D A Case

Summary

Affiliation: The Scripps Research Institute
Country: USA

Publications

  1. ncbi Density functional and reduction potential calculations of Fe4S4 clusters
    Rhonda A Torres
    Department of Molecular Biology TPC 15, The Scripps Research Institute, La Jolla, California 92037, USA
    J Am Chem Soc 125:1923-36. 2003
  2. 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
  3. ncbi Interpretation of chemical shifts and coupling constants in macromolecules
    D A Case
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Curr Opin Struct Biol 10:197-203. 2000
  4. ncbi Calculations of NMR dipolar coupling strengths in model peptides
    D A Case
    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    J Biomol NMR 15:95-102. 1999
  5. ncbi The use of chemical shifts and their anisotropies in biomolecular structure determination
    D A Case
    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    Curr Opin Struct Biol 8:624-30. 1998
  6. ncbi High-resolution solution structures of oxidized and reduced Escherichia coli thioredoxin
    M F Jeng
    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037
    Structure 2:853-68. 1994
  7. ncbi Three-dimensional solution structure of a single zinc finger DNA-binding domain
    M S Lee
    Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037
    Science 245:635-7. 1989
  8. ncbi Automated prediction of 15N, 13Calpha, 13Cbeta and 13C' chemical shifts in proteins using a density functional database
    X P Xu
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Biomol NMR 21:321-33. 2001
  9. ncbi Structural basis for DNA bending by the architectural transcription factor LEF-1
    J J Love
    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA
    Nature 376:791-5. 1995
  10. ncbi High-resolution solution structure of Bacillus subtilis IIAglc
    Y Chen
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Proteins 31:258-70. 1998

