Tag: Scoring

SPIDER – Scoring Protein Interaction Decoys using Exposed Residues

SPIDER

:: DESCRIPTION

SPIDER is developed as a knowledge-based scoring function for protein-protein interaction decoys. SPIDER is a novel multi-body pose-scoring function that has no theoretical limit on the number of residues contributing to the individual interaction terms. SPIDER’s score relies on the geometric similarity of interfacial residues between docking poses and naturally occuring (native) poses.

::DEVELOPER

SPIDER Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPIDER

:: MORE INFORMATION

Citation

Raed Khashan, Weifan Zheng, and Alexander Tropsha.
Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues.
Proteins: Structure, Function, and Bioinformatics, Volume 80, Issue 9, Pages 2207-2217, August 2012.

FastContact 2.0 – Energy Scoring tool for Protein-protein Complex Structures

FastContact 2.0

:: DESCRIPTION

FastContact provides a fast estimate of the interaction free energy between two proteins. Because it is based on folding data, the estimate is robust and does not require to be re-parameterized as more complex structures become available.

::DEVELOPER

Carlos J. Camacho

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  FastContact

:: MORE INFORMATION

Citation

Camacho CJ and Zhang C (2005).
FastContact: rapid estimate of contact and binding free energies.
Bioinformatics, 21(10):2534-6.

pantherScore 1.03 – PANTHER HMM Scoring tool

pantherScore 1.03

:: DESCRIPTION

 pantherScore scores protein sequences against the entire PANTHER HMM library and analyze your sequences.

::DEVELOPER

Paul D. Thomas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 pantherScore

:: MORE INFORMATION

SELECTpro 1.0 – Protein Model Scoring/Selection and Side-Chain Prediction

SELECTpro 1.0

:: DESCRIPTION

SELECTpro is a novel structure-based model selection method derived from an energy function comprising physical, statistical, and predicted structural terms. Novel and unique energy terms include predicted secondary structure, predicted solvent accessibility, predicted contact map, beta-strand pairing, and side-chain hydrogen bonding.

::DEVELOPER

Institute for Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SELECTpro

:: MORE INFORMATION

Citation:

A. Randall, P. Baldi.
SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs.
BMC Structural Biology, 8, 52, 2008