title: Comparison of different torsion angle approaches for NMR structure determination.
abstract: A new procedure for NMR structure determination, based on the Internal Coordinate Molecular Dynamics (ICMD) approach, is presented. The method finds biopolymer conformations that satisfy usual NMR-derived restraints by using high temperature dynamics in torsion angle space. A variable target function algorithm gradually increases the number of NOE-based restraints applied, with the treatment of ambiguous and floating restraints included. This soft procedure allows combining artificially high temperature with a general purpose force-field including Coulombic and Lennard-Jones non-bonded interactions, which improves the quality of the ensemble of conformations obtained in the gas-phase. The new method is compared to existing algorithms by using the structures of eight ribosomal proteins earlier obtained with state-of-the-art procedures and included into the RECOORD database [Nederveen, A., Doreleijers, J., Vranken, W., Miller, Z., Spronk, C., Nabuurs, S., Guntert, P., Livny, M., Markley, M., Nilges, M., Ulrich, E., Kaptein, R. and Bonvin, A.M. (2005) Proteins, 59, 662-672]. For the majority of tested proteins, the ICMD algorithm shows similar convergence and somewhat better quality Z scores for the phi, psi distributions. The new method is more computationally demanding although the overall load is reasonable.
authors.affiliation: Institut Pasteur Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur 25-28 rue du Dr Roux, F-75724, Paris Cedex 15, France.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Bardiaux
authors.forename: Thérèse E
authors.initials: TE
authors.lastname: Malliavin
authors.forename: Michael
authors.initials: M
authors.lastname: Nilges
authors.forename: Alexey K
authors.initials: AK
authors.lastname: Mazur
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D030562:Databases, Protein; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins