PeptideReranking – Peptide Re-ranking with Protein-peptide Correspondence and Precursor Peak Intensity Information

PeptideReranking

:: DESCRIPTION

PeptideReranking includes three peptide reranking methods: PPMRanker, PPIRanker, and MIRanker. PPMRanker only uses Protein-Peptide Map (PPM) information from the protein database, PPIRanker only uses Precursor Peak Intensity (PPI) information, and MIRanker employs both PPM information and PPI information.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PeptideReranking

:: MORE INFORMATION

Citation:

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1212-9. doi: 10.1109/TCBB.2012.29.
Peptide reranking with protein-peptide correspondence and precursor peak intensity information.
Yang C1, He Z, Yang C, Yu W.

Netter – Re-ranking Gene Network Inference Predictions

Netter

:: DESCRIPTION

Netter is a software for re-ranking gene network inference predictions using structural network properties.

::DEVELOPER

Joeri Ruyssinck (Email: joeri.ruyssinck@intec.ugent.be)

:: SCREENSHOTS

netter

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Netter

:: MORE INFORMATION

Citation:

Netter: re-ranking gene network inference predictions using structural network properties.
Ruyssinck J, Demeester P, Dhaene T, Saeys Y.
BMC Bioinformatics. 2016 Feb 9;17(1):76. doi: 10.1186/s12859-016-0913-0.

SymmRef – Refinement and re-ranking of symmetric docking solutions

SymmRef

:: DESCRIPTION

SymmRef is a method for refinement and re-ranking of symmetric docking solutions, with Cn symmetry. The method models backbone and side-chain movements and optimizes the rigid-body orientations of the monomers. The backbone movements are modeled by normal modes minimization and the conformations of the side-chains are modeled by selecting optimal rotamers.

::DEVELOPER

 the BioInfo3D group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SymmRef

:: MORE INFORMATION

Citation:

Efrat Mashiach-Farkash, Ruth Nussinov and Haim J. Wolfson.
SymmRef: A flexible refinement method for symmetric multimers .
Proteins: Structure, Function, and Bioinformatics Volume 79, Issue 9, pages 2607–2623, September 2011