Molecular dynamics simulations of ligand-induced flap closing in HIV-1 protease approach X-ray resolution: establishing the role of bound water in the flap closing …
G Singh, S Senapati - Biochemistry, 2008 - ACS Publications
The necessity of understanding the detailed mechanism of flap dynamics in designing HIV-1
protease inhibitors is immense. Crystal structures have provided us with a static overview of …
protease inhibitors is immense. Crystal structures have provided us with a static overview of …
Clarifying allosteric control of flap conformations in the 1TW7 crystal structure of HIV‐1 protease
KW Lexa, KL Damm, JJ Quintero… - Proteins: Structure …, 2009 - Wiley Online Library
HIV-1 protease (HIVp) inhibitors are essential for current AIDS treatments, and new
compounds are still a very active area of research. The conformational behavior of the flap …
compounds are still a very active area of research. The conformational behavior of the flap …
Atomistic simulations of the HIV-1 protease folding inhibition
Biochemical experiments have recently revealed that the p-S8 peptide, with an amino-acid
sequence identical to the conserved fragment 83–93 (S8) of the HIV-1 protease, can inhibit …
sequence identical to the conserved fragment 83–93 (S8) of the HIV-1 protease, can inhibit …
Exploring the flap dynamics of the South African HIV subtype C protease in presence of FDA‐approved inhibitors: MD study
SI Maphumulo, AK Halder, T Govender… - Chemical biology & …, 2018 - Wiley Online Library
HIV‐1 protease (HIV PR) is considered as one of the most attractive targets for the treatment
of HIV and the impact of flap dynamics of HIV PR on the binding affinities of protease …
of HIV and the impact of flap dynamics of HIV PR on the binding affinities of protease …
Exploration of the Structural Asymmetry Induced by the Intrinsic Flexibility of HIV-2 Protease
A Badel, L Breuil, P Laville, L Regad - Symmetry, 2022 - mdpi.com
HIV-2 protease (PR2) is a homodimer targeted by drugs in the treatment of HIV-2 infections.
This dimer is often considered symmetric. However, exploration of crystallographic …
This dimer is often considered symmetric. However, exploration of crystallographic …
Reconstruction of the binding pathway of an anti-HIV drug, Indinavir, in complex with the HTLV-1 protease by Unaggregated Unbiased Molecular Dynamics simulation
F Sohraby, H Aryapour - bioRxiv, 2021 - biorxiv.org
Retroviruses are a growing concern for the health of human beings, and one of the
dangerous members of this family is the Human T-cell Leukemia Virus 1 (HTLV-1) virus. It …
dangerous members of this family is the Human T-cell Leukemia Virus 1 (HTLV-1) virus. It …
New 1(2H)-phthalazinone derivatives as potent nonpeptidic HIV-1 protease inhibitors: molecular docking studies, molecular dynamics simulation, oral bioavailability …
D Sroczyński, Z Malinowski, AK Szcześniak… - Molecular …, 2016 - Taylor & Francis
Molecular docking simulations of compounds 1–7, the newly synthesised 1 (2 H)-
phthalazinone derivatives with N-(dimethylamino) ethyl pendant arm, as potent inhibitors of …
phthalazinone derivatives with N-(dimethylamino) ethyl pendant arm, as potent inhibitors of …
Toward in silico biomolecular manipulation through static modes: atomic scale characterization of HIV-1 protease flexibility
Probing biomolecular flexibility with atomic-scale resolution is a challenging task in current
computational biology for fundamental understanding and prediction of biomolecular …
computational biology for fundamental understanding and prediction of biomolecular …
Computational approach to site‐directed ligand discovery
G Tóth, K Mukhyala, JA Wells - Proteins: Structure, Function …, 2007 - Wiley Online Library
A computational approach, Systematic Conformational Search & Induced Fit (SCI&FI), to site‐
directed ligand discovery (Tethering®) is presented. SCI&FI has the ability to predict the …
directed ligand discovery (Tethering®) is presented. SCI&FI has the ability to predict the …
Fragment and protein simulation methods in fragment based drug design
AE Klon, Z Konteatis, SN Meshkat, J Zou… - Drug Development …, 2011 - Wiley Online Library
Fragment‐based drug design (FBDD) has become an important and successful approach to
drug discovery. In this review, we discuss two classes of simulation technologies that we …
drug discovery. In this review, we discuss two classes of simulation technologies that we …