In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented.

[1]  Adrian J Mulholland,et al.  Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions. , 2012, Journal of chemical theory and computation.

[2]  Robin Oliver,et al.  A stochastic finite element model for the dynamics of globular macromolecules , 2012, J. Comput. Phys..

[3]  Adrian J Mulholland,et al.  Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling. , 2005, Journal of the American Chemical Society.

[4]  A. Mulholland,et al.  A practical guide to modelling enzyme-catalysed reactions. , 2012, Chemical Society reviews.

[5]  P. T. F. Williamson,et al.  Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers , 2011, European Biophysics Journal.

[6]  Christopher J. Woods,et al.  Analysis and assay of oseltamivir-resistant mutants of influenza neuraminidase via direct observation of drug unbinding and rebinding in simulation. , 2013, Biochemistry.

[7]  F. Young Biochemistry , 1955, The Indian Medical Gazette.

[8]  Joseph A. Bank,et al.  Supporting Online Material Materials and Methods Figs. S1 to S10 Table S1 References Movies S1 to S3 Atomic-level Characterization of the Structural Dynamics of Proteins , 2022 .

[9]  Lisa D. Cabrita,et al.  Protein folding on the ribosome. , 2010, Current opinion in structural biology.

[10]  V. Lučić,et al.  Cryo-electron tomography: The challenge of doing structural biology in situ , 2013, The Journal of cell biology.

[11]  Peter Schuck,et al.  Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT , 2015, Acta crystallographica. Section D, Biological crystallography.

[12]  W G Noid,et al.  Perspective: Coarse-grained models for biomolecular systems. , 2013, The Journal of chemical physics.

[13]  Richard Lonsdale,et al.  A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes , 2014, PLoS Comput. Biol..

[14]  Jonathan W. Essex,et al.  The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes , 2011, PloS one.

[15]  M. W. van der Kamp,et al.  Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. , 2013, Biochemistry.

[16]  Karsten Suhre,et al.  ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement , 2004, Nucleic Acids Res..

[17]  Karolina A Majorek,et al.  Double trouble—Buffer selection and His‐tag presence may be responsible for nonreproducibility of biomedical experiments , 2014, Protein science : a publication of the Protein Society.

[18]  M. Karplus,et al.  Dynamics of folded proteins , 1977, Nature.

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

[20]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[21]  Syma Khalid,et al.  Coarse-grained molecular dynamics simulations of membrane proteins and peptides. , 2007, Journal of structural biology.

[22]  D. Tieleman,et al.  Perspective on the Martini model. , 2013, Chemical Society reviews.

[23]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[24]  J. Chaires,et al.  Calorimetry and thermodynamics in drug design. , 2008, Annual review of biophysics.

[25]  Daniel M Zuckerman,et al.  Equilibrium sampling in biomolecular simulations. , 2011, Annual review of biophysics.

[26]  Syma Khalid,et al.  Coarse-grained MD simulations of membrane protein-bilayer self-assembly. , 2008, Structure.

[27]  I. Bahar,et al.  Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions. , 2013, The Journal of chemical physics.

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

[29]  Alan Brown,et al.  Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions , 2015, Acta crystallographica. Section D, Biological crystallography.

[30]  R. Dror,et al.  How Fast-Folding Proteins Fold , 2011, Science.

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

[32]  J. Harvey,et al.  Spin-forbidden CO ligand recombination in myoglobin. , 2004, Faraday discussions.

[33]  R. Ellis,et al.  Macromolecular crowding: an important but neglected aspect of the intracellular environment. , 2001 .

[34]  Peter J Bond,et al.  Insertion and assembly of membrane proteins via simulation. , 2006, Journal of the American Chemical Society.

[35]  Klaus Schulten,et al.  Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics , 2013, Nature.

[36]  S. Griffis EDITOR , 1997, Journal of Navigation.

[37]  Christine M. Bathelt,et al.  Quantum Mechanics/Molecular Mechanics Modeling of Regioselectivity of Drug Metabolism in Cytochrome P450 2C9 , 2013, Journal of the American Chemical Society.

[38]  Modesto Orozco,et al.  MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. , 2010, Structure.

[39]  Alexander D. MacKerell,et al.  Development and current status of the CHARMM force field for nucleic acids , 2000, Biopolymers.

[40]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[41]  M. Bathe A finite element framework for computation of protein normal modes and mechanical response , 2007, Proteins.

[42]  Adrian J. Mulholland,et al.  Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods , 2010 .

[43]  A. Mark,et al.  Coarse grained model for semiquantitative lipid simulations , 2004 .

[44]  Mark Bathe,et al.  Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies , 2010, Nucleic Acids Res..

[45]  Emanuele Paci,et al.  Understanding the apparent stator‐rotor connections in the rotary ATPase family using coarse‐grained computer modeling , 2014, Proteins.

[46]  Faraday Discuss , 1985 .

[47]  Andreas W. Götz,et al.  SPFP: Speed without compromise - A mixed precision model for GPU accelerated molecular dynamics simulations , 2013, Comput. Phys. Commun..

[48]  J. P. Grossman,et al.  Biomolecular simulation: a computational microscope for molecular biology. , 2012, Annual review of biophysics.

[49]  Peter V Coveney,et al.  Modelling biological complexity: a physical scientist's perspective , 2005, Journal of The Royal Society Interface.

[50]  Valentina Tozzini,et al.  Minimalist models for proteins: a comparative analysis , 2010, Quarterly Reviews of Biophysics.

[51]  Jeremy N. Harvey,et al.  Inclusion of Dispersion Effects Significantly Improves Accuracy of Calculated Reaction Barriers for Cytochrome P450 Catalyzed Reactions , 2010 .

[52]  S. Tzeng,et al.  Protein activity regulation by conformational entropy , 2012, Nature.

[53]  Thomas L. Rodgers,et al.  Modulation of Global Low-Frequency Motions Underlies Allosteric Regulation: Demonstration in CRP/FNR Family Transcription Factors , 2013, PLoS biology.

[54]  Modesto Orozco,et al.  A consensus view of protein dynamics , 2007, Proceedings of the National Academy of Sciences.

[55]  N. Linden,et al.  Self-Assembling Cages from Coiled-Coil Peptide Modules , 2013, Science.

[56]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[57]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[58]  A. Mulholland,et al.  QM/MM modelling of drug-metabolizing enzymes. , 2014, Current topics in medicinal chemistry.