Zobrazeno 1 - 10
of 12
pro vyhledávání: '"Pranav M Khade"'
Publikováno v:
Applied Sciences, Vol 12, Iss 5, p 2344 (2022)
Elastic network models (ENMs) have been widely used in the last decades to investigate protein motions and dynamics. There the intrinsic fluctuations based on the isolated structures are obtained from the normal modes of these elastic networks, and t
Externí odkaz:
https://doaj.org/article/b7de164743c54cf9b8bdd329977a14e2
Autor:
Alberto Carpinteri, Robert L. Jernigan, Domenico Scaramozzino, Giuseppe Lacidogna, Pranav M. Khade, Ambuj Kumar
Publikováno v:
Biophys J
Hinge motions are essential for many protein functions, and their dynamics are important to understand underlying biological mechanisms. The ways that these motions are represented by various computational methods differ significantly. By focusing on
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::37eeb8eb401e10fb3d93ea6c4b200414
https://doi.org/10.1016/j.bpj.2021.10.017
https://doi.org/10.1016/j.bpj.2021.10.017
Publikováno v:
Journal of Molecular Biology. 432:508-522
The functioning of proteins requires highly specific dynamics, which depend critically on the details of how amino acids are packed. Hinge motions are the most common type of large motion, typified by the opening and closing of enzymes around their s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c7633b1c03bf258895674970fbc6bee0
https://doi.org/10.1016/j.jmb.2019.11.018
https://doi.org/10.1016/j.jmb.2019.11.018
Autor:
Pranav M Khade, Robert L Jernigan
Publikováno v:
Bioinformatics Advances.
PACKMAN-molecule is a Structural Bioinformatics toolbox in the form of an Application Programming Interface (API) that contains several utilities that can be used for structural bioinformatics applications. It has already been used in several applica
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::be5c8caa60692f0bd7df1f7eeecacb2e
https://doi.org/10.1093/bioadv/vbac007
https://doi.org/10.1093/bioadv/vbac007
Publikováno v:
Bioinformatics (Oxford, England).
Summary A new dynamic community identifier (DCI) is presented that relies upon protein residue dynamic cross-correlations generated by Gaussian elastic network models to identify those residue clusters exhibiting motions within a protein. A number of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bf49568f70f56d3b1690926ffa8f7adb
https://pubmed.ncbi.nlm.nih.gov/35298588
https://pubmed.ncbi.nlm.nih.gov/35298588
Autor:
Pranav M. Khade, Robert L. Jernigan
Publikováno v:
Biophysical Journal. 121:17a-18a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::59fc972b4758c984aff96671ac1d88aa
https://doi.org/10.1016/j.bpj.2021.11.2614
https://doi.org/10.1016/j.bpj.2021.11.2614
Autor:
Domenico Scaramozzino, Giuseppe Lacidogna, Pranav M. Khade, Robert L. Jernigan, Alberto Carpinteri
Publikováno v:
Proteins
Proteins are the active players in performing essential molecular activities throughout biology, and their dynamics has been broadly demonstrated to relate to their mechanisms. The intrinsic fluctuations have often been used to represent their dynami
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0121093eab2245ccedffb79859f06c5b
http://hdl.handle.net/11583/2847748
http://hdl.handle.net/11583/2847748
Publikováno v:
Biophysical Journal. 121:323a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::471a0130ef2342f5fe5e5b3234fd7466
https://doi.org/10.1016/j.bpj.2021.11.1159
https://doi.org/10.1016/j.bpj.2021.11.1159
Publikováno v:
Biophysical Journal. 120:115a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::84f390311c7fca9b1a47ae8aba2bfe42
https://doi.org/10.1016/j.bpj.2020.11.915
https://doi.org/10.1016/j.bpj.2020.11.915