MoSuMo: A Semantic Web service to generate electrostatic potentials across solvent excluded protein surfaces and binding pockets

Investigations of molecular interactions can benefit from knowledge of the regions that correspond to binding sites and electrostatic potentials across molecular surfaces. In support of simulations aimed at a coarser level of granularity than molecular dynamics, we have developed MoSuMo, a SADI-based Semantic Web service for generating molecular surfaces from a set of 3D atomic coordinates. MoSuMo's service input requires a Protein Data Bank (PDB) identifier from which it obtains the PDB entry and for which it generates electrostatic potentials as vertex values across a geometric mesh that represents the molecular surface. Service inputs and outputs are specified as restrictions on classes from the Semanticscience Integrated Ontology (SIO), which is formalized using the Web Ontology Language (OWL). Binding sites containing their ligands are identified and described as sub-collections of surface vertices. Thus, MoSuMo provides a semantic web service for investigating molecular interactions including visualization. (C) 2011 Elsevier Ltd. All rights reserved.