Zobrazeno 1 - 10
of 275
pro vyhledávání: '"Li L. Duan"'
Publikováno v:
Scientific Reports
Molecular dynamics simulations in explicit water are carried out to study the binding of six inhibitors to HIV-1 protease (PR) for up to 700 ns using the standard AMBER force field and polarized protein-specific charge (PPC). PPC is derived from quan
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce9fe43a03eeb572b1feb7be961555ec
https://doi.org/10.1038/srep42223
https://doi.org/10.1038/srep42223
Publikováno v:
Science China Chemistry. 57:1708-1715
MD simulation study of several peptides including a polyalanine, a helix (pdb:2I9M), and a leucine zipper were carried out to investigate hydrogen bond energetics using dynamic polarized protein-specific charge (DPPC) to account for the polarization
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ee805e798a10ed424995d3024c57072d
https://doi.org/10.1007/s11426-014-5246-0
https://doi.org/10.1007/s11426-014-5246-0
Publikováno v:
Journal of Molecular Modeling. 19:2605-2612
MD simulations of five proteins in which helical chains are held together by hydrophobic packing were carried out to investigate the effect of hydrophobic force on simulated structures of these protein complexes in implicit generalized Born (GB) mode
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c4f587820fd0a6bb5e818fe9252c39ef
https://doi.org/10.1007/s00894-013-1798-8
https://doi.org/10.1007/s00894-013-1798-8
Publikováno v:
Scientific Reports
Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derive
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::12055b91d734279280398bdff05f9f82
https://doi.org/10.1038/srep31488
https://doi.org/10.1038/srep31488
Publikováno v:
Journal of the American Chemical Society. 132:11159-11164
We report direct folding of a 17-residue helix protein (pdb:2I9M) by standard molecular dynamics simulation (single trajectory) at room temperature with implicit solvent. Starting from a fully extended structure, 2I9M successfully folds into the nati
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b2a76b56dbcc0cd22a508884fdce00db
https://doi.org/10.1021/ja102735g
https://doi.org/10.1021/ja102735g
Publikováno v:
Journal of Theoretical and Computational Chemistry. :1265-1279
HIV-1 protease (PR) is a primary target for anti-HIV therapeutics. A well conserved water molecule, denoted as W301, is found in almost all the crystallographic structures of PR/inhibitor complexes and it plays an important role in PR/inhibitor bindi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::10d9a5d176a42d667fb296b894929540
https://doi.org/10.1142/s0219633609005313
https://doi.org/10.1142/s0219633609005313
Publikováno v:
Journal of Molecular Modeling
Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::339424ae7bc0cfc5eb13dbde4788a7a3
http://europepmc.org/articles/PMC3996369
http://europepmc.org/articles/PMC3996369
Publikováno v:
The journal of physical chemistry. B. 116(10)
Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M ) using a polarized charge scheme that includes electronic polarization
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0511d51cd7bf4d463ec211df8dd301d
https://pubmed.ncbi.nlm.nih.gov/22369598
https://pubmed.ncbi.nlm.nih.gov/22369598
Publikováno v:
The Journal of chemical physics. 130(11)
Molecular dynamics (MD) simulation has been carried out to study dynamical stability of intra-protein hydrogen bonds based on two set of atomic charges, the standard AMBER charge and the polarized protein-specific charge (PPC). The latter is derived
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4e3771c9e3aacbf225cb1ba439309f34
https://pubmed.ncbi.nlm.nih.gov/19317568
https://pubmed.ncbi.nlm.nih.gov/19317568
Publikováno v:
Journal of Theoretical and Computational Chemistry. 13:1440005
In this paper, molecular dynamics (MD) simulations were performed for a number of benchmark proteins using both the standard assisted model building with energy refinement (AMBER) charge and the dynamically adjusted polarized protein-specific charge
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::50f79595822afe19eb475f86fbc9f352
https://doi.org/10.1142/s0219633614400057
https://doi.org/10.1142/s0219633614400057