PIVOT 2.0 – Protein Interactions VisualizatiOn Tool

PIVOT 2.0

:: DESCRIPTION

PIVOT (Protein Interactions VisualizatiOn Tool) is a Java-based tool, for visualizing protein-protein interactions. It is rich in features that help the users navigate and interpret the interactions map, as well as graph-theory algorithms for easily connecting remote proteins to the displayed map.PIVOT is not limited to the data present in any database, but instead allows the users to create their own dataset, by importing any available lists of interactions and combining them together. PIVOT is currently configured to work with proteins from four different species (human, yeast, drosophila and mouse), and present functional annotations, designations of homologs from the four species, and links to information pages. The protein data is stored in an MS-Access file, easily modifiable by the users to enter their own data.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PIVOT

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Feb 12;20(3):424-5.
PIVOT: protein interacions visualizatiOn tool.
Orlev N1, Shamir R, Shiloh Y.

PESCADOR – Extract and Analyse a Network of Gene and Protein Interactions from a set of Medline abstracts

PESCADOR

:: DESCRIPTION

PESCADOR (Platform for Exploration of Significant Concepts AssociateD to co-Occurrences Relationships) is a web tool that extracts a network of interactions from a set of PubMed abstracts given by a user, and allows filtering the interaction network according to user-defined concepts.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Nov 9;12:435. doi: 10.1186/1471-2105-12-435.
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.
Barbosa-Silva A1, Fontaine JF, Donnard ER, Stussi F, Ortega JM, Andrade-Navarro MA.

SPRINT – Scoring PRotein INTeractions

SPRINT

:: DESCRIPTION

SPRINT is a C++/OpenMP program that predicts protein-protein interactions.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SPRINT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2017 Nov 15;18(1):485. doi: 10.1186/s12859-017-1871-x.
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome.
Li Y, Ilie L

Alloscore 1.02 – Evaluation of Allosteric Ligand-Protein Interactions

Alloscore 1.02

:: DESCRIPTION

Alloscore is a web server that predicts the binding affinities of allosteric ligand-protein interactions.

::DEVELOPER

Molecular Design Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Alloscore: a tool for predicting allosteric ligand-protein interactions.
Li S, Shen Q, Su M, Liu X, Lu S, Chen Z, Wang R, Zhang J.
Bioinformatics. 2016 Jan 22. pii: btw036.

PiType 2.0 – Protein Interaction Classifier

PiType 2.0

:: DESCRIPTION

PiType is an accurate 3D structure-independent computational method for classifying protein interactions into simultaneously possible (SP) and mutually exclusive (ME) as well as into obligate and non-obligate.

::DEVELOPER

PiType team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Python

:: DOWNLOAD

  PiType

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013;7 Suppl 6:S5. doi: 10.1186/1752-0509-7-S6-S5. Epub 2013 Dec 13.
Prediction of protein interaction types based on sequence and network features.
Goebels F, Frishman D.

PIMiner – Extract Protein-interaction (PI) Information from Raw Text

PIMiner

:: DESCRIPTION

PIMiner is an online tool for the extraction of PI relationships from PubMed-abstracts

::DEVELOPER

PIMiner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Int J Data Min Bioinform. 2013;7(4):450-62.
PIMiner: a web tool for extraction of protein interactions from biomedical literature.
Chowdhary R1, Zhang J, Tan SL, Osborne DE, Bajic VB, Liu JS.

FlexDock – Docking Algorithm for Automatic prediction of protein interactions with large scale motion.

FlexDock

:: DESCRIPTION

FlexDock is a fully automated method for flexible docking with large scale motion in one of the docked molecules. The method automatically identifies hinge regions and rigid parts using HingeProt and then docks the input molecules while explicitly considering the hinges and possible protein motions.

::DEVELOPER

 the BioInfo3D group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  FlexDock

:: MORE INFORMATION

Citation:

Automatic prediction of protein interactions with large scale motion.
Schneidman-Duhovny D, Nussinov R, Wolfson HJ.
Proteins. 2007 Dec 1;69(4):764-73.

DatasetAssess – Estimate Error Rates in High-throughput Protein Interaction datasets

DatasetAssess

:: DESCRIPTION

 DatasetAssess is a tool to estimate error rates in high-throughput protein interaction datasets and other functional genomic data.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 DatasetAssess

:: MORE INFORMATION

Citation:

Gilchrist, M.A., Salter, L.A., Wagner, A. (2004)
A statistical framework for combining and interpreting proteomic datasets.
Bioinformatics 20, 689-700

GWAS Pathway Identifier 1.0.0 – Pathway- and Protein-Interaction-Based Identification of Disease Specific SNP Sets in GWAS

GWAS Pathway Identifier 1.0.0

:: DESCRIPTION

GWAS Pathway Identifier combines GWAS(Genome-Wide Accociation Studies) and pathway data as well as known and predicted protein-interaction data to identify disease specific SNP sets.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 GWAS Pathway Identifier

:: MORE INFORMATION

InferPPI 1.0 – Predict Protein Interactions based on Parsimony Tendency of Domain Interactions

InferPPI 1.0

:: DESCRIPTION

InferPPI aims to infer protein-protein interaction based on the parsimony principle of domain-domain interactions. Specifically, inferring domain interactions is a first step and formulated as an integer linear programming with different searching degree of training protein interaction. Then the model is solved by relaxed linear programming. By using the obtained domain interactions, novel protein interactions can be predicted by a formula. In contrast to probabilistic algorithms, InferPPI is an algorithm based on a deterministic model.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

   InferPPI

:: MORE INFORMATION

Citation

Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yong Wang, Shihua Zhang, Luonan Chen.
Predicting protein interactions based on parsimony tendency of domain interactions.
Manuscript, 2006.