Acta Crystallogr B 45:488–499Ĭanduri F, de Azevedo WF (2008) Protein crystallography in drug discovery. Gros P, Fujinaga M, Dijkstra BW, Kalk KH, Hol WG (1989) Crystallographic refinement by incorporation of molecular dynamics: thermostable serine protease thermitase complexed with eglin c. Postma JP, Parker MW, Tsernoglou D (1989) Application of molecular dynamics in the crystallographic refinement of colicin A. Ichiye T, Karplus M (1988) Anisotropy and anharmonicity of atomic fluctuations in proteins: implications for X-ray analysis. Wendoloski JJ, Wasserman ZR, Salemme FR (1988) Computer simulation of biological interactions and reactivity. Westhof E, Chevrier B, Gallion SL, Weiner PK, Levy RM (1986) Temperature-dependent molecular dynamics and restrained X-ray refinement simulations of a Z-DNA hexamer. Kuriyan J, Petsko GA, Levy RM, Karplus M (1986) Effect of anisotropy and anharmonicity on protein crystallographic refinement. Gros P, Betzel C, Dauter Z, Wilson KS, Hol WG (1989) Molecular dynamics refinement of a thermitase-eglin-c complex at 1.98 A resolution and comparison of two crystal forms that differ in calcium content. Acta Crystallogr D Biol Crystallogr 50:24–36 Proteins 19:277–290Ĭlarage JB, Phillips GN Jr (1994) Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography. Rice LM, Brünger AT (1994) Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Structure 13:1311–1319Īdams PD, Pannu NS, Read RJ, Brünger AT (1997) Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. ![]() VMD provides a wide variety of methods for rendering and coloring a molecule and can be used to animate and analyze the trajectory of a molecular dynamics simulation.Depristo MA, de Bakker PI, Johnson RJ, Blundell TL (2005) Crystallographic refinement by knowledge-based exploration of complex energy landscapes. It may be used to view more general molecules, as VMD can read standard Protein DataBank (PDB) files and display the contained structure. ![]() The program VMD isdesigned for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters. NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. The tutorial shows you how to use NAMD and VMD for biomolecular modeling. All participants are required to bring their own laptop, prepared for use in workshop tutorial sessions. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level.
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