Zobrazeno 1 - 10
of 87
pro vyhledávání: '"Petras J Kundrotas"'
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:
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
Publikováno v:
PLoS Computational Biology, Vol 11, Iss 12, p e1004630 (2015)
The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structu
Externí odkaz:
https://doaj.org/article/0a35e61809894e0988c38352238545a8
Publikováno v:
PLoS ONE, Vol 7, Iss 2, p e31349 (2012)
The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities
Externí odkaz:
https://doaj.org/article/6aa121e202674204a75f4d657eb83227
Autor:
Petras J Kundrotas, Ilya A Vakser
Publikováno v:
PLoS Computational Biology, Vol 6, Iss 4, p e1000727 (2010)
The accuracy of protein structures, particularly their binding sites, is essential for the success of modeling protein complexes. Computationally inexpensive methodology is required for genome-wide modeling of such structures. For systematic evaluati
Externí odkaz:
https://doaj.org/article/39d7305f1afd4bd1be3d984bb6ae30a6
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
Publikováno v:
Frontiers in Molecular Biosciences. 9
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://explore.openaire.eu/search/publication?articleId=doi_dedup___::6108c83872cab229fd739f2fcc1a9c3e
https://doi.org/10.3389/fmolb.2022.1031225
https://doi.org/10.3389/fmolb.2022.1031225
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