Vedani, A.Minireceptors and Pseudoreceptors. In 3D QSAR in Drug Design. Theory, Methods and Applications, Kubinyi, H., Ed.; Escom: Leiden, 1993, pp. 336-354. For more information, contact:
- Angelo Vedani
SIAT Biographics Laboratory
Missions str. 60
CH-4055 Basel, Switzerland
Tel (061) 321 05 33
Fax (061) 321 05 40
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