Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations

(2020) Gert-Jan Bekker et al.   Scientific Reports

Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

(2020) Gert‐Jan Bekker et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Targeting the cryptic sites: NMR-based strategy to improve protein druggability by controlling the conformational equilibrium

(2020) Yumiko Mizukoshi et al.   Science Advances

Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations

(2019) Gert-Jan Bekker et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Structural Biology of Bcl-xL

(2019) Erinna F. Lee et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

More bang for your buck: Improved use of GPU nodes for GROMACS 2018

(2019) Carsten Kutzner et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle

(2018) Nobutaka Numoto et al.   BIOCHEMISTRY

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

(2018) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

Thermal stability of single-domain antibodies estimated by molecular dynamics simulations

(2018) Gert-Jan Bekker et al.   PROTEIN SCIENCE

Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor

(2017) Gert-Jan Bekker et al.   Journal of Chemical Theory and Computation

Enhanced Sampling of Intrinsic Structural Heterogeneity of the BH3-Only Protein Binding Interface of Bcl-xL

(2017) Xiaorong Liu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamic Docking: A Paradigm Shift in Computational Drug Discovery

(2017) Dario Gioia et al.   MOLECULES

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

(2017) Akira R. Kinjo et al.   PROTEIN SCIENCE

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

(2016) Peter Cimermancic et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

(2016) Akira R. Kinjo et al.   NUCLEIC ACIDS RESEARCH

Revisiting antibody modeling assessment for CDR-H3 loop

(2016) Hiroshi Nishigami et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Molmil: a molecular viewer for the PDB and beyond

(2016) Gert-Jan Bekker et al.   Journal of Cheminformatics

Application of zero-dipole summation method to molecular dynamics simulations of a membrane protein system

(2013) Narutoshi Kamiya et al.   CHEMICAL PHYSICS LETTERS

Structure-guided design of a selective BCL-XL inhibitor

(2013) Guillaume Lessene et al.   Nature Chemical Biology

Control of apoptosis by the BCL-2 protein family: implications for physiology and therapy

(2013) Peter E. Czabotar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle

(2011) Ikuo Fukuda et al.   JOURNAL OF CHEMICAL PHYSICS

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Conformational Changes in Bcl-2 Pro-survival Proteins Determine Their Capacity to Bind Ligands

(2009) Erinna F. Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2007) Berk Hess   Journal of Chemical Theory and Computation

Conformational transition states of a β-hairpin peptide between the ordered and disordered conformations in explicit water

(2002) Narutoshi Kamiya et al.   PROTEIN SCIENCE