INTREPED 2.0 – DNA Repair Protein Prediction server

INTREPED 2.0

:: DESCRIPTION

The INTREPED (INTeractive dna REPair prEDiction) web server is a collection of services for predicting properties relating to DNA repair. DNA repair is thought to exist in all organisms that have an active metabolism, and repair systems are crucial for repairing many types of DNA damage. External damage includes (but is not limited to) ionizing (UV) radiation, tobacco smoke, and chemical alteration. Examples of internal damage are DNA copying errors, oxygen byproducts resulting from metabolism, and hydrolysis.

::DEVELOPER

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2009 Jan 20;10:25. doi: 10.1186/1471-2105-10-25.
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology.
Brown JB, Akutsu T.

PRORATE – Prediction of Protein Folding Rates

PRORATE

:: DESCRIPTION

PRORATE is a novel approach to predict protein folding rates for two-state and multi-state protein folding kinetics, which combines a variety of structural topology and complex network properties that are calculated from protein three-dimensional structures.

::DEVELOPER

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Song J, Takemoto K, Shen H, Tan H, Gromiha MM, Akutsu T.
Prediction of protein folding rates from structural topology and complex network properties.
IPSJ Transactions on Bioinformatics 3, 40-53, 2010-05-12

HSEpred – Prediction of Half-Sphere Exposure from Protein Sequences

HSEpred

:: DESCRIPTION

HSEpred is a web server to predict the HSE(Half-Sphere Exposure) measures and infer residue contact numbers using the predicted HSE values, based on a well-prepared non-homologous protein structure dataset.

::DEVELOPER

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Web Server

:: DOWNLOAD

HSEpred

:: MORE INFORMATION

Citation:

Bioinformatics. 2008 Jul 1;24(13):1489-97. doi: 10.1093/bioinformatics/btn222.
HSEpred: predict half-sphere exposure from protein sequences.
Song J, Tan H, Takemoto K, Akutsu T.

ProteinEvolverABC – Estimation of Recombination and Substitution Rates in Alignments of Protein Sequences

ProteinEvolverABC

:: DESCRIPTION

The package ProteinEvolverABC is a computer framework to estimate recombination and substitution rates in multiple alignments of protein sequences by approximate Bayesian computation.

::DEVELOPER

CME Group

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

ProteinEvolverABC

:: MORE INFORMATION

Citation

Arenas M.
ProteinEvolverABC: Coestimation of Recombination and Substitution Rates in Protein Sequences by approximate Bayesian computation.
Bioinformatics. 2021 Aug 27:btab617. doi: 10.1093/bioinformatics/btab617. Epub ahead of print. PMID: 34450622.

SST – Secondary Structural Assignment Program

SST

:: DESCRIPTION

SST is a web server to assign secondary structures to protein coordinate data using the Bayesian method of Minimum Message Length (MML) inference

::DEVELOPER

Laboratory of Computational Biology (LCB), Monash University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jun 15;28(12):i97-105. doi: 10.1093/bioinformatics/bts223.
Minimum message length inference of secondary structure from protein coordinate data.
Konagurthu AS, Lesk AM, Allison L.

PairwiseStatSig 20110801 – Pairwise Statistical Significance

PairwiseStatSig 20110801

:: DESCRIPTION

PairwiseStatSig estimates the pairwise statistical significance of a pairwise local alignment of two protein sequences independent of any database using censored Maximum Likelihood Fitting.

::DEVELOPER

The Brendel Group @ Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PairwiseStatSig

:: MORE INFORMATION

Citation

Agrawal, A., Brendel, V. & Huang, X. (2008)
Pairwise statistical significance versus database statistical significance for local alignment of protein sequences.
BMC Bioinformatics 2009, 10(Suppl 3):S1

PresCont – Predicting Protein-protein Interfaces

PresCont

:: DESCRIPTION

PresCont is a web service which predicts in a robust manner amino acids that constitute protein-protein interfaces (PPIs)

::DEVELOPER

Computational Protein Design and Evolution at the University of Regensburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Proteins. 2012 Jan;80(1):154-68. doi: 10.1002/prot.23172.
PresCont: predicting protein-protein interfaces utilizing four residue properties.
Zellner H, Staudigel M, Trenner T, Bittkowski M, Wolowski V, Icking C, Merkl R.

CLIPS-1D / CLIPS-4D – Predicting Functionally and Structurally Important Residue-positions based on 1D / and 3D data

CLIPS-1D / CLIPS-4D

:: DESCRIPTION

CLIPS-1D / CLIPS-4D: Predicting functionally and structurally importand residues by means of a multiclass support vector machine

::DEVELOPER

Computational Protein Design and Evolution at the University of Regensburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Apr 5;13:55. doi: 10.1186/1471-2105-13-55.
CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure.
Janda JO, Busch M, Kück F, Porfenenko M, Merkl R.

Bioinformatics. 2013 Oct 4.
CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data.
Janda JO, Meier A, Merkl R.

H2r – Identification of Evolutionary Important Residues

H2r

:: DESCRIPTION

H2r is a online web server of identification of important residue-sites by means of an entropy based analysis of multiple sequence alignments

::DEVELOPER

Computational Protein Design and Evolution at the University of Regensburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

MC Bioinformatics. 2008 Mar 18;9:151. doi: 10.1186/1471-2105-9-151.
H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.
Merkl R, Zwick M.

QFC – Quasi-Periodic Feature Classifier algorithm for G protein-coupled receptors

QFC

:: DESCRIPTION

QFC (quasi-periodic feature classifier) is a new algorithm for identifying multi-transmembrane proteins from genomic databases with a specific application to identifying G protein-coupled receptors (GPCRs).

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ MacOsX/ Windows
java

:: DOWNLOAD

QFC

:: MORE INFORMATION

Citation

J. Kim, E.N. Moriyama, C.G. Warr, P.J. Clyne, and J.R. Carlson. 2000.
“Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties.”
Bioinformatics., 16(9): 767-775.