POLYPHEN 2.2.3 – Prediction of Functional Effects of Human nsSNPs

POLYPHEN 2.2.3

:: DESCRIPTION

PolyPhen (Polymorphism Phenotyping) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.

::DEVELOPER

SUNYAEV LAB

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 POLYPHEN

:: MORE INFORMATION

Citation

Ivan A Adzhubei , Steffen Schmidt , Leonid Peshkin , Vasily E Ramensky , Anna Gerasimova , Peer Bork , Alexey S Kondrashov & Shamil R Sunyaev
A method and server for predicting damaging missense mutations
Nat Methods 7, 248-9 (2010)

piRPred 1.0 – piwi interacting RNA (piRNA) Prediction

piRPred 1.0

:: DESCRIPTION

piRPred is a new modular and extensible machine learning method based on multiple kernels and a support vector machine (SVM) classifier for piRNA identification.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 piRPred

:: MORE INFORMATION

Citation

Towards a piRNA prediction using multiple kernel fusion and support vector machine.
Brayet J, Zehraoui F, Jeanson-Leh L, Israeli D, Tahi F.
Bioinformatics. 2014 Sep 1;30(17):i364-i370. doi: 10.1093/bioinformatics/btu441.

GPS-YNO2 1.0.1 – Prediction of Tyrosine Nitration Sites

GPS-YNO2 1.0.1

:: DESCRIPTION

GPS-YNO2 is a software package to predict PTN sites. The software demonstrated a promising accuracy of 76.51%, a sensitivity of 50.09% and a specificity of 80.18% from the leave-one-out validation.

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

  • WIndows / Linux / MacOsX
  • Java

:: DOWNLOAD

 GPS-YNO2

:: MORE INFORMATION

Citation

GPS-YNO2: Computational prediction of tyrosine nitration sites in proteins
Zexian Liu, Jun Cao, Qian Ma, Xinjiao Gao, Jian Ren and Yu Xue.
Molecular BioSystems, 2011, 7(4): 1197-1204

Geptop 2.0 – Gene Essentiality Prediction tool for COMPLETE-GENOME based on Orthology and Phylogeny

Geptop 2.0

:: DESCRIPTION

Geptop is a webserver, which first provides a platform to detect essential gene sets over bacterial species, by comparing orthology and phylogeny of query protein sets with essential gene datasets determined experimentally (from DEG database).

::DEVELOPER

Microbe and Drug Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Python
  • BioPython

:: DOWNLOAD

 Geptop

:: MORE INFORMATION

Citation

PLoS One. 2013 Aug 15;8(8):e72343. doi: 10.1371/journal.pone.0072343. eCollection 2013.
Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny.
Wei W1, Ning LW, Ye YN, Guo FB.

HemeNet – Heme Binding Residue Prediction using Sequence, Structure, and Residue Interaction Network

HemeNet

:: DESCRIPTION

HemeNet, a support vector machine (SVM) based predictor, was developed to identify heme-binding residues by combining topological features with existing sequence and structural features.

::DEVELOPER

Machine Learning and Evolution Laboratory (MLEG)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2011;6(10):e25560. doi: 10.1371/journal.pone.0025560. Epub 2011 Oct 3.
Computational prediction of heme-binding residues by exploiting residue interaction network.
Liu R1, Hu J.

TANGLE – Protein Backbone Torsion Angle Prediction from Primary Sequences

TANGLE

:: DESCRIPTION

TANGLE (Torsion ANGLE) predictor works by integrating multiple local sequence profiles in combination with global sequence features within a two-level SVR learning framework. Input features include evolutionary profiles in the form of position-specific scoring matrices (PSSMs), predicted secondary structure, solvent accessibility and native disorder information. Moreover, other global sequence information such as sequence length and sequence weight were also used as input to TANGLE.

::DEVELOPER

Akutsu Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(2):e30361. doi: 10.1371/journal.pone.0030361.
TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences.
Song J, Tan H, Wang M, Webb GI, Akutsu T.

Phosfinder – Phosphate Binding Sites prediction on Protein Structures

Phosfinder

:: DESCRIPTION

Phosfinder is a bioinformatic web server for the prediction of phosphate-binding sites in protein structures.

::DEVELOPER

Phosfinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W278-82. doi: 10.1093/nar/gkr389. Epub 2011 May 26.
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.
Parca L1, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2011 Mar;39(4):1231-42. doi: 10.1093/nar/gkq987. Epub 2010 Oct 24.
Phosphate binding sites identification in protein structures.
Parca L1, Gherardini PF, Helmer-Citterich M, Ausiello G.

SABLE v4 – Accurate sequence-based prediction of relative Solvent AccessiBiLitiEs

SABLE v4

:: DESCRIPTION

The SABLE server can be used for predicting real valued relative Solvent AccessiBiLitiEs of amino acid residues in proteins, and for improved prediction of secondary structures using evolutionary profiles and predicted relative solvent accessibility of an amino acid residue as a fingerprint of the overall packing.

::DEVELOPER

Meller Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SABLE 

:: MORE INFORMATION

Citation

Adv Exp Med Biol. 2010;680:307-19. doi: 10.1007/978-1-4419-5913-3_35.
Enhanced prediction of conformational flexibility and phosphorylation in proteins.
Swaminathan K1, Adamczak R, Porollo A, Meller J.

Accurate prediction of solvent accessibility using neural networks-based regression.
Adamczak R, Porollo A, Meller J.
Proteins. 2004 Sep 1;56(4):753-67.

Agos – GW Argonaute-binding Domain Prediction

Agos

:: DESCRIPTION

Agos is an alignment-free approach to detect Argonaute-binding WG/GW domains in protein sequence. The identification method is based on the amino-acid composition specificity of the domain. The initial sequence dataset of experimentally-confirmed AGO-binding proteins was used to introduce two-parameter scoring system that help to discriminate genuine GW repeat proteins.

::DEVELOPER

ComGen lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 1;27(9):1318-9. doi: 10.1093/bioinformatics/btr128. Epub 2011 Mar 8.
Agos–a universal web tool for GW Argonaute-binding domain prediction.
Zielezinski A1, Karlowski WM.

Sann – Solvent Accessibility Prediction by Nearest Neighbor Method

Sann

:: DESCRIPTION

Sann is a web server for prediction of protein solvent accessibility by nearest neighbor method.

::DEVELOPER

Korea Institute for Advanced Study

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Sann

:: MORE INFORMATION

Citation

Proteins. 2012 Jul;80(7):1791-7. doi: 10.1002/prot.24074. Epub 2012 May 8.
Sann: solvent accessibility prediction of proteins by nearest neighbor method.
Joo K1, Lee SJ, Lee J.