Welcome to NetSci's
List of Conformational Searching and Analysis Software
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The Software Section of NetSci is accessed by hundreds of scientists every week. Our goal is to make this resource as comprehensive as possible. If your software program is not included, please send e-mail with a brief description, the categories under which your program should appear, the platforms supported, and contact information.
For programs currently listed in NetSci, please check the table and description and notify us of any changes or additions.
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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. Conformational searching components include:
- C2*Conformers provides conformational search algorithms and associated analysis tools, allowing you to characterize molecular conformation and flexibility, and gain insight into geometric and energetic properties.
The program is available from Accelrys
COBRA is a "smart" conformational analysis program which utilizes heuristic techniques to automate conformational analysis and 3D structure generation. COBRA was developed by Oxford Molecular Group but is no longer available.
Concord is used to quickly generate 3D structures from 2D or 2.5D connection tables. Concord is available from Tripos, Inc.
Constrictor is a suite of distance geometry programs for the generation of 3-D structures of small molecules and proteins from distance information. Constrictor was developed by Oxford Molecular Group but is no longer available
CORINA is a 2D-to-3D conversion utility which is available for use through the CORINA website.
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DGEOM is a distance geometry program developed by Blaney, Crippen, Dearing and Dixon for building molecular models and receptor models. Utilizes the algorithms developed by Kuntz, Havel and Crippen. DGEOM runs on a wide variety of computer systems and is available as program number 590 from QCPE
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 person: prof. Werner Braun, (E-mail: werner@tocsy.utmb.edu; phone: (409) 747-6810).
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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.
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.
- Search/Compare generates and compares the conformers of different molecules. You can operate on molecular fields and volumes, superimpose two or more molecules, and search systematically for sterically allowed conformations.
The program is available from Accelrys
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There are no software packages listed in this section
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MOLGEN is used to construct all isomers corresponding to a given brutto formula and further side conditions.
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PADRE - Population Analysis and Duplicate Removal is a general purpose utility that can be used to analyse the results of conformational searches, and to measure similarity and differences between molecules. The program will be made available for a number of Unix platforms (Irix, Ultrix, Linux, more to come...). Some of the highlighted capabilities include:
- molecular overlap based on sterics and electronics
- cluster analysis
- Tcl/Tk based dendogram viewer interface to RASMOL and other programs
- automatic removal of duplicates from a multi-conformer file
- RMS distance/torsional difference measurement
- automatic detection of topologically equivalent atoms (automorphisms)
- support for numerous input and output file types
- simple command line interface
Availability: PADRE is freeware and can be retreived from the Ohio Supercomputer Center computational chemistry archive (infomeister.osc.edu).
Installation: Retrieve the file padre_beta_(platform).tar.Z from infomeister.osc.edu using either ftp or a web browser.
ftp ccl.osc.edu
login: anonymous
password: your-e-mail-address
cd /pub/chemistry/software/UNIX/PADRE
binary
get padre_beta_(platform).tar.Z
quit
1. uncompress padre_beta_(platform).tar.Z
2. tar -xvf padre_beta_(platform).tar
3. follow the instructions in the PADRE.DOC
Contact:
- Matthew Stahl
Harvard University
stahl@lhasa.harvard.edu
Tel: (617) 495-2654
Fax: (617) 495-1823
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There are currently no software packages listed in this section
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There are currently no software packages listed in this section
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There are currently no software packages listed in this section