Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs

Support Vector Machine model for hERG inhibitory activities based on the integrated hERG database using descriptor selection by NSGA-II

(2019) Keiji Ogura et al.   Scientific Reports

Structural implications of hERG K+channel block by a high-affinity minimally structured blocker

(2018) Matthew V. Helliwell et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules

(2017) Seonghoon Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational Tool for Fast in silico Evaluation of hERG K+ Channel Affinity

(2017) Giulia Chemi et al.   Frontiers in Chemistry

Interactions between amiodarone and the hERG potassium channel pore determined with mutagenesis and in silico docking

(2016) Yihong Zhang et al.   BIOCHEMICAL PHARMACOLOGY

The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors

(2016) Mitsugu Araki et al.   Journal of Chemical Information and Modeling

Structure of the voltage-gated K+ channel Eag1 reveals an alternative voltage sensing mechanism

(2016) J. R. Whicher et al.   SCIENCE

New potential binding determinant for hERG channel inhibitors

(2016) P. Saxena et al.   Scientific Reports

All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations

(2016) Yutaka Kuroda et al.   Scientific Reports

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Kv11.1 (hERG)-induced cardiotoxicity: a molecular insight from a binding kinetics study of prototypical Kv11.1 (hERG) inhibitors

(2014) Z Yu et al.   BRITISH JOURNAL OF PHARMACOLOGY

Assessing hERG Pore Models As Templates for Drug Docking Using Published Experimental Constraints: The Inactivated State in the Context of Drug Block

(2014) Christopher E. Dempsey et al.   Journal of Chemical Information and Modeling

Ranolazine inhibition of hERG potassium channels: Drug–pore interactions and reduced potency against inactivation mutants

(2014) Chunyun Du et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Bioisosteres and Scaffold Hopping in Medicinal Chemistry

(2014) Nathan Brown   Molecular Informatics

Recent Developments in Computational Prediction of hERG Blockage

(2013) Sichao Wang et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

hERG K+ Channels: Structure, Function, and Clinical Significance

(2012) Jamie I. Vandenberg et al.   PHYSIOLOGICAL REVIEWS

Computer Simulations of Structure–Activity Relationships for hERG Channel Blockers

(2011) Lars Boukharta et al.   BIOCHEMISTRY

Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst

(2010) I-Jen Chen et al.   Journal of Chemical Information and Modeling

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Massively parallel computation of absolute binding free energy with well-equilibrated states

(2009) Hideaki Fujitani et al.   PHYSICAL REVIEW E

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation