Category: Protein Sequence Analysis

MASKER – Molecular Surface Area Calculator

MASKER

:: DESCRIPTION

MASKER is a program for calculating solvent accessible surface (SAS)  solvent excluded surface (SES) and solvation energy. Three program that use the MASKER module are included in this package:

pdbmask — calculates the solvent excluded surface of atoms in PDB format
maskercm — calculates the pairwise buried surface of residues in a protein
voidmask — finds the locations of buried empty spaces with in a protein, or any molecule.

MASKER contact map server

MASKER buried void calculator

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MASKER

:: MORE INFORMATION

Citaiton

C. Bystroff (2002)
MASKER: Improved solvent excluded molecular surface area estimations using Boolean masks
Protein Engineering, 15:959-965

HMMSUM – Structure-based Substitution Matrices

HMMSUM

:: DESCRIPTION

HMMSUM (HMMSTR-based SUbstitution matrices) is a new model for structural context-based amino acid substitution probabilities consisting of a set of 281 matrices, each for a different sequence-structure context. HMMSUM does not require the structure of the protein to be known. Instead, predictions of local structure are made using HMMSTR, a hidden Markov model for local structure. Alignments using the HMMSUM matrices compare favorably to alignments carried out using the BLOSUM50 matrix when validated against curated remote homolog alignments from BAliBASE. HMMSUM has been implemented using local Dynamic Programming and with the Bayesian Adaptive alignment method. The download package contains the essential programs from HMMSTR (see above) and the HMMSTR model itself, alng with Smith-Waterman local dynamic programming and Bayesian Adaptive alignment programs, modified to use the HMMSUM matrices.

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HMMSUM

:: MORE INFORMATION

Citaiton

Huang, Y-M, & Bystroff, C. (2006)
Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions.
Bioinformatics 22(4):413-422

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