:: DESCRIPTION
BPSpot is a tool to identify RBP binding spots in RNA.
::DEVELOPER
SCBB-LAB (Studio of Computational Biology and Bioinformatics)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sharma NK, Gupta S, Kumar A, Kumar P, Pradhan UK, Shankar R.
RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery.
iScience. 2021 Oct 30;24(12):103381. doi: 10.1016/j.isci.2021.103381. PMID: 34841226; PMCID: PMC8605353.
:: DESCRIPTION
Motif-Raptor, a TF-centric computational tool that integrates sequence-based predic-tive models, chromatin accessibility, gene expression datasets and GWAS summary statistics to systematically investigate how TF function is affected by genetic variants
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yao Q, Ferragina P, Reshef Y, Lettre G, Bauer DE, Pinello L.
Motif-Raptor: A Cell Type-Specific and Transcription Factor Centric Approach for Post-GWAS Prioritization of Causal Regulators.
Bioinformatics. 2021 Feb 3:btab072. doi: 10.1093/bioinformatics/btab072. Epub ahead of print. PMID: 33532840.
:: DESCRIPTION
RNAProt is a computational RBP binding site prediction framework based on recurrent neural networks (RNNs). Conceived as an end-to-end method, RNAProt includes all necessary functionalities, from dataset generation over model training to the evaluation of binding preferences and binding site prediction.
::DEVELOPER
Bioinformatics Group Albert-Ludwigs-University Freiburg
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Uhl M, Tran VD, Heyl F, Backofen R.
RNAProt: an efficient and feature-rich RNA binding protein binding site predictor.
Gigascience. 2021 Aug 18;10(8):giab054. doi: 10.1093/gigascience/giab054. PMID: 34406415; PMCID: PMC8372218.
:: DESCRIPTION
BEST is a suite of motif-finding programs, including four motif-finding programs: AlignACE, BioProspector, Consensus, MEME, and the optimization program BioOptimizer configured for each of these program
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Che D., Jensen, S., Cai, L. and Liu JS.
BEST: Binding-site Estimation Suite of Tools.
Bioinformatics, 21(12):2909-2911.
:: DESCRIPTION
MITSU (Motif discovery by ITerative Sampling and Updating) is a command line application for the discovery of transcription factor binding site (TFBS) motifs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Jun 15;30(12):i310-i318. doi: 10.1093/bioinformatics/btu286.
Stochastic EM-based TFBS motif discovery with MITSU.
Kilpatrick AM, Ward B, Aitken S.
:: DESCRIPTION
P-Binder is a tool for predicting the binding sites on pair of given proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Curr Protein Pept Sci. 2014;15(6):540-52.
Identifying protein-protein binding sites with a combined energy function.
Guo F, Li SC, Fan Y, Wang L
:: DESCRIPTION
Pro-BS is a tool for predicting the binding sites for the given proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Chem Inf Model. 2011 Dec 27;51(12):3287-94. doi: 10.1021/ci200206n. Epub 2011 Nov 28.
Protein-protein binding sites prediction by 3D structural similarities.
Guo F1, Li SC, Wang L.
:: DESCRIPTION
DoBi is a tool for predicting the binding sites on pair of given proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2012 Jul 6;13:158. doi: 10.1186/1471-2105-13-158.
Protein-protein binding site identification by enumerating the configurations.
Guo F1, Li SC, Wang L, Zhu D.
:: DESCRIPTION
BsFinder is a tool for predicting the binding sites for the given proteins.
::DEVELOPER
Fei Guo, Lusheng Wang
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S2. doi: 10.1186/1471-2105-13-S10-S2.
Computing the protein binding sites.
Guo F, Wang L.
:: DESCRIPTION
MotifAdjuster is a tool for computational reassessment of transcription factor binding site annotations
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2009;10(5):R46. doi: 10.1186/gb-2009-10-5-r46. Epub 2009 May 1.
MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations.
Keilwagen J1, Baumbach J, Kohl TA, Grosse I.
