Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes

Conformational diversity and ligand tunnels of mammalian cytochrome P450s

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

Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents

(2013) Veronika Stepankova et al.   CHEMBIOCHEM

Behavior of Human Cytochromes P450 on Lipid Membranes

(2013) Karel Berka et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Solvent fluctuations in hydrophobic cavity–ligand binding kinetics

(2013) Piotr Setny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

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

Software tools for identification, visualization and analysis of protein tunnels and channels

(2012) Jan Brezovsky et al.   BIOTECHNOLOGY ADVANCES

Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations

(2012) Tereza Hendrychova et al.   CURRENT DRUG METABOLISM

A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB

(2012) Lada Biedermannová et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Potential and Limitations of Ensemble Docking

(2012) Oliver Korb 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

Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations

(2012) A. V. Vargiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Eva Chovancova et al.   PLoS Computational Biology

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

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

(2011) Vlad Cojocaru et al.   PLoS Computational Biology

The influence of key residues in the tunnel entrance and the active site on activity and selectivity of toluene-4-monooxygenase

(2010) Moran Brouk et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

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

(2009) Martina Pavlova et al.   Nature Chemical Biology

Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride

(2009) Albert Guskov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Flexible ligand docking to multiple receptor conformations: a practical alternative

(2008) Maxim Totrov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase

(2008) Lily S. Cheng et al.   JOURNAL OF MEDICINAL CHEMISTRY

Flexibility of Human Cytochromes P450: Molecular Dynamics Reveals Differences between CYPs 3A4, 2C9, and 2A6, which Correlate with Their Substrate Preferences

(2008) Josef Skopalík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crystal structure of poxvirus thymidylate kinase: An unexpected dimerization has implications for antiviral therapy

(2008) C. Caillat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MolAxis: Efficient and accurate identification of channels in macromolecules

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