Exploring the concerted mechanistic pathway for HIV-1 PR—substrate revealed by umbrella sampling simulation

Theoretical Model for HIV-1 PR That Accounts for Substrate Recognition and Preferential Cleavage of Natural Substrates

(2019) Zainab K. Sanusi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations

(2018) Shuichiro Tsukamoto et al.   JOURNAL OF CHEMICAL PHYSICS

An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant

(2018) Zainab K. Sanusi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

From recognition to reaction mechanism: an overview on the interactions between HIV-1 protease and its natural targets

(2018) Monsurat M. Lawal et al.   CURRENT MEDICINAL CHEMISTRY

Unraveling the concerted catalytic mechanism of the human immunodeficiency virus type 1 (HIV-1) protease: a hybrid QM/MM study

(2018) Monsurat M. Lawal et al.   STRUCTURAL CHEMISTRY

Investigation of the binding free energies of FDA approved drugs against subtype B and C-SA HIV PR: ONIOM approach

(2017) Z.K. Sanusi et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Computational model for the acylation step of the β -lactam ring: Potential application for l , d -transpeptidase 2 in mycobacterium tuberculosis

(2017) Zeynab Fakhar et al.   JOURNAL OF MOLECULAR STRUCTURE

Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease

(2016) Agnieszka Krzemińska et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations

(2015) Francesco Di Palma et al.   BMC BIOINFORMATICS

Simulating the inhibition reaction of Mycobacterium tuberculosisl,d-transpeptidase 2 by carbapenems

(2015) José Rogério A. Silva et al.   CHEMICAL COMMUNICATIONS

The effect of N-methylation of amino acids (Ac-X-OMe) on solubility and conformation: a DFT study

(2015) Shah Md. Abdur Rauf et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Catalytic Mechanism of L,D-Transpeptidase 2 from Mycobacterium tuberculosis Described by a Computational Approach: Insights for the Design of New Antibiotics Drugs

(2014) José Rogério A. Silva et al.   Journal of Chemical Information and Modeling

pH-REMD Simulations Indicate That the Catalytic Aspartates of HIV-1 Protease Exist Primarily in a Monoprotonated State

(2014) T. Dwight McGee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanistic insights into Pin1 peptidyl-prolylcis-transisomerization from umbrella sampling simulations

(2014) Giovanni Paolo Di Martino et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

On the Active Site Protonation State in Aspartic Proteases: Implications for Drug Design

(2013) Fredy Sussman et al.   CURRENT PHARMACEUTICAL DESIGN

Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

(2013) Tai-Sung Lee et al.   Journal of Chemical Theory and Computation

A Dynamic Structural Model of Expanded RNA CAG Repeats: A Refined X-ray Structure and Computational Investigations Using Molecular Dynamics and Umbrella Sampling Simulations

(2013) Ilyas Yildirim et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural insights into the South African HIV-1 subtype C protease: impact of hinge region dynamics and flap flexibility in drug resistance

(2012) Previn Naicker et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

(2012) Tai-Sung Lee et al.   Journal of Chemical Theory and Computation

Understanding the HIV-1 Protease Reactivity with DFT: What Do We Gain from Recent Functionals?

(2011) J. Garrec et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mass-Dependent Bond Vibrational Dynamics Influence Catalysis by HIV-1 Protease

(2011) D. Randal Kipp et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Nine Crystal Structures Determine the Substrate Envelope of the MDR HIV-1 Protease

(2011) Zhigang Liu et al.   PROTEIN JOURNAL

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations

(2010) Christopher B. Barnett et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography

(2009) M. Adachi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA