Zobrazeno 1 - 10
of 25
pro vyhledávání: '"Savvas Polydorides"'
Autor:
Savvas Polydorides, Georgios Archontis
Publikováno v:
STAR Protocols, Vol 3, Iss 2, Pp 101254- (2022)
Summary: The present protocol describes the computational design of the SARS-CoV-2 receptor binding motif (RBD) to identify mutations that can potentially improve binding affinity for the human ACE2 (hACE2) receptor. We focus on four positions locate
Externí odkaz:
https://doaj.org/article/d46b855f790f4a49acd2c25f8e80c3c1
Autor:
Savvas Polydorides, Georgios Archontis
Publikováno v:
Biophysical Journal
The coronavirus SARS-CoV-2, that is responsible for the COVID-19 pandemic, and the closely related SARS-CoV coronavirus enter cells by binding at the human angiotensin converting enzyme 2 (hACE2). The stronger hACE2 affinity of SARS-CoV-2 has been co
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::56ac955c0021d813c0751bc1280326d3
https://doi.org/10.1016/j.bpj.2021.02.049
https://doi.org/10.1016/j.bpj.2021.02.049
Autor:
Haichao Huang, Joseph Sperling, Savvas Polydorides, Alexander Kotlyar, Linda A. Zotti, Spiros S. Skourtis, Georgia Polycarpou, Roman Zhuravel, Phani Motamarri, Juan Carlos Cuevas, Dvir Rotem, Liat Katrivas, Vikram Gavini, Danny Porath
Publikováno v:
Nature Nanotechnology. 15:836-840
Understanding charge transport in DNA molecules is a long-standing problem of fundamental importance across disciplines1,2. It is also of great technological interest due to DNA’s ability to form versatile and complex programmable structures. Charg
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b07d647eb8eaa790d9b6d1bf8d2b741b
https://doi.org/10.1038/s41565-020-0741-2
https://doi.org/10.1038/s41565-020-0741-2
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 2405
We describe a two-stage computational protein design (CPD) methodology for the design of peptides binding to the FAT domain of the protein focal adhesion kinase. The first stage involves high-throughput CPD calculations with the Proteus software. The
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::28d25253ee8136bb37952d1e74e6c85b
https://pubmed.ncbi.nlm.nih.gov/35298823
https://pubmed.ncbi.nlm.nih.gov/35298823
Publikováno v:
Methods in Molecular Biology ISBN: 9781071618547
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d87cfb6fcdfe6f2f90437104e7f0ba22
https://doi.org/10.1007/978-1-0716-1855-4_18
https://doi.org/10.1007/978-1-0716-1855-4_18
Autor:
David Mignon, Georgios Archontis, Vaitea Opuu, Nicolas Panel, Karen Druart, Francesco Villa, Thomas Gaillard, Thomas Simonson, Eleni Michael, Savvas Polydorides
Publikováno v:
Journal of Physical Chemistry A
Journal of Physical Chemistry A, American Chemical Society, 2020, 124 (51), pp.10637-10648. ⟨10.1021/acs.jpca.0c07605⟩
Journal of Physical Chemistry A, American Chemical Society, 2020, 124 (51), pp.10637-10648. ⟨10.1021/acs.jpca.0c07605⟩
We describe methods for physics-based protein design and some recent applications from our work. We present the physical interpretation of a MC simulation in sequence space and show that sequences and conformations form a well-defined statistical ens
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c3bc7d58ed993f5160ffa45936a019bc
https://pubmed.ncbi.nlm.nih.gov/33170681
https://pubmed.ncbi.nlm.nih.gov/33170681
Autor:
Thomas Gaillard, David Mignon, Eleni Michael, Savvas Polydorides, Francesco Villa, Georgios Archontis, Karen Druart, Vaitea Opuu, Thomas Simonson
We describe methods and software for physics-based protein design. The folded state energy combines molecular mechanics with Generalized Born solvent. Sequence and conformation space are sampled with Replica Exchange Monte Carlo, assuming one or a fe
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::74f726f15192ebd759ba85172f5ed573
https://doi.org/10.1101/2020.06.30.179549
https://doi.org/10.1101/2020.06.30.179549
Autor:
Vasilis J. Promponas, Georgios Archontis, Savvas Polydorides, Paris A. Skourides, Eleni Michael
Publikováno v:
ProteinsREFERENCES.
The focal adhesion kinase (FAK) and the proline-rich tyrosine kinase 2-beta (PYK2) are implicated in cancer progression and metastasis and represent promising biomarkers and targets for cancer therapy. FAK and PYK2 are recruited to focal adhesions (F
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::95a4a0a6067fb2abbbe97bc22a4e10bf
https://pubmed.ncbi.nlm.nih.gov/32776636
https://pubmed.ncbi.nlm.nih.gov/32776636
Publikováno v:
The Journal of Chemical Physics. 153:054113
Computational protein design relies on simulations of a protein structure, where selected amino acids can mutate randomly, and mutations are selected to enhance a target property, such as stability. Often, the protein backbone is held fixed and its d
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::20c8598c2e0d97b8cc44b6e448ec5479
https://doi.org/10.1063/5.0013320
https://doi.org/10.1063/5.0013320
Publikováno v:
Journal of Computational Chemistry
Journal of Computational Chemistry, Wiley, 2017, 38 (29), pp.2509-2519. ⟨10.1002/jcc.24910⟩
Journal of Computational Chemistry, Wiley, 2017, 38 (29), pp.2509-2519. ⟨10.1002/jcc.24910⟩
Implicit solvent models are important for many biomolecular simulations. The polarity of aqueous solvent is essential and qualitatively captured by continuum electrostatics methods like Generalized Born (GB). However, GB does not account for the solv
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::72c6df68fc8fd8402052ccefedb7d0ca
https://hal-polytechnique.archives-ouvertes.fr/hal-01955056
https://hal-polytechnique.archives-ouvertes.fr/hal-01955056