Biologically Relevant Computational Chemistry: New Methods and Applications

Call for Papers

Present available computational power offers increased opportunities to carry out simulations of molecular systems in a more realistic and precise way allowing to interact efficiently with experimentalists, to bring new views for the description of molecular processes involved in living organisms, to build large molecular assemblies at atomic level and unravel their dynamical properties, to design new ligands or proteins with new or altered properties, to build and understand the functional properties of protein-protein networks, and to explain through large scale simulations how the information flow triggered by microscopic perturbations (i.e., point mutations, pH variation, etc.) affects macroscopic behavior of a biological system. As biological processes occur generally largely beyond microsecond time scales, brute standard molecular dynamics simulations are computationally demanding and still not sufficient in most of cases, and new methodological approaches are now necessary through the new available computing possibilities (i.e., distributed computing). Many challenges still have to be relieved, such as how to deal with large scale conformational changes that might affect binding properties of macromolecules, how to design allosteric inhibitors that might affect these properties, or how to better understand and model protein-DNA or RNA interactions and better describe the large scale conformational properties of membrane proteins. This call for papers is concerned with new methodological and computational developments and their applications in these fields in close connection with biochemical or biological processes. Potential topics include, but are not limited to:

• Protein ligand interactions, including enzyme studies
• Protein-protein and protein-DNA interactions
• Target-based drug discovery and design
• Protein flexibility
• Protein design
• DNA and RNA structures and reactions
• Water interactions with biomolecules
• Membrane interactions
• Ion-specific interactions with charged interfaces of biological relevance

Before submission authors should carefully read over the journal's Author Guidelines, which are located at http://www.hindawi.com/journals/oci/guidelines/. Prospective authors should submit an electronic copy of their complete manuscript through the journal Manuscript Tracking System at http://mts.hindawi.com/ according to the following timetable:

Lead Guest Editor

• Rafik Karaman, Medicinal and Pharmaceutical Chemistry Department, College of Pharmacy, Al-Quds University, Abu-Dies, P.O. Box 20002, Jerusalem, Palestine

Guest Editors

• Amiram Goldblum, Laboratory of Molecular Modeling and Drug Design, The Institute of Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
• David Perahia, CNRS, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), Equipe BioInformatique, Modélisation et Dynamique Moléculaire (BIMoDyM), Ecole Normale Supérieure de Cachan, Cachan, France