iELM--a web server to explore short linear motif-mediated interactions [PDF]
Nucleic Acids Research, 2012 The recent expansion in our knowledge of protein-protein interactions (PPIs) has allowed the annotation and prediction of hundreds of thousands of interactions. However, the function of many of these interactions remains elusive. The interactions of Eukaryotic Linear Motif (iELM) web server provides a resource for predicting the function and positional
Weatheritt, RJ +3 more
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Structural Details of BH3 Motifs and BH3-Mediated Interactions: an Updated Perspective
Frontiers in Molecular Biosciences, 2022 Apoptosis is a mechanism of programmed cell death crucial in organism development, maintenance of tissue homeostasis, and several pathogenic processes.
Valentina Sora +3 more
doaj +1 more source
The eukaryotic linear motif resource - 2018 update. [PDF]
, 2018 Short linear motifs (SLiMs) are protein binding modules that play major roles in almost all cellular processes. SLiMs are short, often highly degenerate, difficult to characterize and hard to detect.
Gouw, Marc +5 more
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Evidence for the concerted evolution between short linear protein motifs and their flanking regions. [PDF]
PLoS ONE, 2009 BACKGROUND: Linear motifs are short modules of protein sequences that play a crucial role in mediating and regulating many protein-protein interactions. The function of linear motifs strongly depends on the context, e.g. functional instances mainly occur
Claudia Chica +2 more
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GibbsCluster: unsupervised clustering and alignment of peptide sequences [PDF]
, 2017 Receptor interactions with short linear peptide fragments (ligands) are at the base of many biological signaling processes. Conserved and information-rich amino acid patterns, commonly called sequence motifs, shape and regulate these interactions ...
Alvarez, Bruno +2 more
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QSLiMFinder: improved short linear motif prediction using specific query protein data [PDF]
Bioinformatics, 2015 Abstract Motivation: The sensitivity of de novo short linear motif (SLiM) prediction is limited by the number of patterns (the motif space) being assessed for enrichment. QSLiMFinder uses specific query protein information to restrict the motif space and thereby increase the sensitivity and specificity of predictions ...
Palopoli, Nicolas +2 more
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Surface guidance of stem cell behavior: Chemically tailored co-presentation of integrin-binding peptides stimulates osteogenic differentiation in vitro and bone formation in vivo [PDF]
, 2016 Surface modification stands out as a versatile technique to create instructive biomaterials that are able to actively direct stem cell fate. Chemical functionalization of titanium has been used in this work to stimulate the differentiation of human ...
Dashnyam, Khandmaa +8 more
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A Review of Functional Motifs Utilized by Viruses
Proteomes, 2016 Short linear motifs (SLiM) are short peptides that facilitate protein function and protein-protein interactions. Viruses utilize these motifs to enter into the host, interact with cellular proteins, or egress from host cells.
Haitham Sobhy
doaj +1 more source
Computational Prediction of Short Linear Motifs from Protein Sequences
, 2014 Short Linear Motifs (SLiMs) are functional protein microdomains that typically mediate interactions between a short linear region in one protein and a globular domain in another. SLiMs usually occur in structurally disordered regions and mediate low affinity interactions.
Edwards, Richard J., Palopoli, Nicolas
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DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences. [PDF]
, 2016 Modeling the properties and functions of DNA sequences is an important, but challenging task in the broad field of genomics. This task is particularly difficult for non-coding DNA, the vast majority of which is still poorly understood in terms of ...
Quang, Daniel, Xie, Xiaohui
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