Welcome to NetSci's
List of Conformational Searching and Analysis Software

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[ A, B, C ] -- [ D, E, F ] -- [ G, H, I ] -- [ J, K, L ]
[ M, N, O ] -- [ P, Q, R ] -- [ S, T, U ] --
[ V, W ] -- [ X, Y, Z]




--- A, B, C ---





 

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.





 

CONFLEX will completely search the conformational space of a flexible molecule to find every optimal structure of chemically significant conformers. Unlike its predecessor; CONFLEX, and other geometry optimization programs CONFLEX is not limited to finding only locally-optimized structures that depend on an initial structure input by the user. Utilizing several unique strategies, CONFLEX can exhaustively search conformational space to identify the most stable structures:

  • Downstream/reservoir-filling
  • A variable search limit
  • Three modes of perturbation (unique corner flap, edge flip, and stepwise rotation)
  • Pre-check

CONFLEX calculation results can be output in a variety of formats permitting their use in applications for ab-initio calculations or visualization applications such as BARISTA(TM).

CONTACT INFO:

Daniel Reid
dreid@conflex.us
Conflex USA
5631 Palmer Way
Suite C
Carlsbad, CA 92010 USA
http://www.conflex.us




 

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).





--- G, H, I ---





 

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





--- J, K, L ---





There are no software packages listed in this section





--- M, N, O ---





 

MOLGEN is used to construct all isomers corresponding to a given brutto formula and further side conditions.





--- P, Q, R ---





 

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




--- S, T, U ---





There are currently no software packages listed in this section





--- V, W ---





       

VeraChem is pleased to announce the release of three new products. All VeraChem products are now licensed free of charge to academic and other non-profit users!

Vconf conformational search for drug-like molecules. In "prep" mode, Vconf quickly generates 3D structures suitable for docking and other torsional search applications, with multiple outputs for distinct ring-puckers. In "search" model, Vconf carries out thorough conformational searches and provides high-quality, low-energy conformations. Special features include:

  • filtering to remove repeat conformations from the output, accounting for internal molecular symmetries
  • option to hold a set of atoms rigidly fixed in the input conformation
  • detailed control of chiral centers and double bond geometries.

For more information and download, go to http://www.verachem.com/vconf.html.

Vfilter conformational filtering for drug-like molecules. Processes the output of Vconf or any other conformational analysis program to remove repeat conformations based upon energy or RMSD, accounting for symmetry. For more information and download, go to http://www.verachem.com/vfilter.html.

Vrms calculation of RMSDs of conformations of a drug-like molecule, accounting for symmetries. RMSD with superposition is suitable for free ligands in solution; RMSD without superposition is suitable for docked ligands. For more information and download, go to http://www.verachem.com/vrms.html

Vcharge rapid generation of RESP-like partial charges, is also available. For more information and download, go to http://www.verachem.com/vcharge.html.





--- X, Y, Z ---





There are currently no software packages listed in this section



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