Binding modes of Bcl-2 homology 3 (BH3) peptides with anti-apoptotic protein A1 and redesign of peptide inhibitors: a computational study

A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide

(2017) Jing-Na Ding et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Deciphering the crucial molecular properties of a series of Benzothiazole Hydrazone inhibitors that targets anti-apoptotic Bcl-xL protein

(2017) Parthiban Marimuthu et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Exploring stereochemical specificity of phosphotriesterase by MM-PBSA and MM-GBSA calculation and steered molecular dynamics simulation

(2016) Jingxuan Zhu et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity

(2016) Stefan M. Ivanov et al.   STRUCTURE

Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment

(2015) Shunzhou Wan et al.   Journal of Chemical Theory and Computation

Exploring the binding mechanisms of MIF to CXCR2 using theoretical approaches

(2015) Lei Xu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Insights into the effects of mutations on Cren7–DNA binding using molecular dynamics simulations and free energy calculations

(2015) Lin Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations

(2015) Huiyong Sun et al.   Scientific Reports

Revealing the binding modes and the unbinding of 14-3-3σ proteins and inhibitors by computational methods

(2015) Guodong Hu et al.   Scientific Reports

Molecular dynamics study of segment peptides of Bax, Bim, and Mcl-1 BH3 domain of the apoptosis-regulating proteins bound to the anti-apoptotic Mcl-1 protein

(2014) Run-Ning Zhao et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Biomimetic Design of Platelet Adhesion Inhibitors to Block Integrin α2β1-Collagen Interactions: I. Construction of an Affinity Binding Model

(2014) Lin Zhang et al.   LANGMUIR

On the accuracy of metadynamics and its variations in a protein folding process

(2014) Yunqiang Bian et al.   MOLECULAR SIMULATION

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex

(2014) Yunqiang Bian et al.   PLoS Computational Biology

Peptide Ligands for Pro-survival Protein Bfl-1 from Computationally Guided Library Screening

(2013) Sanjib Dutta et al.   ACS Chemical Biology

deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis

(2013) D. H. P. Low et al.   BIOINFORMATICS

Localized Frustration and Binding-Induced Conformational Change in Recognition of 5S RNA by TFIIIA Zinc Finger

(2013) Cheng Tan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PUMA binding induces partial unfolding within BCL-xL to disrupt p53 binding and promote apoptosis

(2013) Ariele Viacava Follis et al.   Nature Chemical Biology

Macrostate Identification from Biomolecular Simulations through Time Series Analysis

(2012) Weizhuang Zhou et al.   Journal of Chemical Information and Modeling

Molecular Determinants of Bim(BH3) Peptide Binding to Pro-Survival Proteins

(2012) Laura Delgado-Soler et al.   Journal of Chemical Information and Modeling

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Evolution of Specific Protein–Protein Interaction Sites Following Gene Duplication

(2012) Daniel Aiello et al.   JOURNAL OF MOLECULAR BIOLOGY

Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method

(2012) Nadine Homeyer et al.   Molecular Informatics

Molecular Basis of Bcl-XL-p53 Interaction: Insights from Molecular Dynamics Simulations

(2011) Nagakumar Bharatham et al.   PLoS One

BH3-only proteins: Orchestrators of apoptosis

(2010) Aisha Shamas-Din et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Characterizing Protein Energy Landscape by Self-Learning Multiscale Simulations: Application to a Designed β-Hairpin

(2010) Wenfei Li et al.   BIOPHYSICAL JOURNAL

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

MM-GBSA binding free energy decomposition and T cell receptor engineering

(2010) V. Zoete et al.   JOURNAL OF MOLECULAR RECOGNITION

The BCL-2 Family Reunion

(2010) Jerry E. Chipuk et al.   MOLECULAR CELL

Molecular Basis for Bcl-2 Homology 3 Domain Recognition in the Bcl-2 Protein Family

(2009) Gautier Moroy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Completing the family portrait of the anti-apoptotic Bcl-2 proteins: Crystal structure of human Bfl-1 in complex with Bim

(2008) Maria Dolores Herman et al.   FEBS LETTERS

Multiple Peptide Conformations Give Rise to Similar Binding Affinities: Molecular Simulations of p53-MDM2

(2008) Shubhra Ghosh Dastidar et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

Structural Plasticity Underpins Promiscuous Binding of the Prosurvival Protein A1

(2008) Callum Smits et al.   STRUCTURE