Zobrazeno 1 - 10
of 133
pro vyhledávání: '"Petras J Kundrotas"'
Publikováno v:
Frontiers in Molecular Biosciences, Vol 9 (2022)
Association of proteins to a significant extent is determined by their geometric complementarity. Large-scale recognition factors, which directly relate to the funnel-like intermolecular energy landscape, provide important insights into the basic rul
Externí odkaz:
https://doaj.org/article/cea96feb9c0b460a985b8d5bece21ab8
Publikováno v:
PLoS ONE, Vol 17, Iss 5, p e0267531 (2022)
Membrane proteins are significantly underrepresented in Protein Data Bank despite their essential role in cellular mechanisms and the major progress in experimental protein structure determination. Thus, computational approaches are especially valuab
Externí odkaz:
https://doaj.org/article/f5bc5034f8774af185bdaf4e26ca8ab6
Publikováno v:
BMC Bioinformatics, Vol 19, Iss 1, Pp 1-10 (2018)
Abstract Background Structural modeling of protein-protein interactions produces a large number of putative configurations of the protein complexes. Identification of the near-native models among them is a serious challenge. Publicly available result
Externí odkaz:
https://doaj.org/article/fe32a6b9a16d4c9b8f5f91062e1e42a1
Publikováno v:
Proteins
Protein docking protocols typically involve global docking scan, followed by re-ranking of the scan predictions by more accurate scoring functions that are either computationally too expensive or algorithmically impossible to include in the global sc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cfbd71d04592f2fc0451303f36f67218
https://doi.org/10.1002/prot.26306
https://doi.org/10.1002/prot.26306
Publikováno v:
Bioinformatics
Motivation In the last decade, de novo protein structure prediction accuracy for individual proteins has improved significantly by utilising deep learning (DL) methods for harvesting the co-evolution information from large multiple sequence alignment
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::88c6252c474933932e8e4080f8df675b
https://doi.org/10.1093/bioinformatics/btab760
https://doi.org/10.1093/bioinformatics/btab760
Autor:
Keeley W. Collins, Matthew M. Copeland, Ian Kotthoff, Amar Singh, Petras J. Kundrotas, Ilya A. Vakser
Publikováno v:
Protein science : a publication of the Protein Society. 31(12)
Structural information of protein-protein interactions is essential for characterization of life processes at the molecular level. While a small fraction of known protein interactions has experimentally determined structures, computational modeling o
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9025385e6cb3de2ef09795ada26eecdd
https://pubmed.ncbi.nlm.nih.gov/36281025
https://pubmed.ncbi.nlm.nih.gov/36281025
Publikováno v:
Proceedings of the National Academy of Sciences of the United States of America
Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (41), pp.e2210249119:1-8. ⟨10.1073/pnas.2210249119⟩
Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (41), pp.e2210249119:1-8. ⟨10.1073/pnas.2210249119⟩
Computational methodologies are increasingly addressing modeling of the whole cell at the molecular level. Proteins and their interactions are the key component of cellular processes. Techniques for modeling protein interactions, so far, have include
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ad1d25314a0c7391beb8cf5208bc53e3
https://pubmed.ncbi.nlm.nih.gov/36191203
https://pubmed.ncbi.nlm.nih.gov/36191203
Publikováno v:
PLoS Computational Biology, Vol 12, Iss 9, p e1005120 (2016)
Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discove
Externí odkaz:
https://doaj.org/article/363fd47820c94116be42228bdbac87a2
Autor:
Ilya A. Vakser, Alexander V. Tuzikov, Ivan Anishchenko, A. Yu. Hadarovich, Petras J. Kundrotas
Publikováno v:
Doklady of the National Academy of Sciences of Belarus. 64:150-158
We propose an algorithm for comparing protein-protein complexes based on their functional properties in terms of Gene Ontology. The proposed measure of a functional similarity between complexes is combined with a structural measure to find templates
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::5a0a7a9f8db87fbec63919c9a3095764
https://doi.org/10.29235/1561-8323-2020-64-2-150-158
https://doi.org/10.29235/1561-8323-2020-64-2-150-158
Publikováno v:
Proteins
Comparative docking is based on experimentally determined structures of protein-protein complexes (templates), following the paradigm that proteins with similar sequences and/or structures form similar complexes. Modeling utilizing structure similari
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::41b61cf8fce7f1a62a8b9982c33fbbf8
https://doi.org/10.1002/prot.25875
https://doi.org/10.1002/prot.25875