DLPacker : Deep learning for prediction of amino acid side chain conformations in proteins

Autor: Raghav Shroff, Anatoly B. Kolomeisky, Ross Thyer, Mikita Misiura

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 90:1278-1290

Prediction of side chain conformations of amino acids in proteins (also termed ‘packing’) is an important and challenging part of protein structure prediction with many interesting applications in protein design. A variety of methods for packing

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cff2057b422a2566701d2c4608dcd28a
https://doi.org/10.1002/prot.26311

Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space

Autor: Nick Goldman, Dearbhaile Casey, Umberto Perron, Claudia C. Weber, Ziheng Yang

Publikováno v: Systematic Biology

How can we best learn the history of a protein’s evolution? Ideally, a model of sequence evolution should capture both the process that generates genetic variation and the functional constraints determining which changes are fixed. However, in prac

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::33bbbb79b59b7d28b3c893f807bef895
http://europepmc.org/articles/PMC7744038

Graph transformation for enzymatic mechanisms

Autor: Rolf Fagerberg, Jakob L. Andersen, Juraj Kolčák, Nikolai Nøjgaard, Christophe V. F. P. Laurent, Walter Fontana, Christoph Flamm, Daniel Merkle

Publikováno v: Andersen, J L, Fagerberg, R, Flamm, C, Fontana, W, Kolčák, J, Laurent, C V F P, Merkle, D & Nøjgaard, N 2021, ' Graph transformation for enzymatic mechanisms ', Bioinformatics, vol. 37, no. Suppl. 1, pp. 392-400 . https://doi.org/10.1093/bioinformatics/btab296
Bioinformatics

Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this complex problem

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fecbc82d8324eae7911ccec4b44affa9
https://findresearcher.sdu.dk:8443/ws/files/185247742/btab296.pdf

Binding Profile Mapping of the S100 Protein Family Using a High-throughput Local Surface Mimetic Holdup Assay

Autor: Eszter Boros, Márton A. Simon, Beáta Mag, Éva Bartus, Gergő Gógl, Tamás A. Martinek, Lea Roszjár, László Nyitray, Gilles Travé

S100 proteins are small, typically homodimeric, vertebrate-specific EF-hand proteins that establish Ca2+-dependent protein-protein interactions in the intra- and extracellular environment and are overexpressed in various pathologies. There are about

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::4dd22e61d425d9ae8b1fd8fcc765b04a
https://doi.org/10.1101/2020.12.02.407676

Posttranslational modifications in proteins: resources, tools and prediction methods

Autor: Javad Zahiri, Shahin Ramazi

Publikováno v: Database (Oxford)

Posttranslational modifications (PTMs) refer to amino acid side chain modification in some proteins after their biosynthesis. There are more than 400 different types of PTMs affecting many aspects of protein functions. Such modifications happen as cr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::070d3c700f3f3ec56280a18f30c3708f
https://pubmed.ncbi.nlm.nih.gov/33826699