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Protein–surface interactions: challenging experiments and computations

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Abstract Protein–surface interactions are fundamental in natural processes, and have great potential for applications ranging from nanotechnology to medicine. A recent workshop highlighted the current … achievements and the main challenges in the field. Copyright © 2009 John Wiley & Sons, Ltd.

Authors: Ori Cohavi, Stefano Corni, Francesca De Rienzo, Rosa Di Felice, Kay E. Gottschalk, Martin Hoefling, Daria Kokh, Elisa Molinari, Gideon Schreiber, Alexander Vaskevich, Rebecca C. Wade

Date Published: 2009

Publication Type: Journal

Computational approaches to identifying and characterizing protein binding sites for ligand design

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Abstract Given the three-dimensional structure of a protein, how can one find the sites where other molecules might bind to it? Do these sites have the properties necessary for high affinity binding? … Is this protein a suitable target for drug design? Here, we discuss recent developments in computational methods to address these and related questions. Geometric methods to identify pockets on protein surfaces have been developed over many years but, with new algorithms, their performance is still improving. Simulation methods show promise in accounting for protein conformational variability to identify transient pockets but lack the ease of use of many of the (rigid) shape-based tools. Sequence and structure comparison approaches are benefiting from the constantly increasing size of sequence and structure databases. Energetic methods can aid identification and characterization of binding pockets, and have undergone recent improvements in the treatment of solvation and hydrophobicity. The “druggability” of a binding site is still difficult to predict with an automated procedure. The methodologies available for this purpose range from simple shape and hydrophobicity scores to computationally demanding free energy simulations. Copyright © 2009 John Wiley & Sons, Ltd.

Authors: Stefan Henrich, Outi M. H. Salo-Ahen, Bingding Huang, Friedrich F. Rippmann, Gabriele Cruciani, Rebecca C. Wade

Date Published: 2009

Publication Type: Journal

SYCAMORE--a systems biology computational analysis and modeling research environment

Abstract

Not specified

Authors: A. Weidemann, S. Richter, M. Stein, S. Sahle, R. Gauges, R. Gabdoulline, I. Surovtsova, N. Semmelrock, B. Besson, I. Rojas, R. Wade, U. Kummer

Date Published: 13th Jun 2008

Publication Type: Journal

Protein-protein docking by simulating the process of association subject to biochemical constraints

Abstract

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Authors: Domantas Motiejunas, Razif Gabdoulline, Ting Wang, Anna Feldman-Salit, Tim Johann, Peter J. Winn, Rebecca C. Wade

Date Published: 1st Jun 2008

Publication Type: Journal

webPIPSA: a web server for the comparison of protein interaction properties

Abstract

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Authors: S. Richter, A. Wenzel, M. Stein, R. R. Gabdoulline, R. C. Wade

Date Published: 19th May 2008

Publication Type: Journal

Heterodimer formation of wild-type and amyotrophic lateral sclerosis-causing mutant Cu/Zn-superoxide dismutase induces toxicity independent of protein aggregation

Abstract

Not specified

Authors: Heidrun Witan, Andreas Kern, Ingrid Koziollek-Drechsler, Rebecca Wade, Christian Behl, Albrecht M. Clement

Date Published: 15th May 2008

Publication Type: Journal

The acidic, glutamine-rich Mpn474 protein of Mycoplasma pneumoniae is surface exposed and covers the complete cell

Abstract

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Authors: Jan Hegermann, Sven Halbedel, Roger Dumke, Jörg Regula, Razif R. Gabdoulline, Frank Mayer, Jörg Stülke, Richard Herrmann

Date Published: 1st Apr 2008

Publication Type: Journal

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