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MoDPepInt: an interactive web server for prediction of modular domain–peptide interactions
2014
Computer applications in the biosciences : CABIOS
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MoDPepInt (Modular Domain Peptide Interaction) is a new easy-to-use web server for the prediction of binding partners for modular protein domains. ...
More specifically, our server offers predictions for 51 SH2 human domains and 69 SH3 human domains via single domain models, and predictions for 226 PDZ domains across several species, via 43 multidomain ...
Conflict of interest: none declared. ...
doi:10.1093/bioinformatics/btu350
pmid:24872426
pmcid:PMC4155253
fatcat:42pztpcv75hylpkso54twznfde
An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions
[chapter]
2017
Msphere
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Here, we propose a machine learning approach based on an efficient semisupervised learning technique for the prediction of 51 SH2 domain mediated interactions in human proteome. ...
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. ...
This work was funded by Bundesministerium für Bildung und Forschung (e-bio; FKZ 0316174A to RB), and the Centre for Biological Signalling Studies (BIOSS), University of Freiburg. ...
doi:10.1007/978-1-4939-6762-9_6
pmid:28092029
fatcat:nez4xvsvdfcjhpbyvi6ulrxa6m
Optimizing the Amino Acid Sequences of Peptides and Improving Their Specificity of Binding to SH3 Domains of Target Proteins
2017
Indian Journal of Pharmaceutical Education and Research
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It is always a crucial challenge in biotechnology to avoid promiscuous binding between an anticancer peptide and multiple SH3 domains, thus reducing potential toxic effects. ...
of binding to the SH3 domain of c-Src protein. ...
Prediction of peptide-target interactions The prototype peptides were submitted to MoDPepInt (Modular Domain Peptide Interaction, http://modpepint.informatik.uni-freiburg.de/), an interactive web server ...
doi:10.5530/ijper.51.1.7
fatcat:5cj323gruzh4lb5e2yvxdacc3y
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
2018
Nucleic Acids Research
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Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. ...
The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification ...
ACKNOWLEDGEMENTS We thank the users of the Freiburg RNA tools for their productive feedback.
FUNDING ...
doi:10.1093/nar/gky329
pmid:29788132
pmcid:PMC6030932
fatcat:cmpvl5tygrc27mbc5qyjv7pzaq
Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications
2021
Science Signaling
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Several of these SLiMs have now been validated to mediate the predicted peptide interactions. ...
These SLiM candidates are highly conserved in vertebrates and may interact with the μ2 subunit of the endocytosis-associated AP2 adaptor complex, as well as with various protein domains (namely, I-BAR, ...
Ivarsson from the Uppsala University for testing several motif candidates and sharing their peptide-domain binding data in advance of publication. We thank S. ...
doi:10.1126/scisignal.abd0334
pmid:33436497
fatcat:dvtier5l7vguzhyflmplriixta