MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

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

(2012) Michal Otyepka et al.   CURRENT DRUG METABOLISM

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

(2012) Tereza Hendrychova et al.   CURRENT DRUG METABOLISM

dxTuber: Detecting protein cavities, tunnels and clefts based on protein and solvent dynamics

(2011) Martin Raunest et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site

(2011) Karel Berka et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues

(2011) Po-Hsien Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Interactions of cytochrome P450s with their ligands

(2010) Kip P. Conner et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

(2010) Stéphanie Pérot et al.   DRUG DISCOVERY TODAY

3V: cavity, channel and cleft volume calculator and extractor

(2010) N. R. Voss et al.   NUCLEIC ACIDS RESEARCH

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

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

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

HotSpot Wizard: a web server for identification of hot spots in protein engineering

(2009) A. Pavelka et al.   NUCLEIC ACIDS RESEARCH

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

Finding and Characterizing Tunnels in Macromolecules with Application to Ion Channels and Pores

(2008) Ryan G. Coleman et al.   BIOPHYSICAL JOURNAL

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

MolAxis: a server for identification of channels in macromolecules

(2008) Eitan Yaffe et al.   NUCLEIC ACIDS RESEARCH

MolAxis: Efficient and accurate identification of channels in macromolecules

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

HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures

(2008) Bosco K Ho et al.   BMC STRUCTURAL BIOLOGY