title: Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.
abstract: The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.
authors.affiliation: Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Germany.
authors.forename: Olaf
authors.initials: O
authors.lastname: Schneider
authors.forename: Rasmus H
authors.initials: RH
authors.lastname: Fogh
authors.forename: Ulrich
authors.initials: U
authors.lastname: Sternberg
authors.forename: Konstantin
authors.initials: K
authors.lastname: Klenin
authors.forename: Ivan
authors.initials: I
authors.lastname: Kondov
mesh_terms: D001690:Biological Science Disciplines; D003198:Computer Simulation; D006302:Health Services Research / Q000379:methods; D033181:Information Dissemination / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D008956:Models, Chemical; D008958:Models, Molecular; D012984:Software; D014584:User-Computer Interface; D057188:Workflow