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MoDPepInt: an interactive web server for prediction of modular domain–peptide interactions

Kousik Kundu, Martin Mann, Fabrizio Costa, Rolf Backofen
2014 Computer applications in the biosciences : CABIOS  
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]

Kousik Kundu, Rolf Backofen
2017 Msphere  
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

Yanrong Ren, Qiang Wang, Xiaobo Li
2017 Indian Journal of Pharmaceutical Education and Research  
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

Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu (+10 others)
2018 Nucleic Acids Research  
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

Bálint Mészáros, Hugo Sámano-Sánchez, Jesús Alvarado-Valverde, Jelena Čalyševa, Elizabeth Martínez-Pérez, Renato Alves, Denis C. Shields, Manjeet Kumar, Friedrich Rippmann, Lucía B. Chemes, Toby J. Gibson
2021 Science Signaling  
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