Tag: Protein-protein

HDOCK 1.1 – Protein-protein and Protein-DNA/RNA Docking based on Hybrid Strategy

HDOCK 1.1

:: DESCRIPTION

The HDOCK server is to predict the binding complexes between two molecules like proteins and nucleic acids by using a hybrid docking strategy.

::DEVELOPER

Huang Laboratary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HDOCK 

:: MORE INFORMATION

Citation:

Yan Y, Zhang D, Zhou P, Li B, Huang SY.
HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.
Nucleic Acids Res. 2017 Jul 3;45(W1):W365-W373. doi: 10.1093/nar/gkx407. PMID: 28521030; PMCID: PMC5793843.

Osprey 1.2.0 – Protein-protein Interaction Networks Visualization System

Osprey 1.2.0

:: DESCRIPTION

Osprey is a tool for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale data sets can be readily combined with Osprey for comparison of different methods.

::DEVELOPER

Osprey Partners

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Osprey

:: MORE INFORMATION

Citation

Osprey: a network visualization system.
Breitkreutz BJ, Stark C, Tyers M.
Genome Biol. 2003;4(3):R22. Epub 2003 Feb 27.

DOCKSCORE – Ranking Protein-protein Docked Poses

DOCKSCORE

:: DESCRIPTION

DockScore is a rigorous scoring scheme which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed.

::DEVELOPER

DockScore Team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DOCKSCORE: a webserver for ranking protein-protein docked poses.
Malhotra S, Mathew OK, Sowdhamini R.
BMC Bioinformatics. 2015 Apr 24;16(1):127.

PS-HomPPI v1.3 / NPS-HomPPI – Protein-Protein Binding Site Predictor

PS-HomPPI v1.3 / NPS-HomPPI

:: DESCRIPTION

PS-HomPPI is a sequence-based partner-specific protein-protein interface residue prediction server.

NPS-HomPPI is a sequence-based non-partner-specific protein-protein interface residue prediction server.

::DEVELOPER

Artificial Intelligence Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Jun 17;12:244. doi: 10.1186/1471-2105-12-244.
HomPPI: a class of sequence homology based protein-protein interface prediction methods.
Xue LC1, Dobbs D, Honavar V.

MM-ISMSA – Scoring Function for Protein-Protein and Protein-Ligand Docking and Molecular Dynamics

MM-ISMSA

:: DESCRIPTION

MM-ISMSA is an ultrafast and accurate scoring function for protein-protein and protein-ligand docking

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

MM-ISMSA

:: REQUIREMENTS

  • Windows / Linux
  • Python
  • PyMOL

:: DOWNLOAD

  MM-ISMSA

:: MORE INFORMATION

Citation

Javier Klett, Alfonso Núñez-Salgado, Helena G. Dos Santos, Álvaro Cortés-Cabrera, Almudena Perona, Rubén Gil-Redondo, David Abia, Federico Gago, and Antonio Morreale
MM-ISMSA: an ultra-fast and accurate scoring function for protein-protein docking.
J Chem Theory Comput. 2012 Sep 11;8(9):3395-3408

iPPBS-PseAAC – Prediction of Protein-Protein Binding Sites

iPPBS-PseAAC

:: DESCRIPTION

The web-server iPPBS-PseAAC is used to predict the Protein-Protein Binding Sites(PPBS).

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification of protein-protein binding sites by incorporating the physicochemical properties and stationary wavelet transforms into pseudo amino acid composition.
Jia J, Liu Z, Xiao X, Liu B, Chou KC.
J Biomol Struct Dyn. 2015 Sep 16:1-38

PPI / PPI_RF – Prediction of Protein-Protein Interactions

PPI / PPI_RF

:: DESCRIPTION

The web-server PPI  is used to predict the protein-protein interaction.The protein sequence are represented by chaos game representation and wavelets transform. The chaos game representation encodes the amino acid position of the proteion and then two discrete series are gotten. The wavelets transform is used to analyse the two series. Finally the random forests algorithm is used for PPIs prediction.

The web-server PPI_RF is used to predict the protein-protein interaction. Based on the physicochemical descriptors, a protein could be converted into several digital signals and then wavelet transform was used to analyze them. With such a formulation frame to represent the samples of protein sequences, the random forests algorithm was adopted to conduct prediction.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prediction of protein-protein interactions using chaos game representation and wavelet transform via the random forest algorithm.
Jia JH, Liu Z, Chen X, Xiao X, Liu BX.
Genet Mol Res. 2015 Oct 2;14(4):11791-805. doi: 10.4238/2015.

Prediction of Protein-Protein Interactions with Physicochemical Descriptors and Wavelet Transform via Random Forests.
Jia J, Xiao X, Liu B.
J Lab Autom. 2015 Apr 16. pii: 2211068215581487

NAViGaTOR 3.0 – Visualize and Analyze Protein-protein Interaction Networks.

NAViGaTOR 3.0

:: DESCRIPTION

NAViGaTOR (Network Analysis, Visualization, & Graphing TORonto ) is a software package for visualizing and analyzing protein-protein interaction networks.NAViGaTOR can query OPHID / I2D – online databases of interaction data – and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI).

::DEVELOPER

Jurisica Lab of the Ontario Cancer Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 NAViGaTOR

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Dec 15;25(24):3327-9. doi: 10.1093/bioinformatics/btp595. Epub 2009 Oct 16.
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto.
Brown KR1, Otasek D, Ali M, McGuffin MJ, Xie W, Devani B, Toch IL, Jurisica I.

Djebbari, A., Ali, M., Otasek, D., Kotlyar. M., Fortney, K., Wong, S., Hrvojic, A. and Jurisica, I.
NAViGaTOR: Scalable and Interactive Navigation and Analysis of Large Graphs.
Internet Mathematics, 7(4):314-347, 2011

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.

3D-Garden 1.4 – Protein-protein and Protein-polynucleotide Docking

3D-Garden 1.4

:: DESCRIPTION

3DGarden (Global and Restrained Docking Exploration Nexus) is an integrated software suite for performing protein-protein and protein-polynucleotide docking. For any pair of biomolecules structures specified by the user, 3DGarden’s primary function is to generate an ensemble of putative complexed structures and rank them. The highest-ranking candidates constitute predictions for the structure of the complex. 3DGarden cannot be used to decide whether or not a particular pair of biomolecules interacts. Complexes of protein and nucleic acid chains can also be specified as individual interactors for docking purposes.

::DEVELOPER

Structural Bioinformatics Group, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm.
Lesk VI, Sternberg MJ.
Bioinformatics. 2008 May 1;24(9):1137-44. doi: 10.1093/bioinformatics/btn093.