Molecular dynamics simulations of nucleic acid-protein complexes.

[1]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[2]  B. Montgomery Pettitt,et al.  Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids , 1985 .

[3]  Alexander D. MacKerell,et al.  Protein dynamics. A time-resolved fluorescence, energetic and molecular dynamics study of ribonuclease T1. , 1987, Biophysical chemistry.

[4]  A. Elofsson,et al.  How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin. , 1993, Journal of molecular biology.

[5]  R. Roberts,et al.  Hhal methyltransferase flips its target base out of the DNA helix , 1994, Cell.

[6]  Bernard R. Brooks,et al.  New spherical‐cutoff methods for long‐range forces in macromolecular simulation , 1994, J. Comput. Chem..

[7]  Nobutoshi Ito,et al.  Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin , 1994, Nature.

[8]  L. Nilsson,et al.  High-pressure molecular dynamics of a nucleic acid fragment , 1994 .

[9]  P. Kollman,et al.  Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins , 1995 .

[10]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[11]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[12]  L. Nilsson,et al.  Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution. , 1995, Biophysical journal.

[13]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[14]  T. Halgren.  Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..

[15]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[16]  Thomas Hermann,et al.  Simulations of the dynamics at an RNA–protein interface , 1999, Nature Structural Biology.

[17]  P. Kollman,et al.  A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. , 1999, Journal of biomolecular structure & dynamics.

[18]  L. Nilsson,et al.  Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution. , 1999, Biophysical journal.

[19]  P. Kollman,et al.  Molecular dynamics studies of U1A-RNA complexes. , 1999, RNA.

[20]  L. Nilsson,et al.  On the truncation of long-range electrostatic interactions in DNA. , 2000, Biophysical journal.

[21]  Alexander D. MacKerell,et al.  All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000 .

[22]  Ming-Jing Hwang,et al.  Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds , 2001, J. Comput. Chem..

[23]  R. Friesner,et al.  Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .

[24]  G. Varani,et al.  Molecular dynamics simulation of the RNA complex of a double-stranded RNA-binding domain reveals dynamic features of the intermolecular interface and its hydration. , 2002, Biophysical journal.

[25]  K. Hall,et al.  A functional role for correlated motion in the N-terminal RNA-binding domain of human U1A protein. , 2002, Journal of molecular biology.

[26]  Alexander D. MacKerell,et al.  Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Pavel Hobza,et al.  New parameterization of the Cornell et al. empirical force field covering amino group nonplanarity in nucleic acid bases , 2003, J. Comput. Chem..

[28]  Wei Zhang,et al.  A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations , 2003, J. Comput. Chem..

[29]  J. Christopher Fromme,et al.  Product-assisted catalysis in base-excision DNA repair , 2003, Nature Structural Biology.

[30]  S. Joseph,et al.  Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs. , 2003, Journal of molecular biology.

[31]  Alexander D. MacKerell,et al.  Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations , 2004, J. Comput. Chem..

[32]  K. Réblová,et al.  Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex. , 2004, Biophysical journal.

[33]  Guillaume Paillard,et al.  Analyzing protein-DNA recognition mechanisms. , 2004, Structure.

[34]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[35]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[36]  Alexander D. MacKerell,et al.  Cooperative binding of DNA and CBFβ to the Runt domain of the CBFα studied via MD simulations , 2005, Nucleic acids research.

[37]  S. Joseph,et al.  Simulating movement of tRNA into the ribosome during decoding. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Wei Yang,et al.  Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA , 2005, Nature.

[39]  I. Andricioaei,et al.  Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation , 2005, Nucleic acids research.

[40]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[41]  J. Åqvist,et al.  Mechanism of peptide bond synthesis on the ribosome. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Alexander D. MacKerell,et al.  Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. , 2005, Journal of molecular biology.

[43]  Markus Christen,et al.  The GROMOS software for biomolecular simulation: GROMOS05 , 2005, J. Comput. Chem..

[44]  M. Mezei,et al.  Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI. , 2005, Biophysical journal.

[45]  K. Hall,et al.  Correlated motions in the U1 snRNA stem/loop 2:U1A RBD1 complex. , 2005, Biophysical journal.

[46]  Chris Oostenbrink,et al.  An improved nucleic acid parameter set for the GROMOS force field , 2005, J. Comput. Chem..

[47]  L. Nilsson,et al.  Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain. , 2006, Biochemistry.

[48]  Srikanta Sen,et al.  Exploring the potential of complex formation between a mutant DNA and the wild type protein counterpart: a MM and MD simulation approach. , 2006, Journal of molecular graphics & modelling.

[49]  J. Chocholousová,et al.  Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. , 2006, The journal of physical chemistry. B.

[50]  T. Schlick,et al.  Distinct energetics and closing pathways for DNA polymerase β with 8-oxoG template and different incoming nucleotides , 2007, BMC Structural Biology.

[51]  T. Schlick,et al.  Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding. , 2006, Biophysical journal.

[52]  Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex. , 2006, Journal of the American Chemical Society.

[53]  Peter L. Freddolino,et al.  Molecular dynamics simulations of the complete satellite tobacco mosaic virus. , 2006, Structure.

[54]  Wei Zhang,et al.  Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides , 2006, J. Comput. Chem..

[55]  K. Sanbonmatsu.  Energy landscape of the ribosomal decoding center. , 2006, Biochimie.

[56]  K. Schulten,et al.  Structure-based model of the stepping motor of PcrA helicase. , 2006, Biophysical journal.

[57]  J. Frank,et al.  Functional conformations of the L11-ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations. , 2006, RNA.

[58]  Ying Zhao,et al.  Molecular dynamics simulation studies of a protein–RNA complex with a selectively modified binding interface , 2006, Biopolymers.

[59]  Toshikazu Ebisuzaki,et al.  Structure and dynamics of RNA polymerase II elongation complex. , 2006, Biochemical and biophysical research communications.

[60]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[61]  Lennart Nilsson,et al.  The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA , 2006, Nucleic acids research.

[62]  D. Beveridge,et al.  A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations. , 2007, Journal of structural biology.

[63]  J. Šponer,et al.  Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers , 2007 .

[64]  Kentaro Shimizu,et al.  Mechanism of the difference in the binding affinity of E. coli tRNAGln to glutaminyl-tRNA synthetase caused by noninterface nucleotides in variable loop. , 2007, Biophysical journal.

[65]  R. Nussinov,et al.  Structural Basis for p53 Binding-induced DNA Bending* , 2007, Journal of Biological Chemistry.

[66]  Martin Almlöf,et al.  Energetics of codon-anticodon recognition on the small ribosomal subunit. , 2007, Biochemistry.

[67]  B. Ma,et al.  Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements , 2007, Nucleic acids research.