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

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

Binding Free Energy Calculations of Nine FDA-approved Protease Inhibitors Against HIV-1 Subtype C I36T↑T Containing 100 Amino Acids Per Monomer

(2016) Husain A. Lockhat et al.   Chemical Biology & Drug Design

Purification and characterization of naturally occurring HIV-1 (South African subtype C) protease mutants from inclusion bodies

(2016) Sibusiso B. Maseko et al.   PROTEIN EXPRESSION AND PURIFICATION

The ONIOM Method and Its Applications

(2015) Lung Wa Chung et al.   CHEMICAL REVIEWS

Disubstituted Bis-THF Moieties as New P2 Ligands in Nonpeptidal HIV-1 Protease Inhibitors (II)

(2015) Konrad Hohlfeld et al.   JOURNAL OF MEDICINAL CHEMISTRY

NBO–NEDA, NPA, and QTAIM studies on the interactions between aza-, diaza-, and triaza-12-crown-4 (An-12-crown-4, n=1, 2, 3) and Li+, Na+, and K+ ions

(2015) Reza Behjatmanesh-Ardakani   Computational and Theoretical Chemistry

A Conserved Hydrogen-Bonding Network of P2bis-Tetrahydrofuran-Containing HIV-1 Protease Inhibitors (PIs) with a Protease Active-Site Amino Acid Backbone Aids in Their Activity against PI-Resistant HIV

(2014) Ravikiran S. Yedidi et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Structural Basis for HTLV-1 Protease Inhibition by the HIV-1 Protease Inhibitor Indinavir

(2014) Maren Kuhnert et al.   JOURNAL OF MEDICINAL CHEMISTRY

AIM and NBO analyses on hydrogen bonds formation in sugar-based surfactants (α/β-d-mannose andn-octyl-α/β-d-mannopyranoside): a density functional theory study

(2014) Zahrabatoul Mosapour Kotena et al.   LIQUID CRYSTALS

A fundamental view of enthalpy–entropy compensation

(2014) Ulf Ryde   MedChemComm

The intramolecular cation–π interaction of some aryl amines and its drastic influence on the basicity of them: AIM and NBO analysis

(2014) Somayyeh Kheirjou et al.   Computational and Theoretical Chemistry

Crystallographic study of multi-drug resistant HIV-1 protease lopinavir complex: Mechanism of drug recognition and resistance

(2013) Zhigang Liu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Insights into the mechanism of drug resistance: X-ray structure analysis of multi-drug resistant HIV-1 protease ritonavir complex

(2013) Zhigang Liu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The Impact of Active Site Mutations of South African HIV PR on Drug Resistance: Insight from Molecular Dynamics Simulations, Binding Free Energy and Per-Residue Footprints

(2013) Shaimaa M. Ahmed et al.   Chemical Biology & Drug Design

Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity

(2013) Bahareh Honarparvar et al.   CHEMICAL REVIEWS

Homology modeling, molecular docking and MD simulation studies to investigate role of cysteine protease from Xanthomonas campestris in degradation of Aβ peptide

(2013) Maruti J. Dhanavade et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Relation between flexibility and positively selected HIV-1 protease mutants against inhibitors

(2013) Antônio S. K. Braz et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Hydrogen-bonded complexes of serotonin with methanol and ethanol: a DFT study

(2013) A. Mano Priya et al.   STRUCTURAL CHEMISTRY

Extreme Entropy–Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease

(2012) Nancy M. King et al.   ACS Chemical Biology

Comparison of the Molecular Dynamics and Calculated Binding Free Energies for Nine FDA-Approved HIV-1 PR Drugs Against Subtype B and C-SA HIV PR

(2012) Shaimaa M. Ahmed et al.   Chemical Biology & Drug Design

Pentacycloundecane-diol-Based HIV-1 Protease Inhibitors: Biological Screening, 2D NMR, and Molecular Simulation Studies

(2012) Bahareh Honarparvar et al.   ChemMedChem

Synthesis, screening and computational investigation of pentacycloundecane-peptoids as potent CSA-HIV PR inhibitors

(2012) Maya M. Makatini et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Synthesis and molecular modelling studies of novel carbapeptide analogs for inhibition of HIV-1 protease

