HMMSTR-CM – Protein Contact Map Prediction

HMMSTR-CM

:: DESCRIPTION

HMMSTR-CM is a software for protein contact map predictions. As above a sequence profile is the input. HMMSTR-CM gives you a JPEG image and text file showing the residues that are most likely to come into contact (distance < 8.0A) in the folded structure. This too is a bare-bones package. This script runs as part of the HMMSTR/Rosetta server.

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HMMSTR-CM

:: MORE INFORMATION

Citaiton

Shao Y & Bystroff C. (2003a).
Predicting inter-residue contacts using templates and pathways.
Proteins, Structure, Function and Genetics 53 Suppl 6:497-502.

REPRO – Protein Repeats Analysis

REPRO

:: DESCRIPTION

REPRO (Protein Repeats Analysis) is able to recognise distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring local alignments, followed by a graph-based iterative clustering procedure to delineate the repeat set(s) based on consistency of the pairwise top-alignments.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

REPRO

:: MORE INFORMATION

Citation

George RA. and Heringa J. (2000)
The REPRO server: finding protein internal sequence repeats through the web
Trends Biochem. Sci. 25, 515-517.

TOPO2 – Create Transmembrane Proteins Images

TOPO2

:: DESCRIPTION

TOPO2 is an open source program written in Python for the creation of transmembrane protein 2D topology images. It makes no attempt to predict the TMDs that it displays. The user needs to supply that information. Residues of interest can be highlighted, if desired.

TOPO2 Web Version

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • Python

:: DOWNLOAD

TOPO2

:: MORE INFORMATION

Contact Susan Jean Johns (email: johns@cgl.ucsf.edu) for more information about the software or if you are having problems with the site.

DICROPROT 2000 – DICHROism of PROTeins

DICROPROT 2000

:: DESCRIPTION

DICROPROT (DICHROism of PROTeins) was designed to integrate into a single package most of the methods designed for the estimation of protein sequence secondary structure derivation from circular dichroism experiments.

::DEVELOPER

Pr Gilbert Deléage at France Institute of Biology and Chemistry of Proteins

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DICROPROT

:: MORE INFORMATION

Citation:

An interactive graphic program for calculating the secondary structure content of proteins from circular dichroism spectrum.
Deléage G, Geourjon C
(1993) Comput Appl Biosci. 2, 197-199.

estzmate – Assess Potential for Protein Coding Region

estzmate

:: DESCRIPTION

estzmate is a software to assess the potential for protein-coding regions in ESTs.

::DEVELOPER

Lars Arvestad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • Perl

:: DOWNLOAD

estzmate

:: MORE INFORMATION

Citation:

Savolainen P, Fitzsimmons C, Arvestad L, Andersson L, Lundeberg J (2005)  ESTs from brain and testis of White Leghorn and red junglefowl: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels. Cytogenet Genome Res 111(1), 79—78

MODELESTIMATOR 1.1 – Estimate Amino Acid Replacement Rates

MODELESTIMATOR 1.1

:: DESCRIPTION

MODELESTIMATOR estimates amino acid replacement rates from an input of aligned sequences.

::DEVELOPER

Lars Arvestad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • Perl

:: DOWNLOAD

MODELESTIMATOR Source Code

:: MORE INFORMATION

Citation:

Lars Arvestad, Efficient methods for estimating amino acid replacement rates, 2006, J Mol Evol, 62(6):663–673.

NucPred 1.1 – Predicting Nuclear Localization of Proteins

NucPred 1.1

:: DESCRIPTION

NucPred (pronounced newk-pred) analyses a eukaryotic protein sequence and predicts if the protein: spends at least some time in the nucleus or spends no time in the nucleus. Don’t forget that proteins can have multiple functions and/or multiple subcellular locations. However, if a protein is already known to be secreted or is an integral membrane protein, a second role as a nuclear protein is not likely. NucPred will make a small number of confident but contradictory predictions like this. So please use all sources of biological information (both real and predicted) when interpreting the results.

::DEVELOPER

Stockholm Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

NucPred

:: MORE INFORMATION

The source code to NucPred is freely available to all under the GNU Public License (GPL)

Citation:

NucPred – Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0 – Multiple Sequence Alignment , Viewer & Quality Assessment

Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0

:: DESCRIPTION

Kalign is a fast and accurate multiple sequence alignment software.

Kalignvu is an lightweight viewer for multiple sequence alignments and phylogenetic trees.

Mumsa is a program to assess the quality of multiple sequence alignments.

::DEVELOPER

Dr. Erik Sonnhammer

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Kalign ;  Kalignvu / Mumsa

:: MORE INFORMATION

Citation:

Kalign – an accurate and fast multiple sequence alignment algorithm.
Lassmann T. and Erik L.L. Sonnhammer (2005)
BMC Bioinformatics, 6:298

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.
Lassmann T. and Erik L.L. Sonnhammer (2006)
Nucleic Acids Research, 34:W596-W599

DASher 1.3.4 – Protein Sequence Client for DAS

DASher 1.3.4

:: DESCRIPTION

DASher is a Java DAS (the Distributed Annotation System) client for displaying annotations on a protein sequence. Enter a protein ID and DASher automatically gathers information about it from DAS servers around the world.

::DEVELOPER

David N. Messina (David.Messina@sbc.su.se) and Erik L. L. Sonnhammer

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

DASher

:: MORE INFORMATION

Citation:

David N. Messina and Erik L. L. Sonnhammer
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System
Bioinformatics (2009) 25 (10): 1333-1334.

SPICE 0.9 – Protein Sequences, Structures & Annotations Browser

SPICE 0.9

:: DESCRIPTION

SPICE is a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information.

::DEVELOPER

Andreas Prlic, Thomas Down, Tim Hubbard.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

SPICE

:: MORE INFORMATION

Citation:

Adding some SPICE to DAS
Bioinformatics Volume 21, suppl_2 Pp. ii40-ii41
Andreas Prlic, Thomas A. Down and Tim J. P. Hubbard