GOMEP – Gene Ontology-based Missing Enzyme Predictor

GOMEP

:: DESCRIPTION

GOMEP Predicts Missing Enzymes using functional coherence scores of Gene Ontology (GO) terms

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

GOMEP

:: MORE INFORMATION

Citation

Sci Rep. 2016 Aug 24;6:31725. doi: 10.1038/srep31725.
Missing gene identification using functional coherence scores.
Chitale M, Khan IK, Kihara D

MPFit – Moonlighting protein Prediction with Missing Feature Imputation

MPFit

:: DESCRIPTION

MPFit Predicts Moonlighting Proteins from Gene Ontology (GO) and diverse omics-based protein association features.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MPFit

:: MORE INFORMATION

Citation

Methods Mol Biol. 2017;1611:45-57. doi: 10.1007/978-1-4939-7015-5_5.
MPFit: Computational Tool for Predicting Moonlighting Proteins.
Khan I, McGraw J, Kihara D

DextMP – Moonlighting Protein Prediction by Deep Dive into Text

DextMP

:: DESCRIPTION

DextMP Text-mining tool to find Moonlighting Proteins from publication titles, abstract and functional description in UniProt.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DextMP

:: MORE INFORMATION

Citation

DextMP: deep dive into text for predicting moonlighting proteins.
Khan IK, Bhuiyan M, Kihara D.
Bioinformatics. 2017 Jul 15;33(14):i83-i91. doi: 10.1093/bioinformatics/btx231.

FlexPred – Protein Fluctuation Prediction using SVR

FlexPred

:: DESCRIPTION

FlexPred predicts real-value fluctuation of each residues in a query protein structure. Predication can be performed for single-chain, complex proteins, and computational models.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Methods Mol Biol. 2017;1484:175-186. doi: 10.1007/978-1-4939-6406-2_13.
Predicting Real-Valued Protein Residue Fluctuation Using FlexPred.
Peterson L, Jamroz M, Kolinski A, Kihara D

BindML/BindML+ – Detecting Protein-Protein Interaction Interface Propensity

BindML/BindML+

:: DESCRIPTION

BindML predicts protein-protein interaction sites in a query protein structure by using evolutionary information.

BindML+ further classifies a binding site to permanent and transient interaction.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns.
Wei Q, La D, Kihara D.
Methods Mol Biol. 2017;1529:279-289.

GMQ – Prediction of Local Quality of Protein Structure Models Considering Spatial Neighbors

GMQ

:: DESCRIPTION

GMQ (Graph-based Model Quality assessment method) is a protein quality assessment program which employs conditional random field. The program gives a binary prediction that predicts a modeled residue has an error within a C-alpha distance cutoff or not.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

GMQ

:: MORE INFORMATION

Citation

Sci Rep. 2017 Jan 11;7:40629. doi: 10.1038/srep40629.
Prediction of Local Quality of Protein Structure Models Considering Spatial Neighbors in Graphical Models.
Shin WH, Kang X, Zhang J, Kihara D.

NaviGO – An analytic tool for Gene Ontology Visualization and Similarity

NaviGO

:: DESCRIPTION

NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.
Wei Q, Khan IK, Ding Z, Yerneni S, Kihara D.
BMC Bioinformatics. 2017 Mar 20;18(1):177. doi: 10.1186/s12859-017-1600-5.

PhyloPFP – Gene Ontology Prediction Using Phylogenomics

PhyloPFP

:: DESCRIPTION

PhyloPFP is a phylogenomics based protein function prediction server

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Mar 1;35(5):753-759. doi: 10.1093/bioinformatics/bty704.
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences.
Jain A, Kihara D.

Dove – A Deep-learning based dOcking decoy eValuation mEthod

Dove

:: DESCRIPTION

Dove is a deep learning based protein docking model evluation method.It will use the atom information such as postions, types, energy scores in the interface area to judge if the docking model is reasonable.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Dove

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Nov 20. pii: btz870. doi: 10.1093/bioinformatics/btz870. [Epub ahead of print]
Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks.
Wang X, Terashi G, Christoffer CW, Zhu M, Kihara D.

EM-SURFER – Navigating 3D Electron Microscopy Maps

EM-SURFER

:: DESCRIPTION

EM-SURFER is a web platform for real-time electron microscopy database search. It compares isosurface shape of a query EM map against maps in the latest EMDB.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Navigating 3D electron microscopy maps with EM-SURFER.
Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D.
BMC Bioinformatics. 2015 May 30;16:181. doi: 10.1186/s12859-015-0580-6.