Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Hatice Gökcan"'
Autor:
Théo Jaffrelot Inizan, Thomas Plé, Olivier Adjoua, Pengyu Ren, Hatice Gökcan, Olexandr Isayev, Louis Lagardère, Jean-Philip Piquemal
Publikováno v:
Chemical Science
Chemical Science, 2023, ⟨10.1039/D2SC04815A⟩
Chemical Science, 2023, ⟨10.1039/D2SC04815A⟩
International audience; Deep-HP is a scalable extension of the Tinker-HP multi-GPUs molecular dynamics (MD) package enabling the use of Pytorch/TensorFlow Deep Neural Networks (DNNs) models. Deep-HP increases DNNs MD capabilities by orders of magnitu
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e3204c37f45afbf96b891d166d560cc0
https://hal.science/hal-03738403
https://hal.science/hal-03738403
Autor:
Hatice Gökcan, Olexandr Isayev
Publikováno v:
Chemical Science. 13:2462-2474
We developed new empirical ML model for protein pKa prediction with MAEs below 0.5 for all amino acid types.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::da4503af54bc6d0773d03e284b56ebb5
https://doi.org/10.1039/d1sc05610g
https://doi.org/10.1039/d1sc05610g
Autor:
Hatice Gökcan, Olexandr Isayev
The behavior of proteins is closely related to the protonation states of the residues. Therefore, prediction and measurement of pKa are essential to understand the basic functions of proteins. In this work, we develop a new empirical scheme for prote
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7c9799eda74469eeca9ea5580dbfaaca
https://doi.org/10.33774/chemrxiv-2021-tcn0f-v2
https://doi.org/10.33774/chemrxiv-2021-tcn0f-v2
Autor:
Hatice Gökcan, Olexandr Isayev
Publikováno v:
WIREs Computational Molecular Science. 12
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::977674d35002649f3696db3e1c6e0261
https://doi.org/10.1002/wcms.1564
https://doi.org/10.1002/wcms.1564
Publikováno v:
J Chem Theory Comput
The QM/MM method has become a useful tool to investigate various properties of complex systems. We previously introduced the layered interacting chemical models (LICHEM) package to enable QM/MM simulations with advanced potentials by combining variou
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::81fc095a52d090200ed16eec8b7eaff3
https://pubmed.ncbi.nlm.nih.gov/30908049
https://pubmed.ncbi.nlm.nih.gov/30908049
Autor:
Melissa Lizette Liriano, Alessandro A. Rizzo, Kevin Jeanne Dit Fouque, Bilyana N. Koleva, G. Andrés Cisneros, Hatice Gökcan, Dmitry M. Korzhnev, Francisco Fernandez-Lima, Socheata Lim, Penny J. Beuning, Angelina Choy
Publikováno v:
Biophys J
The ring-shaped sliding clamp proteins have crucial roles in the regulation of DNA replication, recombination, and repair in all organisms. We previously showed that the Escherichia coli β-clamp is dynamic in solution, transiently visiting conformat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::71095f61c4e992742ea101035aa5d950
https://pubmed.ncbi.nlm.nih.gov/31349986
https://pubmed.ncbi.nlm.nih.gov/31349986
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 84:875-891
The pyridoxal 5-phosphate (PLP) cofactor is a significant organic molecule in medicinal chemistry. It is often found covalently bound to lysine residues in proteins to form PLP dependent enzymes. An example of this family of PLP dependent enzymes is
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::74bf8085c9ed97ed97158aa7113764e6
https://doi.org/10.1002/prot.24991
https://doi.org/10.1002/prot.24991
Publikováno v:
Journal of Chemical Information and Modeling
Journal of Chemical Information and Modeling, American Chemical Society, 2018, 59 (1), pp.206-214. ⟨10.1021/acs.jcim.8b00605⟩
Journal of Chemical Information and Modeling, American Chemical Society, 2018, 59 (1), pp.206-214. ⟨10.1021/acs.jcim.8b00605⟩
International audience; Semi-empirical quantum methods from the neglect of differential diatomic overlap (NDDO) family such as MNDO, AM1, or PM3 are fast albeit approximate quantum methods. By combining them with linear scaling methods like the divid
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::11785d2ef81e9d76a50026ea7b803409
https://hal.univ-lorraine.fr/hal-02188215/document
https://hal.univ-lorraine.fr/hal-02188215/document
Publikováno v:
Journal of Physical Chemistry Letters
Journal of Physical Chemistry Letters, American Chemical Society, 2018, 9 (11), pp.3062-3067. ⟨10.1021/acs.jpclett.8b01412⟩
Journal of Physical Chemistry Letters, American Chemical Society, 2018, 9 (11), pp.3062-3067. ⟨10.1021/acs.jpclett.8b01412⟩
The use of advanced polarizable potentials in quantum mechanical/molecular mechanical (QM/MM) simulations has been shown to improve the overall accuracy of the calculation. We have developed a density-based potential called the Gaussian electrostatic
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::da6901e112cc67633b23cdabf1af716c
https://hal.archives-ouvertes.fr/hal-02126841
https://hal.archives-ouvertes.fr/hal-02126841
Publikováno v:
Proteins. 84(7)
The pyridoxal 5-phosphate (PLP) cofactor is a significant organic molecule in medicinal chemistry. It is often found covalently bound to lysine residues in proteins to form PLP dependent enzymes. An example of this family of PLP dependent enzymes is
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::960819c064f2b6f502288b3f36c8c2c2
https://pubmed.ncbi.nlm.nih.gov/26800298
https://pubmed.ncbi.nlm.nih.gov/26800298