Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory
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[1] Jeanmarie Guenot,et al. Variability of conformations at crystal contacts in BPTI represent true low‐energy structures: Correspondence among lattice packing and molecular dynamics structures , 1992, Proteins.
[2] John Kuriyan,et al. Exploration of disorder in protein structures by X‐ray restrained molecular dynamics , 1991, Proteins.
[3] M Karplus,et al. Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation. , 1985, Biophysical journal.
[4] R L Somorjai,et al. Fuzzy cluster analysis of molecular dynamics trajectories , 1992, Proteins.
[5] D J Barlow,et al. RAMBLE: a conformational search program. , 1990, Journal of molecular graphics.
[6] Peter Murray-Rust,et al. Computer analysis of molecular geometry: Part VI: Classification of differences in conformation , 1985 .
[7] A. Lesk,et al. Structural mechanisms for domain movements in proteins. , 1994, Biochemistry.
[8] P A Kollman,et al. Molecular dynamics studies of a DNA‐binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor , 1992, Protein science : a publication of the Protein Society.
[9] C. Brooks,et al. Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. , 1993, Biochemistry.
[10] H Frauenfelder,et al. Conformational substates and motions in myoglobin. External influences on structure and dynamics. , 1990, Biophysical journal.
[11] H. Berendsen,et al. Essential dynamics of proteins , 1993, Proteins.
[12] Robin Taylor,et al. Automated Conformational Analysis from Crystallographic Data. 3.* Three-Dimensional Pattern Recognition within the Cambridge Structural Database System: Implementation and Practical Examples , 1991 .
[13] P. Wolynes,et al. The energy landscapes and motions of proteins. , 1991, Science.
[14] M. Sternberg,et al. On the prediction of protein structure: The significance of the root-mean-square deviation. , 1980, Journal of molecular biology.
[15] A Wlodawer,et al. Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor. , 1987, Journal of molecular biology.
[16] Philip M. Dean,et al. An exploration of a novel strategy for superposing several flexible molecules , 1993, J. Comput. Aided Mol. Des..
[17] R. Ornstein,et al. An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme , 1994, Proteins.
[18] Peter A. Kollman,et al. Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation , 1993, J. Comput. Chem..
[19] A Kitao,et al. Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis , 1994, Protein science : a publication of the Protein Society.
[20] M Levitt,et al. Molecular dynamics of native protein. II. Analysis and nature of motion. , 1983, Journal of molecular biology.
[21] N Go,et al. Structural basis of hierarchical multiple substates of a protein. I: Introduction , 1989, Proteins.
[22] L Laaksonen,et al. A graphics program for the analysis and display of molecular dynamics trajectories. , 1992, Journal of molecular graphics.
[23] Peter S. Shenkin,et al. Cluster analysis of molecular conformations , 1994, J. Comput. Chem..
[24] M. Karplus,et al. Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. , 1987, Science.
[25] W. Kabsch. A discussion of the solution for the best rotation to relate two sets of vectors , 1978 .