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Lists of Software for
Bioinformatics: Structure Prediction

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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]




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--- D, E, F ---





 

FGENEH from the Baylor College of Medicine predicts a single complete gene and the corresponding amino acid sequence.





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GENSCAN, available from MIT, predicts complete gene structures in genomic sequences.



 

IDT's Biotools provides freely usable Internet access to software for oligonucleotide design for the PCR, secondary structure prediction, sequence similarity, and several other biophysical properties of nucleotide sequences.

Contact:

Integrated DNA Technologies Inc.
1710 Commercial Park
Coralville, IA 52241
319-626-9696
http://www.idtdna.com/program/gateway/gateway.asp




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--- M, N, O ---





 

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.



 

MSEQ is a user-friendly program which combines novel graphics and integration of predictive parameters from several sources for the prediction and display of protein secondary structures. A full description of the software can be found in Analytical Biochemistry, 193, 72-82, 1991. The software runs under DOS on IBM and compatibles. Contact:

Colleen Healy
University of Michigan Software
Room 2354
475 E. Jefferson Street
Ann Arbor, MI 48109-1248 USA
Tel: (313)936-0435
Fax: (313)936-1330



 

MZEF, from CSHL, is a program that predicts internal protein coding exons in genomic DNA sequences.



 

NAB was designed to construct models of helical and non-helical nucleic acids from a few dozen to a few hundred nucleotides in size. The program uses a combination of rigid body transformations and distance geometry to create candidate structures that match input criteria.



 

NAMOT(Nucleic Acid MOdeling Tool) is a tool developed at Los Alamos National Laboratory for the structural manipulation of single or double stranded, RNA or DNA. NAMOT uses a set of reduced co-ordinates to describe base/unit, sugar and phosphate geometry. Detailed description of these parameters can be found in the references listed at the bottom of this announcement.

Namot features an X11 graphics interface for display of the molecule while modifications are being carried out. Both Motif and XView toolkit versions exist, which should allow namot to be easily ported to most unix machines.

Namot is availible over the internet via anonymous ftp. To get namot:

ftp namot.lanl.gov
login: anonymous
Password:(Your email address)
cd pub/namot
get <which ever version you want>

Note: SGI users may need to use "nlist" and not "ls" to list files.

NAMOT 1. and NAMOT 1.2 have been tested on:

  • Sun SparcStation 1+ running SunOS 4.1.3
  • Sun SparcStation LX running SunOS 2,3
  • Sun SparcClassic running SunOS 2,2

NAMOT 1.2s has been tested on SGI Iris Indigo

Feedback on NAMOT is greatly appreciated, email can be sent to namot@temin.lanl.gov, Gene Carter (esc@temin.lanl.gov) or Chang-Shung Tung (cst@temin.lanl.gov)



 

NAOMI is no longer available.



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Peptool is a software program which assists in the identification of protein function. The program provides for alignment, homology building, structure prediction, etc. It is available from

BioTools, Inc.
420 Sun Life Place
Edmonton, Alberta
Canada T5J 3H1
403-423-1133


 

PoPMuSiC, has been developed to predict protein stability changes upon single-site mutations and is available through a web interface. PoPMuSiC is an efficient tool for rational computer-aided design of single-site mutations in proteins and peptides. Two types of queries can be submitted. The first option allows to estimate the changes in folding free energy for specific point mutations given by the user. In the second option, all possible point mutations in a given protein or protein region are performed and the most stabilizing or destabilizing mutations, or the neutral mutations with respect to thermodynamic stability, are selected. For each sequence position or secondary structure the deviation from the most stable sequence is moreover evaluated, which helps to identify the most suitable sites for the introduction of mutations. Additional information available from:

Dimitri Gilis, PhD
Biomolecular Engineering
Free University of Brussels
Avenue Franklin Roosevelt 50 - CP165/64
B-1050 Bruxelles
Belgium
Tel: +32 2 650 20 67
Fax: +32 2 650 36 06
E-mail: dgilis@ulb.ac.be


 

PROSPECT Pro is the latest release of the R&D 100 award-winning protein structure prediction tool. Derived from decades of recognized and well-respected research, PROSPECT Pro combines sequence to sequence and sequence to structure search methods with advanced analysis tools into one integrated software solution. Highly efficient in pinpointing target template proteins, PROSPECT Pro can give your organization the upper hand in drug discovery or research.

Platforms: Windows, Linux, SGI, Solaris, Mac OS
Categories: Bioinformatics, Drug Discovery, Proteomics, Protein Structure Prediction.

For additional information, contact:

Bioinformatics Solutions Inc.
145 Columbia St. West, Suite 2B
Waterloo, ON Canada N2L 3L2
Tel: (519) 885-8288
Fax: (519) 885-9075
http://www.bioinformaticssolutions.com


 

RAPTOR is an innovative software tool designed to predict protein structures from their sequence information. Based on a novel linear programming method, RAPTOR combines sequence-to-sequence and sequence-to-structure search methods with advanced analysis tools in one integrated software solution. Highly efficient in pinpointing target template proteins, RAPTOR can give your organization the upper hand in drug discovery or research.

Platforms: Windows, Linux, Mac OS, other platforms available on request.
Categories: Bioinformatics, Drug Discovery, Proteomics, Protein Structure Prediction.

For additional information, contact:

Bioinformatics Solutions Inc.
145 Columbia St. West, Suite 2B
Waterloo, ON Canada N2L 3L2
Tel: (519) 885-8288
Fax: (519) 885-9075
http://www.bioinfor.com/raptor




--- S, T, U ---





 

SegMod provides the user with a completely automated method for homology modeling. SegMod is no longer available.



 

SIGNALSCAN, a service from the NIH, finds homologies in published signal sequences based on the sequence submitted. The program is an excellent method to learn the identity of unknown proteins bound to characterized binding sites in DNA sequences.



 

SOPMA (Self Optimized Prediction Method from Alignment) is a package to make secondary structure predictions of proteins. This program is developed for Unix workstations and has been successfully checked onto IBM RS6000 workstations and SGI.



 

STRAP is a free comprehensive workbench for protein sequences and structures. With 200 different users each day it is one of the leading programs in this field. With a simplified appearance it serves as a Web-based viewer in seven different Bioinformatics resources including Prodom, PDBSum, ViperDB and JenaLib. The system features: mixed sequence and structure alignment, evolutionary dendrogram, 3D-Visualization, export as HTML, highlighting of sequence features from Expasy and DAS servers, structure prediction, export as HTML, PDF and MS-Word. The Drag-and-Drop handling makes data import and export very intuitive.



 

3D-PSSM is a Browser-based protein fold recognition program which uses 1D and 3D sequence profiles coupled with secondary structure information (Foldfit). The program is available at the Biomolecular Modelling Laboratory homepage.





--- V, W ---





 

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. Contact:

G. Vriend
E.M.B.L.
Meyerhofstrasse 2
D-6900 Heidelberg
GERMANY
Tel: +49-622-138-7473
Fax: +49-6221-387517
E-mail: VRIEND@EMBL-Heidelberg.de
URL: http://www.cmbi.kun.nl/

The program is also available from Suhaib M. Siddiqi (ssiddiqi@inspirepharm.com) for Windows from the Inspire Pharmaceuticals Web page at http://www.inspirepharm.com/whatif





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