LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor

CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories

(2018) Adam Jurcik et al.   BIOINFORMATICS

CONAN: A Tool to Decode Dynamical Information from Molecular Interaction Maps

(2018) Davide Mercadante et al.   BIOPHYSICAL JOURNAL

Steered Molecular Dynamics Simulation in Rational Drug Design

(2018) Phuc-Chau Do et al.   Journal of Chemical Information and Modeling

Targeting estrogen receptor beta (ERβ) for treatment of ovarian cancer: importance of KDM6B and SIRT1 for ERβ expression and functionality

(2018) Giulia Pinton et al.   Oncogenesis

farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods

(2018) Zhe Wang et al.   BIOINFORMATICS

Protein–Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics

(2017) Duy Phuoc Tran et al.   Journal of Chemical Theory and Computation

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets

(2017) Antonia Stank et al.   NUCLEIC ACIDS RESEARCH

Estrogen receptor beta and ovarian cancer: a key to pathogenesis and response to therapy

(2016) Ioannis Kyriakidis et al.   ARCHIVES OF GYNECOLOGY AND OBSTETRICS

Discovery of DNA dyes Hoechst 34580 and 33342 as good candidates for inhibiting amyloid beta formation: in silico and in vitro study

(2016) Nguyen Quoc Thai et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

(2016) Michael R. Shirts et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

ACFIS: a web server for fragment-based drug discovery

(2016) Ge-Fei Hao et al.   NUCLEIC ACIDS RESEARCH

NAPS: Network Analysis of Protein Structures

(2016) Broto Chakrabarty et al.   NUCLEIC ACIDS RESEARCH

Jmol SMILES and Jmol SMARTS: specifications and applications

(2016) Robert M. Hanson   Journal of Cheminformatics

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

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

iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics

(2015) Hongchun Li et al.   NUCLEIC ACIDS RESEARCH

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity

(2014) Teresa Paramo et al.   Journal of Chemical Theory and Computation

COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures

(2014) Mohd Firdaus-Raih et al.   NUCLEIC ACIDS RESEARCH

iMODS: internal coordinates normal mode analysis server

(2014) José Ramón López-Blanco et al.   NUCLEIC ACIDS RESEARCH

The DynaMine webserver: predicting protein dynamics from sequence

(2014) Elisa Cilia et al.   NUCLEIC ACIDS RESEARCH

A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex

(2014) Kota Kasahara et al.   PLoS One

Estrogen receptors alpha (ERα) and beta (ERβ): Subtype-selective ligands and clinical potential

(2014) Ilaria Paterni et al.   STEROIDS

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

Native contacts determine protein folding mechanisms in atomistic simulations

(2013) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations

(2012) Adam Hospital et al.   BIOINFORMATICS

A Toolkit for the Analysis of Free-Energy Perturbation Calculations

(2012) Peng Liu et al.   Journal of Chemical Theory and Computation

NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins

(2012) D. M. Kruger et al.   NUCLEIC ACIDS RESEARCH

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

(2012) Eva Chovancova et al.   PLoS Computational Biology

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

Development of subtype-selective oestrogen receptor-based therapeutics

(2011) Stefan Nilsson et al.   NATURE REVIEWS DRUG DISCOVERY

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

(2011) Daniel-Adriano Silva et al.   PLoS Computational Biology

Selectively targeting estrogen receptors for cancer treatment

(2010) Erin K. Shanle et al.   ADVANCED DRUG DELIVERY REVIEWS

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

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Molecular Recognition and Drug-Lead Identification: What Can Molecular Simulations Tell Us?

(2009) G. Morra et al.   CURRENT MEDICINAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Understanding the Mechanism of Drug Resistance Due to a Codon Deletion in Protoporphyrinogen Oxidase through Computational Modeling

(2009) Ge-Fei Hao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational Insights into the Mechanism of Ligand Unbinding and Selectivity of Estrogen Receptors

(2009) Jie Shen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Estrogen receptor β ligands: Recent advances and biomedical applications

(2009) Filippo Minutolo et al.   MEDICINAL RESEARCH REVIEWS

PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure

(2009) Marialuisa Pellegrini-Calace et al.   PLoS Computational Biology

A novel switch region regulates H-ras membrane orientation and signal output

(2008) Daniel Abankwa et al.   EMBO JOURNAL

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Insights into Ligand Selectivity in Estrogen Receptor Isoforms:  Molecular Dynamics Simulations and Binding Free Energy Calculations

(2008) Juan Zeng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modeling the Catalysis of Anti-Cocaine Catalytic Antibody: Competing Reaction Pathways and Free Energy Barriers

(2008) Yongmei Pan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Radius of gyration as an indicator of protein structure compactness

(2008) M. Yu. Lobanov et al.   MOLECULAR BIOLOGY

MolAxis: Efficient and accurate identification of channels in macromolecules

(2008) Eitan Yaffe et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE