chemical models

Summary

Summary: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.

Top Publications

  1. pmc The Amber biomolecular simulation programs
    David A Case
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA
    J Comput Chem 26:1668-88. 2005
  2. ncbi GROMACS: fast, flexible, and free
    David van der Spoel
    Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S 75124 Uppsala, Sweden
    J Comput Chem 26:1701-18. 2005
  3. ncbi The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M Hucka
    Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 19:524-31. 2003
  4. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
    Bioinformatics 21:951-60. 2005
  5. ncbi HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
    Cyril Dominguez
    Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CH, Utrecht, The Netherlands
    J Am Chem Soc 125:1731-7. 2003
  6. pmc Length-dependent prediction of protein intrinsic disorder
    Kang Peng
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Bioinformatics 7:208. 2006
  7. ncbi Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    Alasdair T R Laurie
    School of Biochemistry and Microbiology, University of Leeds, UK
    Bioinformatics 21:1908-16. 2005
  8. ncbi OPM: orientations of proteins in membranes database
    Mikhail A Lomize
    College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI 48109 1065, USA
    Bioinformatics 22:623-5. 2006
  9. ncbi Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates
    Leslie L Chavez
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, California 92093, USA
    J Am Chem Soc 126:8426-32. 2004
  10. pmc iFoldRNA: three-dimensional RNA structure prediction and folding
    Shantanu Sharma
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Bioinformatics 24:1951-2. 2008

Research Grants

  1. Chemical Models of Protein beta-Sheet Interactions
    James Nowick; Fiscal Year: 2009
  2. REGULATION OF SYNAPTIC TRANSMISSION
    Robert Zucker; Fiscal Year: 2002
  3. CHEMICAL MODELS FOR BIOLOGICAL ELECTRON TRANSFER
    John Dawson; Fiscal Year: 1991
  4. Splicing, Folding, and Stretching Nucleic Acids
    DANIEL AALBERTS; Fiscal Year: 2003
  5. CHEMICAL MODELS OF PRESYNAPTIC NEUROMUSCULAR DISEASE
    WILLIAM ATCHISON; Fiscal Year: 1999
  6. MECHANISMS OF INHERITED MEMBRANE TRANSPORT DISORDERS
    Stanton Segal; Fiscal Year: 1992
  7. REACTION CENTER DYNAMICS
    CRAIG SCHENCK; Fiscal Year: 1992
  8. Effects of phosphoinositides on cytoskeletal structure
    Paul Janmey; Fiscal Year: 2006
  9. Binding and Splicing mRNA
    DANIEL AALBERTS; Fiscal Year: 2009

Detail Information

Publications238 found, 100 shown here

  1. pmc The Amber biomolecular simulation programs
    David A Case
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA
    J Comput Chem 26:1668-88. 2005
    ....
  2. ncbi GROMACS: fast, flexible, and free
    David van der Spoel
    Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S 75124 Uppsala, Sweden
    J Comput Chem 26:1701-18. 2005
    ..It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org...
  3. ncbi The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M Hucka
    Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 19:524-31. 2003
    ..Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively...
  4. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
    Bioinformatics 21:951-60. 2005
    ..Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution...
  5. ncbi HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
    Cyril Dominguez
    Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CH, Utrecht, The Netherlands
    J Am Chem Soc 125:1731-7. 2003
    ..In all cases, the best structures generated by HADDOCK, that is, the structures with the lowest intermolecular energies, were the closest to the published structure of the respective complexes (within 2.0 A backbone RMSD)...
  6. pmc Length-dependent prediction of protein intrinsic disorder
    Kang Peng
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Bioinformatics 7:208. 2006
    ..However, these predictors are less successful on short disordered regions (< or =30 residues). A probable cause is a length-dependent amino acid compositions and sequence properties of disordered regions...
  7. ncbi Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    Alasdair T R Laurie
    School of Biochemistry and Microbiology, University of Leeds, UK
    Bioinformatics 21:1908-16. 2005
    ..Energetically favourable probe sites are clustered according to their spatial proximity and clusters are then ranked according to the sum of interaction energies for sites within each cluster...
  8. ncbi OPM: orientations of proteins in membranes database
    Mikhail A Lomize
    College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI 48109 1065, USA
    Bioinformatics 22:623-5. 2006
    ..All coordinate files with the calculated membrane boundaries are available for downloading...
  9. ncbi Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates
    Leslie L Chavez
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, California 92093, USA
    J Am Chem Soc 126:8426-32. 2004
    ....
  10. pmc iFoldRNA: three-dimensional RNA structure prediction and folding
    Shantanu Sharma
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Bioinformatics 24:1951-2. 2008
    ..We expect iFoldRNA will serve as a useful resource for RNA structure prediction and folding thermodynamic analyses...
  11. pmc Geometric nomenclature and classification of RNA base pairs
    N B Leontis
    Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Ohio 43403, USA
    RNA 7:499-512. 2001
    ..Graphical conventions are proposed for displaying non-Watson-Crick interactions on a secondary structure diagram. The utility of the classification in homology modeling of RNA tertiary motifs is illustrated...
  12. ncbi Improved treatment of the protein backbone in empirical force fields
    Alexander D MacKerell
    Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
    J Am Chem Soc 126:698-9. 2004
    ..The developed approach is suggested to lead to significant improvements in the accuracy of empirical force fields to treat peptides and proteins...
  13. ncbi IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    Zsuzsanna Dosztanyi
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, PO Box 7, H 1518 Budapest, Hungary
    Bioinformatics 21:3433-4. 2005
    ..Optional to the prediction are built-in parameter sets optimized for predicting short or long disordered regions and structured domains...
  14. pmc Bayesian statistical analysis of protein side-chain rotamer preferences
    R L Dunbrack
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco 94143 0450, USA
    Protein Sci 6:1661-81. 1997
    ..The new library is suitable for use in homology modeling, protein folding simulations, and the refinement of X-ray and NMR structures...
  15. pmc THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures
    Douglas L Theobald
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
    Bioinformatics 22:2171-2. 2006
    ..THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble...
  16. ncbi FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded
    Jaime Prilusky
    Biological Services, Weizmann Institute of Science, Rehovot 76100, Israel
    Bioinformatics 21:3435-8. 2005
    ..Sliding windows permit identification of large regions within a protein that possess folding propensities different from those of the whole protein...
  17. ncbi Why are "natively unfolded" proteins unstructured under physiologic conditions?
    V N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Proteins 41:415-27. 2000
    ....
  18. pmc Natively unfolded proteins: a point where biology waits for physics
    Vladimir N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
    Protein Sci 11:739-56. 2002
    ..In this respect, the Protein Quartet model, with function arising from four specific conformations (ordered forms, molten globules, premolten globules, and random coils) and transitions between any two of the states, is discussed...
  19. ncbi The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
    Zsuzsanna Dosztanyi
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, 1518 Budapest, PO Box 7, Hungary
    J Mol Biol 347:827-39. 2005
    ..This application we term IUPred and compare its performance with three generally accepted predictors, PONDR VL3H, DISOPRED2 and GlobPlot on a database of disordered proteins...
  20. ncbi Predicting protein functional sites with phylogenetic motifs
    David La
    Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, USA
    Proteins 58:309-20. 2005
    ..Further, phylogenetic motif results are also shown to be consistent with evolutionary trace results, and bootstrapping is used to demonstrate tree significance...
  21. ncbi Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    I Bahar
    Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
    Fold Des 2:173-81. 1997
    ..The elements of the inverse of the Kirchhoff matrix give directly the auto-correlations or cross-correlations of atomic fluctuations...
  22. ncbi What are the dielectric "constants" of proteins and how to validate electrostatic models?
    C N Schutz
    Department of Chemistry, University of Southern California, Los Angeles, California, USA
    Proteins 44:400-17. 2001
    ..These include the effect of water penetration and the effect of the protein reorganization. Finally, we show that the optimal dielectric constant for self-energies is not the optimal constant for charge-charge interactions...
  23. ncbi Prediction of protein B-factor profiles
    Zheng Yuan
    Institute for Molecular Bioscience and ARC Centre in Bioinformatics, The University of Queensland, St Lucia, Australia
    Proteins 58:905-12. 2005
    ..flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods...
  24. pmc STITCH: interaction networks of chemicals and proteins
    Michael Kuhn
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D684-8. 2008
    ..5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.de/...
  25. ncbi Virtual computational chemistry laboratory--design and description
    Igor V Tetko
    Institute of Bioorganic and Petroleum Chemistry, Kyiv, Ukraine
    J Comput Aided Mol Des 19:453-63. 2005
    ..In this article we review the main features and statistics of the developed system that can be used as a prototype for academic and industry models...
  26. pmc RNA STRAND: the RNA secondary structure and statistical analysis database
    Mirela Andronescu
    Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada
    BMC Bioinformatics 9:340. 2008
    ..Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures...
  27. ncbi Local structural disorder imparts plasticity on linear motifs
    Monika Fuxreiter
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary
    Bioinformatics 23:950-6. 2007
    ..These results establish a connection between LMs and molecular recognition elements of intrinsically unstructured proteins (IUPs), which realize a non-conventional mode of partner binding mostly in regulatory functions...
  28. ncbi Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions
    S Teng
    Department of Physics, Clemson University, Clemson, SC 29634, USA
    Curr Pharm Biotechnol 9:123-33. 2008
    ..The importance of understanding the effects caused by nsSNP mutations at the protein-protein and protein-DNA interfaces is outlined...
  29. ncbi Global mapping of pharmacological space
    Gaia V Paolini
    The Department of Knowledge Discovery, Pfizer Global Research and Development, Sandwich, Kent CT13 9NJ, UK
    Nat Biotechnol 24:805-15. 2006
    ..The relationships between proteins, chemical structures and drug-like properties provide a framework for developing a probabilistic approach to drug discovery that can be exploited to increase research productivity...
  30. pmc Maximum likelihood estimation of ion channel kinetics from macroscopic currents
    Lorin S Milescu
    Department of Physiology and Biophysics, State University of New York, Buffalo, New York, USA
    Biophys J 88:2494-515. 2005
    ..Given appropriate stimulation protocols, our method chose a reasonable model size and topology...
  31. ncbi COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures
    Jason Vertrees
    Department of Human Biological Chemistry and Genetics, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
    Bioinformatics 21:3318-9. 2005
    ..AVAILABILITY: The COREX/BEST Server may be accessed through a typical web browser by visiting http://best.utmb.edu/BEST/...
  32. ncbi Serine protease mechanism and specificity
    Lizbeth Hedstrom
    Department of Biochemistry, MS 009, Brandeis University, Waltham, Massachusetts 02454, USA
    Chem Rev 102:4501-24. 2002
  33. ncbi What controls the melting properties of DNA-linked gold nanoparticle assemblies?
    Rongchao Jin
    Department of Chemistry and Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
    J Am Chem Soc 125:1643-54. 2003
    ....
  34. pmc Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation
    P Schuck
    Bioengineering and Physical Science Program, National Institutes of Health, Bethesda, Maryland 20892, USA
    Biophys J 75:1503-12. 1998
    ..In addition, in the case of a protein in rapid monomer-dimer equilibrium, this configuration was found to reveal the most precise estimate of the association constant...
  35. ncbi Nucleated conformational conversion and the replication of conformational information by a prion determinant
    T R Serio
    Department of Molecular Genetics and Cell Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
    Science 289:1317-21. 2000
    ..This model for replicating protein-based genetic information, nucleated conformational conversion, may be applicable to other protein assembly processes...
  36. ncbi A perspective on enzyme catalysis
    Stephen J Benkovic
    Department of Chemistry, 152 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Science 301:1196-202. 2003
    ..Such coupled networks have important implications for the origin and evolution of enzymes, as well as for protein engineering...
  37. ncbi Multiple Alignment of protein structures and sequences for VMD
    John Eargle
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, 607 South Mathews Avenue, Urbana, IL 61801, USA
    Bioinformatics 22:504-6. 2006
    ..It is implemented as a plugin for VMD (Visual Molecular Dynamics), which is distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics at the University of Illinois...
  38. ncbi Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing
    Jens Harborth
    Department of Biochemistry and Cell Biology, Max Planck Institute for Biophysical Chemistry, D 37077 Gottingen, Germany
    Antisense Nucleic Acid Drug Dev 13:83-105. 2003
    ....
  39. pmc Line tension and interaction energies of membrane rafts calculated from lipid splay and tilt
    Peter I Kuzmin
    Laboratory of Cellular and Molecular Biophysics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    Biophys J 88:1120-33. 2005
    ..This barrier can kinetically stabilize the rafts against merger. Our physical theory thus quantifies conditions that allow rafts to form, and further, defines the parameters that control raft merger...
  40. pmc Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation
    Patrick H Brown
    Protein Biophysics Resource, Division of Bioengineering and Physical Science, ORS, Office of the Director, National Institutes of Health, Bethesda, Maryland 20892, USA
    Biophys J 90:4651-61. 2006
    ..We show that this can be used to determine average molar masses of macromolecules and characterize macromolecular distributions, without the approximation of any scaling relationship between hydrodynamic and thermodynamic parameters...
  41. ncbi Analysis of heterologous interacting systems by sedimentation velocity: curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and kinetic constants
    Walter F Stafford
    Analytical Ultracentrifugation Research Laboratory, Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA
    Biophys Chem 108:231-43. 2004
    ..sedanal fits to time-difference data to eliminate time-independent systematic errors inherent in AUC data. The sedanal software package is based on the use of finite-element numerical solutions of the Lamm equation...
  42. pmc Sphingomyelin-cholesterol domains in phospholipid membranes: atomistic simulation
    Sagar A Pandit
    Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, USA
    Biophys J 87:1092-100. 2004
    ..The calculated difference in thickness is consistent with data obtained in atomic force microscopy experiments...
  43. ncbi RNAshapes: an integrated RNA analysis package based on abstract shapes
    Peter Steffen
    Faculty of Technology and, Bielefeld University, 33594 Bielefeld, Germany
    Bioinformatics 22:500-3. 2006
    ..Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach...
  44. ncbi Strength of the Calpha H..O hydrogen bond of amino acid residues
    S Scheiner
    Department of Chemistry and Biochemistry, Utah State University, Logan 84322 0300, USA
    J Biol Chem 276:9832-7. 2001
    ..32 A. Formation of each interaction results in a downfield shift of the bridging hydrogen's chemical shift and a blue shift in the C(alpha)H stretching frequency, potential diagnostics of the presence of such an H-bond within a protein...
  45. ncbi A tale of two tails: why are terminal residues of proteins exposed?
    Etai Jacob
    The Mina and Everard Goodman Faculty of Life Sciences, bar Ilan University Ramat Gan, 52900, Israel
    Bioinformatics 23:e225-30. 2007
    ..Progressively, each selection raises the proportion of proteins with termini on the surface, resulting in similar proportions to those observed for real proteins...
  46. pmc A diffusional bimolecular propensity function
    Daniel T Gillespie
    Dan T Gillespie Consulting, 30504 Cordoba Pl, Castaic, California 91384, USA
    J Chem Phys 131:164109. 2009
    ....
  47. ncbi Thermodynamics of RNA-RNA binding
    Ulrike Mückstein
    Institute for Theoretical Chemistry, University of Vienna Währingerstrasse 17, A 1090 Vienna, Austria
    Bioinformatics 22:1177-82. 2006
    ..The thermodynamics of such RNA-RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to 'open' the binding site and (2) the energy gained from hybridization...
  48. ncbi Force fields for protein simulations
    Jay W Ponder
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Adv Protein Chem 66:27-85. 2003
  49. ncbi An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations
    Tihamer Geyer
    Zentrum fur Bioinformatik, Universitat des Saarlandes, D 66123 Saarbrucken, Germany
    J Chem Phys 130:114905. 2009
    ..This now allows to include HI into large many-particle Brownian dynamics simulations, where until now the runtime scaling of the correlated random motion was prohibitive...
  50. ncbi Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms
    Jianlin Cheng
    Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, CA 92697, USA
    Bioinformatics 21:i75-84. 2005
    ..Previous approaches for predicting beta-sheet topological features, such as beta-strand alignments, in general have not exploited the global covariation and constraints characteristic of beta-sheet architectures...
  51. ncbi A neural-network-based method for predicting protein stability changes upon single point mutations
    Emidio Capriotti
    Laboratory of Biocomputing, CIRB Department of Biology, University of Bologna, Bologna, Italy
    Bioinformatics 20:i63-8. 2004
    ..This allows the application of machine learning techniques to predicting free energy stability changes upon mutation starting from the protein sequence...
  52. ncbi Taming of a poison: biosynthesis of the NiFe-hydrogenase cyanide ligands
    Stefanie Reissmann
    Department Biologie I, Mikrobiologie, University of Munich, Maria Ward Strasse 1a, D 80638 Munich, Germany
    Science 299:1067-70. 2003
    ..This finding underscores a striking parallel between biochemistry and organometallic chemistry in the formation of an iron-cyano complex...
  53. pmc Assessing the impact of secondary structure and solvent accessibility on protein evolution
    N Goldman
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
    Genetics 149:445-58. 1998
    ....
  54. ncbi Constrained geometric simulation of diffusive motion in proteins
    Stephen Wells
    Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287 1504, USA
    Phys Biol 2:S127-36. 2005
    ..We additionally show how FRODA can be used to find a pathway from one conformation to another. This directed dynamics is illustrated with the protein dihydrofolate reductase...
  55. ncbi Vesicle fluctuation analysis of the effects of sterols on membrane bending rigidity
    Jonas Henriksen
    MEMPHYS Centre for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, 2800, Lyngby, Denmark
    Eur Biophys J 33:732-41. 2004
    ..These recent modifications render vesicle fluctuation analysis an efficient and accurate method for determining how cholesterol, lanosterol, and ergosterol increase membrane bending rigidity...
  56. ncbi A statistical thermodynamic model of the protein ensemble
    Vincent J Hilser
    Department of Biochemistry and Molecular Biology and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555 1068, USA
    Chem Rev 106:1545-58. 2006
  57. ncbi Anisotropic network model: systematic evaluation and a new web interface
    Eran Eyal
    Department of Computational Biology, School of Medicine, University of Pittsburgh, PA 15213, USA
    Bioinformatics 22:2619-27. 2006
    ..Despite its broad use for exploring biomolecular collective motions, ANM has not been systematically evaluated to date. A lack of a convenient interface has been an additional obstacle for easy usage...
  58. ncbi Stochastic modeling of RNA pseudoknotted structures: a grammatical approach
    Liming Cai
    Department of Computer Science, The University of Georgia, Athens, Georgia 30602, USA
    Bioinformatics 19:i66-73. 2003
    ..Formally a context-sensitive grammar is required, which would impose a large increase in complexity...
  59. pmc Electrostatic steering and ionic tethering in enzyme-ligand binding: insights from simulations
    R C Wade
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 95:5942-9. 1998
    ..Ionic tethering can provide a control mechanism for substrate binding that is sensitive to the electrostatic properties of the enzyme's surroundings even when the substrate is nonpolar...
  60. ncbi OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar
    Håkan Viklund
    Department of Biochemistry and Biophysics Center for Biomembrane Research Stockholm Bioinformatics Center, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE 10691 Stockholm, Sweden
    Bioinformatics 24:1662-8. 2008
    ..Because structural knowledge of transmembrane proteins is difficult to attain experimentally, improved methods for prediction of structural features of these proteins are important...
  61. ncbi Mechanisms and free energies of enzymatic reactions
    Jiali Gao
    Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Chem Rev 106:3188-209. 2006
  62. pmc The protein folding problem
    Ken A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
    Annu Rev Biophys 37:289-316. 2008
    ....
  63. pmc DNA translocation governed by interactions with solid-state nanopores
    Meni Wanunu
    Department of Biomedical Engineering and Department of Physics, Boston University, Boston, Massachusetts, USA
    Biophys J 95:4716-25. 2008
    ..These findings shed light on the transport properties of DNA in small pores, relevant for future nanopore applications, such as DNA sequencing and genotyping...
  64. pmc Cooperative transition between open and closed conformations in potassium channels
    Turkan Haliloglu
    Polymer Research Center, Bogazici University, Bebek Istanbul, Turkey
    PLoS Comput Biol 4:e1000164. 2008
    ....
  65. ncbi Porter: a new, accurate server for protein secondary structure prediction
    Gianluca Pollastri
    Computer Science Department, University College Dublin, Belfield, Dublin 4, Ireland
    Bioinformatics 21:1719-20. 2005
    ..Porter's accuracy, tested by rigorous 5-fold cross-validation on a large set of proteins, exceeds 79%, significantly above a copy of the state-of-the-art SSpro server, better than any system published to date...
  66. ncbi Stochastic reaction-diffusion simulation with MesoRD
    Johan Hattne
    Department of Cell and Molecular Biology, BMC, Uppsala University, 75124 Uppsala, Sweden
    Bioinformatics 21:2923-4. 2005
    ..In particular, it is an implementation of the next subvolume method, which is an exact method to simulate the Markov process corresponding to the reaction-diffusion master equation...
  67. ncbi Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking
    Sheng You Huang
    Dalton Cardiovascular Research Center and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
    Proteins 66:399-421. 2007
    ....
  68. pmc Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models
    Wen Liu
    Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Bioinformatics 7:182. 2006
    ....
  69. ncbi Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
    Petr Jurecka
    Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo namesti 2, 166 10, Prague 6, Czech Republic
    Phys Chem Chem Phys 8:1985-93. 2006
    ..In this case larger basis sets were used for extrapolation to the CBS limit and also CCSD(T) and counterpoise-corrected MP2 optimized geometries were sometimes adopted...
  70. ncbi A revised mechanism for the alkaline phosphatase reaction involving three metal ions
    B Stec
    Department of Biochemistry and Cell Biology, W M Keck Center for Computational Biology, Rice University, Houston, TX, 77005, USA
    J Mol Biol 299:1303-11. 2000
    ..A revised mechanism for the catalytic reaction of alkaline phosphatase is proposed on the basis of the two new X-ray crystal structures reported...
  71. ncbi Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase
    J E Ferrell
    Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, California 94305 5332, USA
    J Biol Chem 272:19008-16. 1997
    ....
  72. ncbi Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states
    Frank Noe
    Computational Molecular Biophysics Group, Interdisciplinary Center for Scientific Computing IWR, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
    J Chem Phys 126:155102. 2007
    ..The model hierarchy yields a qualitative understanding of the multiple time and length scales in the dynamics of biomolecules...
  73. ncbi On entropy-based molecular descriptors: statistical analysis of real and synthetic chemical structures
    Matthias Dehmer
    Institute for Bioinformatics and Translational Research, UMIT, Eduard Wallnoefer Zentrum 1, A 6060, Hall in Tyrol, Austria
    J Chem Inf Model 49:1655-63. 2009
    ..Instead, an analysis based on real chemical structures is favorable. Further, we find strong hints that molecular descriptors can be partitioned into distinct classes capturing complementary information...
  74. ncbi Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
    Ana Maria Fernandez-Escamilla
    Nat Biotechnol 22:1302-6. 2004
    ..Furthermore, the algorithm opens the door to a fully automated, sequence-based design strategy to improve the aggregation properties of proteins of scientific or industrial interest...
  75. pmc Ligand configurational entropy and protein binding
    Chia en A Chang
    Department of Chemistry and Biochemistry, and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 104:1534-9. 2007
    ..The results highlight the potential to gain affinity by designing conformationally restricted ligands and have implications for the formulation of energy models for ligand scoring...
  76. pmc Activation mechanism of a signaling protein at atomic resolution from advanced computations
    Liang Ma
    Graduate program in Biophysics and Department of Chemistry and Theoretical Chemical Institute, University of Wisconsin Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
    J Am Chem Soc 129:10261-8. 2007
    ..The computational strategy used and mechanistic insights obtained have an impact on the study of signaling proteins and allosteric systems in general...
  77. pmc Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport
    Johan Lagerqvist
    Department of Physics, University of California, San Diego, La Jolla, California, USA
    Biophys J 93:2384-90. 2007
    ..Finally, water in the environment has negligible direct influence on the transverse electrical current...
  78. ncbi Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
    Hongwu Ma
    GBF German Research Center for Biotechnology, Microbial Systems, Mascheroder Weg 1, 38124 Braunschweig, Germany
    Bioinformatics 19:270-7. 2003
    ..These networks are often very large and complex. To properly understand and analyze the global properties of metabolic networks, methods for rationally representing and quantitatively analyzing their structure are needed...
  79. pmc Fretting about FRET: correlation between kappa and R
    Darren B VanBeek
    Hope College, Department of Chemistry, Holland, Michigan, USA
    Biophys J 92:4168-78. 2007
    ..6. The observed correlation between kappa and R is caused by the succinimide linkage between the D and HEWL, which is found to be relatively inflexible...
  80. ncbi Riboswitches: emerging themes in RNA structure and function
    Rebecca K Montange
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    Annu Rev Biophys 37:117-33. 2008
    ....
  81. pmc Measuring internal friction of an ultrafast-folding protein
    Troy Cellmer
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
    Proc Natl Acad Sci U S A 105:18320-5. 2008
    ..This finding is consistent with the excellent correlation found between experimental and calculated folding rates based on free energy barrier heights using the same diffusion coefficient for every protein...
  82. pmc The crystal structure of xanthine oxidoreductase during catalysis: implications for reaction mechanism and enzyme inhibition
    Ken Okamoto
    Department of Biochemistry and Molecular Biology, Nippon Medical School, 1 1 5 Sendagi, Bunkyo ku, Tokyo 113 8602, Japan
    Proc Natl Acad Sci U S A 101:7931-6. 2004
    ..A water molecule usually seen in the active site of the enzyme is absent in the present structure, which probably accounts for the stability of this intermediate toward ligand displacement by hydroxide...
  83. ncbi In silico prediction of ADME and pharmacokinetics. Report of an expert meeting organised by COST B15
    Alan Boobis
    Section on Clinical Pharmacology, Imperial College, London, UK
    Eur J Pharm Sci 17:183-93. 2002
    ..Controlled access to these data could be particularly helpful in validating new in silico approaches...
  84. pmc Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness
    Maximilian Schlosshauer
    Department of Physics, University of Washington, Seattle, WA 98195, USA
    Protein Sci 13:1660-9. 2004
    ..The transparent physical interpretation of our approach that computes association rates directly from the size and geometry of protein-protein binding funnels makes it a useful complement to Brownian dynamics simulations...
  85. pmc Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils
    Nicolae Viorel Buchete
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520
    Biophys J 92:3032-9. 2007
    ..The interior C-terminal beta-sheets in the hydrophobic core remain largely intact, indicating that their formation and stability is crucial to the dissociation/elongation and stability of Abeta fibrils...
  86. ncbi ISIS: interaction sites identified from sequence
    Yanay Ofran
    CUBIC and North East Structural Genomics Consortium, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
    Bioinformatics 23:e13-6. 2007
    ..Therefore, for the vast majority of proteins, for which there is no high-resolution structure, there is no effective way of identifying interface residues...
  87. ncbi Neutral evolution of model proteins: diffusion in sequence space and overdispersion
    U Bastolla
    HLRZ, Forschungszentrum Julich, Julich, D 52425, Germany
    J Theor Biol 200:49-64. 1999
    ..This result is in contrast with the simplest model of neutral evolution, which assumes a Poisson process for substitutions, and in qualitative agreement with the biological data...
  88. pmc Protein-DNA binding specificity predictions with structural models
    Alexandre V Morozov
    Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 33:5781-98. 2005
    ..Use of homology modeling can significantly increase the extent of our approach, making it a useful tool for studying regulatory pathways in many organisms and cell types...
  89. pmc Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes
    Basak Isin
    Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
    Biophys J 95:789-803. 2008
    ....
  90. pmc Mechanics of channel gating of the nicotinic acetylcholine receptor
    Xinli Liu
    Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian, Liaoning, China
    PLoS Comput Biol 4:e19. 2008
    ..The present MD simulations explore the structural dynamics of the receptor under its gating process and provide a new insight into the gating mechanism of nAChR at the atomic level...
  91. pmc Probing the flexibility of large conformational changes in protein structures through local perturbations
    Bosco K Ho
    Howard Hughes Medical Institute and the Department of Biochemistry, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 5:e1000343. 2009
    ..RIP analysis has the potential to discover sites of functional conformational changes and the linchpin residues critical in determining these conformational states...
  92. ncbi Natively unfolded proteins
    Anthony L Fink
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    Curr Opin Struct Biol 15:35-41. 2005
    ..New algorithms have been developed to identify disordered regions of proteins and have demonstrated their presence in cancer-associated proteins and proteins regulated by phosphorylation...
  93. ncbi Quantifying the kinetic parameters of prion replication
    J Masel
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, UK
    Biophys Chem 77:139-52. 1999
    ..Published kinetic data are all compatible with our mathematical model, so the nucleated polymerisation hypothesis cannot be ruled out on dynamic grounds...
  94. ncbi Mitochondria and Huntington's disease pathogenesis: insight from genetic and chemical models
    Susan E Browne
    Merck Research Laboratories, West Point, PA 19486, USA
    Ann N Y Acad Sci 1147:358-82. 2008
    ....
  95. ncbi Replica exchange molecular dynamics simulations of amyloid peptide aggregation
    M Cecchini
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    J Chem Phys 121:10748-56. 2004
    ..The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides..
  96. ncbi The role of active site glutamate residues in catalysis of Rhodobacter capsulatus xanthine dehydrogenase
    Silke Leimkuhler
    Department of Plant Biology, Technical University Braunschweig, 38023 Braunschweig, Germany
    J Biol Chem 279:40437-44. 2004
    ..This result is fully consistent with the proposed role of this residue as an active site base that initiates catalysis...
  97. ncbi Sterically locked synthetic bilin derivatives and phytochrome Agp1 from Agrobacterium tumefaciens form photoinsensitive Pr- and Pfr-like adducts
    Katsuhiko Inomata
    Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920 1192, Japan
    J Biol Chem 280:24491-7. 2005
    ..In this way, physiological action of Pfr can be studied in vivo and separated from Pr/Pfr cycling and other light effects...
  98. ncbi Symmetry, form, and shape: guiding principles for robustness in macromolecular machines
    Florence Tama
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biophys Biomol Struct 35:115-33. 2006
    ..Emerging from such studies is a control principle for robustness in Nature's machines. We discuss this idea in the context of large-scale functional reorganization of the ribosome, virus particles, and the muscle protein myosin...
  99. ncbi A new type of bacteriophytochrome acts in tandem with a classical bacteriophytochrome to control the antennae synthesis in Rhodopseudomonas palustris
    Eric Giraud
    Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, AGRO M, INRA, UM2, TA 10 J, Campus de Baillarguet, Montpellier France
    J Biol Chem 280:32389-97. 2005
    ....
  100. ncbi Setting up and running molecular dynamics simulations of membrane proteins
    Christian Kandt
    Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary AB, Canada T2N 1N4
    Methods 41:475-88. 2007
    ..The main advantages of these methods are that they minimize equilibration time and can be almost completely automated, nearly eliminating one time consuming step in MD simulations of membrane proteins...
  101. ncbi Comparing and combining predictors of mostly disordered proteins
    Christopher J Oldfield
    Molecular Kinetics, Inc, 6201 La Pas Trail, Suite 160, Indianapolis, Indiana 46268, USA
    Biochemistry 44:1989-2000. 2005
    ....

Research Grants10

  1. Chemical Models of Protein beta-Sheet Interactions
    James Nowick; Fiscal Year: 2009
    ..The investigators will gain insight into interactions between protein beta-sheets by developing and studying chemical models of beta-sheets that bind proteins by means of beta-sheet interactions...
  2. REGULATION OF SYNAPTIC TRANSMISSION
    Robert Zucker; Fiscal Year: 2002
    ..Effects of a rise in presynaptic [Ca2+]i on facilitation and secretion will be simulated to test chemical models of these processes...
  3. CHEMICAL MODELS FOR BIOLOGICAL ELECTRON TRANSFER
    John Dawson; Fiscal Year: 1991
    ....
  4. Splicing, Folding, and Stretching Nucleic Acids
    DANIEL AALBERTS; Fiscal Year: 2003
    ..The following three proposals will expand the predictive power of physical chemical models of nucleic acid conformations. (1) Gene finding algorithms are currently statistics based...
  5. CHEMICAL MODELS OF PRESYNAPTIC NEUROMUSCULAR DISEASE
    WILLIAM ATCHISON; Fiscal Year: 1999
    ....
  6. MECHANISMS OF INHERITED MEMBRANE TRANSPORT DISORDERS
    Stanton Segal; Fiscal Year: 1992
    ..Segal, Principal Investigator, Project 2, Chemical Models of the Fanconi Syndrome: Studies with 15N-GC-MS and 13C-NMR, Principal Investigator, Dr...
  7. REACTION CENTER DYNAMICS
    CRAIG SCHENCK; Fiscal Year: 1992
    ..novel reaction intermediates in the electron transport sequence and interpreting these events with physical chemical models. The molecular nature of the forces that determine the spectroscopic, kinetic and thermodynamic ..
  8. Effects of phosphoinositides on cytoskeletal structure
    Paul Janmey; Fiscal Year: 2006
    ..between the PI of the parent grant and each of the two Latvian collaborators suggest that physical-chemical models may account for domain formation by the phosphoinositide systems studied in the parent project, and this ..
  9. Binding and Splicing mRNA
    DANIEL AALBERTS; Fiscal Year: 2009
    ..We propose to: (1) Develop physical-chemical models of small RNAs and proteins binding that modulate gene expression through mRNA binding...