Including ligand-induced protein flexibility into protein tunnel prediction

Conformational diversity and ligand tunnels of mammalian cytochrome P450s

(2013) Xiaofeng Yu et al.   BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

(2013) David Sehnal et al.   Journal of Cheminformatics

Is There a Relationship Between the Substrate Preferences and Structural Flexibility of Cytochromes P450?

(2012) Michal Otyepka et al.   CURRENT DRUG METABOLISM

Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study

(2012) Jacopo Sgrignani et al.   Journal of Chemical Information and Modeling

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

(2012) K. Berka et al.   NUCLEIC ACIDS RESEARCH

Investigation of Indazole Unbinding Pathways in CYP2E1 by Molecular Dynamics Simulations

(2012) Zhonghua Shen et al.   PLoS One

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

(2012) Eva Chovancova et al.   PLoS Computational Biology

Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations

(2011) Markus A. Lill   BIOCHEMISTRY

The crystal structure of a voltage-gated sodium channel

(2011) Jian Payandeh et al.   NATURE

Structural basis for alcohol modulation of a pentameric ligand-gated ion channel

(2011) R. J. Howard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9

(2011) Vlad Cojocaru et al.   PLoS Computational Biology

g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

(2010) Jochen S. Hub et al.   Journal of Chemical Theory and Computation

Crystal Structure of a Cytochrome P450 2B6 Genetic Variant in Complex with the Inhibitor 4-(4-Chlorophenyl)imidazole at 2.0-A Resolution

(2010) S. C. Gay et al.   MOLECULAR PHARMACOLOGY

Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism

(2009) Dan Fishelovitch et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

(2009) Martina Pavlova et al.   Nature Chemical Biology

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

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

Target Flexibility: An Emerging Consideration in Drug Discovery and Design†

(2008) Pietro Cozzini et al.   JOURNAL OF MEDICINAL CHEMISTRY

MolAxis: Efficient and accurate identification of channels in macromolecules

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