MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.
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M. Orozco | J. Gelpí | T. Meyer | M. Rueda | Alberto Pérez | M. D’Abramo | Adam Hospital | Jordi Camps | Oliver Carrillo | Dmitry Repchevsky | Carles Fenollosa | Carles Ferrer-Costa
[1] L. Holm,et al. The Pfam protein families database , 2011, Nucleic Acids Res..
[2] Baris E. Suzek,et al. The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..
[3] Guang Song,et al. Protein elastic network models and the ranges of cooperativity , 2009, Proceedings of the National Academy of Sciences.
[4] Adam Hospital,et al. FlexServ: an integrated tool for the analysis of protein flexibility , 2009, Bioinform..
[5] Modesto Orozco,et al. Comparison of molecular dynamics and superfamily spaces of protein domain deformation , 2009, BMC Structural Biology.
[6] Modesto Orozco,et al. United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials. , 2008, Journal of chemical theory and computation.
[7] M. Orozco,et al. Exploring the suitability of coarse-grained techniques for the representation of protein dynamics. , 2008, Biophysical journal.
[8] Valerie Daggett,et al. Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data. , 2008, Protein engineering, design & selection : PEDS.
[9] R Dustin Schaeffer,et al. Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. , 2008, Protein engineering, design & selection : PEDS.
[10] Valerie Daggett,et al. Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations. , 2008, Protein engineering, design & selection : PEDS.
[11] R. Goldstein. The structure of protein evolution and the evolution of protein structure. , 2008, Current opinion in structural biology.
[12] Modesto Orozco,et al. GRID‐MD—A tool for massive simulation of protein channels , 2008, Proteins.
[13] D. van der Spoel,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[14] Alfonso Valencia,et al. Interoperability with Moby 1.0--it's better than sharing your toothbrush! , 2008, Briefings in bioinformatics.
[15] M. Karplus,et al. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis , 2007, Nature.
[16] K. Henrick,et al. Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.
[17] J. Skolnick,et al. Scoring function for automated assessment of protein structure template quality , 2007 .
[18] P. Chacón,et al. Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. , 2007, Structure.
[19] Modesto Orozco,et al. A consensus view of protein dynamics , 2007, Proceedings of the National Academy of Sciences.
[20] Jonathan W. Essex,et al. BioSimGrid: Grid-enabled biomolecular simulation data storage and analysis , 2006, Future Gener. Comput. Syst..
[21] Charles A Laughton,et al. Essential Dynamics: A Tool for Efficient Trajectory Compression and Management. , 2006, Journal of chemical theory and computation.
[22] F. J. Luque,et al. Data Mining of Molecular Dynamics Trajectories of Nucleic Acids , 2006, Journal of biomolecular structure & dynamics.
[23] D. Wishart,et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration , 2005, Nucleic Acids Res..
[24] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[25] I. Bahar,et al. Coarse-grained normal mode analysis in structural biology. , 2005, Current opinion in structural biology.
[26] Werner Dubitzky,et al. Towards Data Warehousing and Mining of Protein Unfolding Simulation Data , 2005, Journal of Clinical Monitoring and Computing.
[27] M. Karplus,et al. Molecular dynamics and protein function. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[28] Valentina Tozzini,et al. Coarse-grained models for proteins. , 2005, Current opinion in structural biology.
[29] D. Zerbino,et al. An analysis of core deformations in protein superfamilies. , 2005, Biophysical journal.
[30] M. DePristo,et al. Simultaneous determination of protein structure and dynamics , 2005, Nature.
[31] Frances M. G. Pearl,et al. The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis , 2004, Nucleic Acids Res..
[32] David Baker,et al. Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[33] R. Abagyan,et al. Optimal docking area: A new method for predicting protein–protein interaction sites , 2004, Proteins.
[34] Jeremy C. Smith,et al. The role of dynamics in enzyme activity. , 2003, Annual review of biophysics and biomolecular structure.
[35] F. J. Luque,et al. Theoretical methods for the simulation of nucleic acids. , 2003, Chemical Society reviews.
[36] Ryan Day,et al. A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary , 2003, Protein science : a publication of the Protein Society.
[37] F. J. Luque,et al. Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins , 2001, Proteins.
[38] M. Orozco,et al. Cooperativity in drug-DNA recognition: a molecular dynamics study. , 2001, Journal of the American Chemical Society.
[39] Ioan Andricioaei,et al. On the calculation of entropy from covariance matrices of the atomic fluctuations , 2001 .
[40] D. Baker,et al. Native protein sequences are close to optimal for their structures. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[41] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[42] M. Karplus,et al. Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. , 1999, Journal of molecular biology.
[43] M Karplus,et al. The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[44] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[45] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[46] Tirion,et al. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.
[47] Karl-Heinz Ott,et al. Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations , 1996, J. Comput. Chem..
[48] Alexander D. MacKerell,et al. An all-atom empirical energy function for the simulation of nucleic acids , 1995 .
[49] P. Kollman,et al. A second generation force field for the simulation of proteins , 1995 .
[50] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[51] J. Schlitter. Estimation of absolute and relative entropies of macromolecules using the covariance matrix , 1993 .
[52] H. Berendsen,et al. Essential dynamics of proteins , 1993, Proteins.
[53] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[54] H. Berendsen,et al. A consistent empirical potential for water–protein interactions , 1984 .
[55] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[56] M. Karplus,et al. Dynamics of folded proteins , 1977, Nature.
[57] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[58] T. Ackermann. C. L. Brooks III, M. Karplus, B. M. Pettitt. Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics, Volume LXXI, in: Advances in Chemical Physics, John Wiley & Sons, New York 1988. 259 Seiten, Preis: US $ 65.25 , 1990 .
[59] M. Karplus,et al. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics , 1988 .