CPORT – Prediction of Protein-protein Interface Residues

CPORT

:: DESCRIPTION

CPORT is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2011 Mar 25;6(3):e17695. doi: 10.1371/journal.pone.0017695.
CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.
de Vries SJ1, Bonvin AM.

DEPTH 2.8.7 – Measure Extent of Atom/Residue Burial within Protein

DEPTH 2.8.7

:: DESCRIPTION

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein–protein interaction hot spots, post-translational modification sites and sequence variability.

::DEVELOPER

Bioinformatics Institute of Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 DEPTH

:: MORE INFORMATION

Citation:

Kuan Pern Tan; Raghavan Varadarajan; M. S. Madhusudhan
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr356

NADbinder – Prediction of NAD interacting residues in proteins

NADbinder

:: DESCRIPTION

NADbinder server discriminate the NAD interacting residues and non-interacting residues from a given sequence. The NADbinder server uses the SVM based method by using the Position Specific Scoring Matrix (PSSM) generated from the query sequence(s).

::DEVELOPER

NADbinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Mar 30;11:160. doi: 10.1186/1471-2105-11-160.
Identification of NAD interacting residues in proteins.
Ansari HR1, Raghava GP.

VitaPred – Prediction of Vitamin Interacting Residues

VitaPred

:: DESCRIPTION

VitaPred is a SVM (Support Vector Machines) based prediction method for the vitamin-interacting residues in protein sequences. Vitamins play vital role in the cell and involves in the various enzymatic reaction and functions as a cofactor. VitaPred predicts that which amino acid residues in the protein sequence will interact with the vitamins. An example of protein-vitamin binding given in the following diagram, where pyridoxal 5′-phosphate (PLP, red color) interacts with specific residues (yellow color) of a protein (cyan color).

VitaPred Online version

::DEVELOPER

VitaPred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  VitaPred

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Feb 7;14:44. doi: 10.1186/1471-2105-14-44.
Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information.
Panwar B1, Gupta S, Raghava GP.

PAIRPred 1.0 – Partner Aware Interacting Residue PREDictor

PAIRPred 1.0

:: DESCRIPTION

PAIRPred is a partner specific protein-protein interaction site predictor that can make accurate predictions of whether a pair of residues from two different proteins interact or not.

::DEVELOPER

PAIRPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 PAIRPred

:: MORE INFORMATION

Citation

PAIRpred: partner-specific prediction of interacting residues from sequence and structure.
Minhas Fu, Geiss BJ, Ben-Hur A.
Proteins. 2014 Jul;82(7):1142-55. doi: 10.1002/prot.24479.

CAB-align – Residue-residue Contact Area Based Alignment

CAB-align

:: DESCRIPTION

CAB-align (contact area-based alignment) is a flexible protein structure alignment method based on the residue-residue contact area.

::DEVELOPER

Takeda-Shitaka Lab (Laboratory of Biomolecular Design)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CAB-align

:: MORE INFORMATION

Citation

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.
Terashi G, Takeda-Shitaka M.
PLoS One. 2015 Oct 26;10(10):e0141440. doi: 10.1371/journal.pone.0141440.

QUASSI – Quantifying Significance of MHC II Residues

QUASSI

:: DESCRIPTION

QUASSI is a project to solve integer linear programming problem proposed in bioinformatics

::DEVELOPER

QUASSI team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JRE

:: DOWNLOAD

 QUASSI

:: MORE INFORMATION

Citation

Quantifying Significance of MHC II Residues.
Ying Fan, Ruoshui Lu, Lusheng Wang, Andreatta M, Shuai Cheng Li.
IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):17-25. doi: 10.1109/TCBB.2013.138.

PrISE 20110723 – Prediction of protein-protein Interface residues using Structural Elements

PrISE 20110723

:: DESCRIPTION

PrISE predict interface residues using local surface structural similarity. PrISe represents a local surface structure using structural elements.

::DEVELOPER

Artificial Intelligence Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012 Mar 18;13:41. doi: 10.1186/1471-2105-13-41.
Predicting protein-protein interface residues using local surface structural similarity.
Jordan RA1, El-Manzalawy Y, Dobbs D, Honavar V.

MotiveValidator 1.1.15.5.12 – Validate Ligand and Residue Structure in Biomolecular Complexes

MotiveValidator 1.1.15.5.12

:: DESCRIPTION

MotiveValidator is a platform for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its models stored in the wwPDB Chemical Component Dictionary (wwPDB CCD).

::DEVELOPER

MotiveValidator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

MotiveValidator

:: MORE INFORMATION

Citation

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.
Vařeková RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horský V, Wimmerová M, Koča J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W227-33. doi: 10.1093/nar/gku426.

FreeContact – Protein Contact Prediction from Residue Co-evolution

FreeContact 1.0.12

:: DESCRIPTION

FreeContact is a protein residue contact predictor optimized for speed.

::DEVELOPER

the Rostlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl /Python

:: DOWNLOAD

 FreeContact

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Mar 26;15:85. doi: 10.1186/1471-2105-15-85.
FreeContact: fast and free software for protein contact prediction from residue co-evolution.
Kaján L, Hopf TA, Kalaš M, Marks DS, Rost B