Decoding the Host–Parasite Protein Interactions Involved in Cerebral Malaria Through Glares of Molecular Dynamics Simulations

Mining of Ebola virus genome for the construction of multi-epitope vaccine to combat its infection

(2021) Uma Shankar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

In silico analysis of antiviral phytochemicals efficacy against Epstein–Barr virus glycoprotein H

(2021) Shweta Jakhmola et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies

(2021) Rajarshi Roy et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Elucidating specificity of an allosteric inhibitor WNK476 among WNK isoforms using molecular dynamic simulations

(2021) Nisha Amarnath Jonniya et al.   Chemical Biology & Drug Design

Identification of Potential Inhibitors against Epstein–Barr Virus Nuclear Antigen 1 (EBNA1): An Insight from Docking and Molecular Dynamic Simulations

(2021) Shweta Jakhmola et al.   ACS Chemical Neuroscience

Plant derived active compounds as potential anti SARS-CoV-2 agents: an in-silico study

(2021) Dharmendra Kashyap et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Dynamical Basis of Allosteric Activation for the Plasmodium falciparum Protein Kinase G

(2021) Jinfeng Huang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations

(2020) Md Fulbabu Sk et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Insights into the Binding Recognition and Susceptibility of Tofacitinib toward Janus Kinases

(2020) Kamonpan Sanachai et al.   ACS Omega

Investigating Conformational Dynamics of Lewis Y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics

(2020) Rajarshi Roy et al.   ACS Omega

Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations

(2020) Md Fulbabu Sk et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations

(2020) Md Fulbabu Sk et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA‐dependent RNA polymerase (RdRp) inhibition: an in-silico analysis

(2020) Satyam Singh et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Investigating the mechanism of recognition and structural dynamics of nucleoprotein-RNA complex from Peste des petits ruminants virus via Gaussian accelerated molecular dynamics simulations

(2020) Rajarshi Roy et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets

(2020) Liya Thurakkal et al.   CHEMICAL PHYSICS LETTERS

Epstein–Barr virus infection modulates blood–brain barrier cells and its co-infection with Plasmodium falciparum induces RBC adhesion

(2020) Omkar Indari et al.   Pathogens and Disease

Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM

(2020) Md Fulbabu Sk et al.   Frontiers in Molecular Biosciences

Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations

(2019) Nisha A. Jonniya et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Prediction of Non-Competitive Inhibitor Binding Mode Reveals Promising Site for Allosteric Modulation of Falcipain-2

(2019) Jorge Enrique Hernandez Gonzalez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Investigating Phosphorylation-Induced Conformational Changes in WNK1 Kinase by Molecular Dynamics Simulations

(2019) Nisha Amarnath Jonniya et al.   ACS Omega

Insight into binding mechanisms of inhibitors MKP56, MKP73, MKP86, and MKP97 to HIV-1 protease by using molecular dynamics simulation

(2017) Shuhua Shi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Variant surface antigens of Plasmodium falciparum and their roles in severe malaria

(2017) Mats Wahlgren et al.   NATURE REVIEWS MICROBIOLOGY

Computational Studies of a Mechanism for Binding and Drug Resistance in the Wild Type and Four Mutations of HIV-1 Protease with a GRL-0519 Inhibitor

(2016) Guodong Hu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structural Conservation Despite Huge Sequence Diversity Allows EPCR Binding by the PfEMP1 Family Implicated in Severe Childhood Malaria

(2015) Clinton K.Y. Lau et al.   Cell Host & Microbe

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Sequence variation and structural conservation allows development of novel function and immune evasion in parasite surface protein families

(2014) Matthew K. Higgins et al.   PROTEIN SCIENCE

Malaria's deadly grip: cytoadhesion ofPlasmodium falciparum-infected erythrocytes

(2013) Joseph D. Smith et al.   CELLULAR MICROBIOLOGY

Molecular Architecture of a Complex between an Adhesion Protein from the Malaria Parasite and Intracellular Adhesion Molecule 1

(2013) Alan Brown et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Importance of Polar Solvation and Configurational Entropy for Design of Antiretroviral Drugs Targeting HIV-1 Protease

(2013) Parimal Kar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Genetic structure of Plasmodium falciparum populations across the Honduras-Nicaragua border

(2013) Nerea Larrañaga et al.   MALARIA JOURNAL

Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir

(2012) Parimal Kar et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Energetics of Mutation-Induced Changes in Potency of Lersivirine against HIV-1 Reverse Transcriptase

(2012) Parimal Kar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mutation-Induced Loop Opening and Energetics for Binding of Tamiflu to Influenza N8 Neuraminidase

(2012) Parimal Kar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Origin of Decrease in Potency of Darunavir and Two Related Antiviral Inhibitors against HIV-2 Compared to HIV-1 Protease

(2012) Parimal Kar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Plasmodium falciparum erythrocyte membrane protein 1 domain cassettes 8 and 13 are associated with severe malaria in children

(2012) T. Lavstsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Importance of Polar Solvation for Cross-Reactivity of Antibody and Its Variants with Steroids

(2011) Parimal Kar et al.   JOURNAL OF PHYSICAL CHEMISTRY B