MORPHEUS – Identify Residues in Predicted Models with a large Error

MORPHEUS

:: DESCRIPTION

MORPHEUS is a tool to identify and rebuild residues in predicted models with a large error. The error in predicted models is estimated using the average pairwise geometric distance per residue computed among selected lowest energy models. This error distribution among residues is employed to guide the rebuilding process that focuses on more error-prone residues of the coarse-grain models.

::DEVELOPER

Structural Bioinformatics Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MORPHEUS

:: MORE INFORMATION

Citation

Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1522-34. doi: 10.1107/S0907444912037961. Epub 2012 Oct 18.
Error-estimation-guided rebuilding of de novo models increases the success rate of ab initio phasing.
Shrestha R1, Simoncini D, Zhang KY.

RNABindRPlus 1.0 – Prediction of RNA-binding Residues in Protein

RNABindRPlus 1.0

:: DESCRIPTION

RNABindRPlus predicts RNA-binding residues from protein sequences by combining the output from a Support Vector Machine (SVM) classifier with the output from a Homology-based method.

::DEVELOPER

Artificial Intelligence Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins.
Walia RR, Xue LC, Wilkins K, El-Manzalawy Y, Dobbs D, Honavar V.
PLoS One. 2014 May 20;9(5):e97725. doi: 10.1371/journal.pone.0097725

eFindSitePPI – Detect Protein Binding Sites and Residues with Meta-threading

eFindSitePPI

:: DESCRIPTION

eFindSitePPI is a program to detect protein binding sites and residues with meta-threading. eFindSitePPI also predicts interfacial geometry and specific interactions stabilizing protein-protein complexes, such as hydrogen bonds, salt bridges, aromatic and hydrophobic interactions.

::DEVELOPER

Computational Systems Biology Group,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

eFindSitePPI

:: MORE INFORMATION

Citation

Maheshwari S, Brylinski M.
Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning.
J Mol Recognit. 2015 Jan;28(1):35-48. doi: 10.1002/jmr.2410. PMID: 26268369.

HotSpot – Hot Spot Residues Prediction

HotSpot

:: DESCRIPTION

Hot Spot is a software of prediction of hot spot residues through physicochemical characteristics of amino acid sequences

::DEVELOPER

Structural and Functional Bioinformatics Group, King Abdullah University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

HotSpot

:: MORE INFORMATION

Citation

Proteins. 2013 Aug;81(8):1351-62. doi: 10.1002/prot.24278.
Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.
Chen P1, Li J, Wong L, Kuwahara H, Huang JZ, Gao X.

NsitePred – Prediction of Nucleotide-binding Residues

NsitePred

:: DESCRIPTION

NsitePred is designed for sequence-based prediction of binding residues for ATP, ADP, AMP, GDP, and GTP.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):331-41. doi: 10.1093/bioinformatics/btr657. Epub 2011 Nov 29.
Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors.
Chen K1, Mizianty MJ, Kurgan L.

GTPbinder – predicting GTP interacting Residues in a Protein

GTPbinder

:: DESCRIPTION

GTPBinder is a web based tool for prediction of GTP binding residue in protein sequence.It takes amino acid sequence in FASTA format as input and predict the GTP-interacting residues with Support Vector Machine (SVM).

::DEVELOPER

GTPbinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Jun 3;11:301. doi: 10.1186/1471-2105-11-301.
Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information.
Chauhan JS1, Mishra NK, Raghava GP.