(2012) Sachin A. Pawar et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Linear and cyclic glycopeptide as HIV protease inhibitors

(2012) Sachin A. Pawar et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Synthesis, 2D-NMR and molecular modelling studies of pentacycloundecane lactam-peptides and peptoids as potential HIV-1 wild type C-SA protease inhibitors

(2012) Maya M. Makatini et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

Hydrogen bonds in galactopyranoside and glucopyranoside: a density functional theory study

(2012) Zahrabatoul Mosapour Kotena et al.   JOURNAL OF MOLECULAR MODELING

Directionality of Inter- and Intramolecular OHO Hydrogen Bonds: DFT Study Followed by AIM and NBO Analysis

(2012) Irena Majerz   JOURNAL OF PHYSICAL CHEMISTRY A

DRASTIC INFLUENCE OF BORON ATOM ON THE ACIDITY OF ALCOHOL IN BOTH GAS PHASE AND SOLUTION PHASE, A DFT STUDY

(2012) SOMAYYEH KHEIRJOU et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

Novel PCU cage diol peptides as potential targets against wild-type CSA HIV-1 protease: synthesis, biological screening and molecular modelling studies

(2012) Rajshekhar Karpoormath et al.   MEDICINAL CHEMISTRY RESEARCH

Critical differences in HIV-1 and HIV-2 protease specificity for clinical inhibitors

(2012) Yunfeng Tie et al.   PROTEIN SCIENCE

Pentacycloundecane derived hydroxy acid peptides: A new class of irreversible non-scissile ether bridged type isoster as potential HIV-1 wild type C-SA protease inhibitors

(2011) Rajshekhar Karpoormath et al.   BIOORGANIC CHEMISTRY

Homology modeling, docking, molecular dynamics simulation, and structural analyses of coxsakievirus B3 2A protease: An enzyme involved in the pathogenesis of inflammatory myocarditis

(2011) Amir Hossein Maghsoudi et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery

(2011) Roman A. Laskowski et al.   Journal of Chemical Information and Modeling

Strength of Hydrogen Bond Network Takes Crucial Roles in the Dissociation Process of Inhibitors from the HIV-1 Protease Binding Pocket

(2011) Dechang Li et al.   PLoS One

An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

(2011) Arvind Marathe et al.   BMC STRUCTURAL BIOLOGY

Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypes

(2010) Arthur H. Robbins et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Computational Study of the Resistance Shown by the Subtype B/HIV-1 Protease to Currently Known Inhibitors

(2010) Alessandro Genoni et al.   BIOCHEMISTRY

Case Studies of ONIOM(DFT:DFTB) and ONIOM(DFT:DFTB:MM) for Enzymes and Enzyme Mimics

(2010) Marcus Lundberg et al.   Journal of Chemical Theory and Computation

Synthesis of New Thienyl Ring Containing HIV-1 Protease Inhibitors: Promising Preliminary Pharmacological Evaluation against Recombinant HIV-1 Proteases§

(2010) Carlo Bonini et al.   JOURNAL OF MEDICINAL CHEMISTRY

QUANTUM CALCULATION OF PROTEIN SOLVATION AND PROTEIN–LIGAND BINDING FREE ENERGY FOR HIV-1 PROTEASE/WATER COMPLEX

(2010) YAN TONG et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

Role of Gag in HIV Resistance to Protease Inhibitors

(2010) François Clavel et al.   Viruses-Basel

Assessment of QM/MM Scoring Functions for Molecular Docking to HIV-1 Protease

(2009) Pedro Fong et al.   Journal of Chemical Information and Modeling

Prevalence of C-terminal gag cleavage site mutations in HIV from therapy-naïve patients

(2008) Jens Verheyen et al.   JOURNAL OF INFECTION

Active-Site Mutations in the South African Human Immunodeficiency Virus Type 1 Subtype C Protease Have a Significant Impact on Clinical Inhibitor Binding: Kinetic and Thermodynamic Study

(2008) S. Mosebi et al.   JOURNAL OF VIROLOGY

Tautomeric Equilibrium, Stability, and Hydrogen Bonding in 2‘-Deoxyguanosine Monophosphate Complexed with Mg2+

(2007) Dmytro Kosenkov et al.   JOURNAL OF PHYSICAL CHEMISTRY B