Collaborators

Detail Information

Publications79

  1. ncbi Density functional and reduction potential calculations of Fe4S4 clusters
    Rhonda A Torres
    Department of Molecular Biology TPC 15, The Scripps Research Institute, La Jolla, California 92037, USA
    J Am Chem Soc 125:1923-36. 2003
    ....
  2. 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
    ....
  3. ncbi Interpretation of chemical shifts and coupling constants in macromolecules
    D A Case
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Curr Opin Struct Biol 10:197-203. 2000
    ..Topics of recent special interest include spin couplings across hydrogen bonds and patterns of chemical shift anisotropies, in both diamagnetic and paramagnetic proteins...
  4. ncbi Calculations of NMR dipolar coupling strengths in model peptides
    D A Case
    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    J Biomol NMR 15:95-102. 1999
    ..The present computational results are compared to both solid- and liquid-state NMR experiments. The analysis suggests that secondary structural elements in many proteins may be more rigid than is commonly thought...
  5. ncbi The use of chemical shifts and their anisotropies in biomolecular structure determination
    D A Case
    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    Curr Opin Struct Biol 8:624-30. 1998
    ..It influences the resonance position in partially-ordered samples and has consequences for spin relaxation, even in isotropic systems. There has been recent progress in measuring and interpreting these anisotropies...
  6. ncbi High-resolution solution structures of oxidized and reduced Escherichia coli thioredoxin
    M F Jeng
    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037
    Structure 2:853-68. 1994
    ..We therefore undertook high-resolution solution structural studies of the two forms of Escherichia coli thioredoxin in order to detect subtle conformational differences...
  7. ncbi Three-dimensional solution structure of a single zinc finger DNA-binding domain
    M S Lee
    Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037
    Science 245:635-7. 1989
    ..A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding...
  8. ncbi Automated prediction of 15N, 13Calpha, 13Cbeta and 13C' chemical shifts in proteins using a density functional database
    X P Xu
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Biomol NMR 21:321-33. 2001
    ..This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement...
  9. ncbi Structural basis for DNA bending by the architectural transcription factor LEF-1
    J J Love
    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA
    Nature 376:791-5. 1995
    ..The structure reveals the HMG domain bound in the widened minor groove of a markedly distorted and bent double helix. The basic region binds across the narrowed major groove and contributes to DNA recognition...
  10. ncbi High-resolution solution structure of Bacillus subtilis IIAglc
    Y Chen
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Proteins 31:258-70. 1998
    ..The active site is located in a concave region of the protein surface. The histidine, which accepts the phosphoryl group (His 83), interacts with a neighboring histidine (His 68) and is surrounded by hydrophobic residues...
  11. ncbi FeMo cofactor of nitrogenase: a density functional study of states M(N), M(OX), M(R), and M(I)
    T Lovell
    Department of Molecular Biology TPC 15, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Am Chem Soc 123:12392-410. 2001
    ....
  12. ncbi Density functional calculation of p K(a) values and redox potentials in the bovine Rieske iron-sulfur protein
    G Matthias Ullmann
    Department of Moleular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Biol Inorg Chem 7:632-9. 2002
    ..The potential biological function of the low p K(a) value of the histidines and the shift upon reduction are briefly discussed...
  13. ncbi Binding modes for the first coupled electron and proton addition to FeMoco of nitrogenase
    Timothy Lovell
    The Scripps Research Institute, La Jolla California 92037, USA
    J Am Chem Soc 124:4546-7. 2002
    ..Under physiological turnover conditions of low electron flux, the formation of this iron-hydride intermediate may represent a first step towards cofactor liberation of dihydrogen in the absence of dinitrogen...
  14. ncbi Biomolecular simulations at constant pH
    John Mongan
    The Center for Theoretical Biological Physics, University of California San Diego, La Jolla, CA 92093 0365, USA
    Curr Opin Struct Biol 15:157-63. 2005
    ....
  15. ncbi A novel view of pH titration in biomolecules
    A Onufriev
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC-15, La Jolla, California 92037, USA
    Biochemistry 40:3413-9. 2001
    ..The application of the new framework to the protein rubredoxin demonstrates its usefulness in calculating and interpreting complicated titration curves...
  16. ncbi The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters
    James A Fee
    Department of Molecular Biology, MB8, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Biol Inorg Chem 8:519-26. 2003
    ....
  17. ncbi Structural, spectroscopic, and redox consequences of a central ligand in the FeMoco of nitrogenase: a density functional theoretical study
    Timothy Lovell
    Department of Molecular Biology TPC 15, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Am Chem Soc 125:8377-83. 2003
    ..97 eV for O(2-) and -1.31 eV for C(4-). The calculated structural parameters and/or redox data suggest either O(2-) or C(4-) is unlikely as a central anion...
  18. ncbi Predicting interactions of winged-helix transcription factors with DNA
    Victoria A Roberts
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Proteins 57:172-87. 2004
    ..Our results show rigid-body docking that includes a rigorous treatment of the electrostatic interaction energy can be effective in predicting protein-DNA interactions...
  19. ncbi Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations
    Thomas Steinbrecher
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, San Diego, California 92037, USA
    J Chem Phys 127:214108. 2007
    ..Additionally, results from a more flexible solute, hexane, will also be discussed...
  20. ncbi Metal substitution in the active site of nitrogenase MFe(7)S(9) (M = Mo(4+), V(3+), Fe(3+))
    Timothy Lovell
    Department of Molecular Biology TPC 15, The Scripps Research Institute, La Jolla, CA 92037, USA
    Inorg Chem 41:5744-53. 2002
    ..The size of the cofactor cluster shows a dependency on the nature of the heterometal and increases in the order FeMoco < FeVco < FeFeco...
  21. ncbi Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach
    Holger Gohlke
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Proteins 56:322-37. 2004
    ..Finally, the sensitivity of FIRST results with respect to the representation of non-covalent interactions used as constraints is probed...
  22. ncbi FeMo cofactor of nitrogenase: energetics and local interactions in the protein environment
    Timothy Lovell
    Department of Molecular Biology TPC 15, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Biol Inorg Chem 7:735-49. 2002
    ..These calculations represent a first step towards the development of a microscopic model of electron and proton transfer events at the nitrogenase active site...
  23. pmc Ligand-bound S = 1/2 FeMo-cofactor of nitrogenase: hyperfine interaction analysis and implication for the central ligand X identity
    Vladimir Pelmenschikov
    The Scripps Research Institute, Department of Molecular Biology TPC 15, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Inorg Chem 47:6162-72. 2008
    ..In addition, our results illustrate structural details and likely spin-coupling patterns for models for early intermediates in the catalytic cycle...
  24. pmc Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: application of density functional theory to cytochrome ba3 of Thermus thermophilus
    James A Fee
    The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Am Chem Soc 130:15002-21. 2008
    ..E. M.; Blomberg, M. A. R. Chem. Rev. 2000, 100, 421-437) and shows how the chemistry of O 2 reduction in the heme a 3 -Cu B dinuclear center can be harnessed to generate an electrochemical proton gradient across the lipid bilayer...
  25. ncbi The structure of calcyclin reveals a novel homodimeric fold for S100 Ca(2+)-binding proteins
    B C Potts
    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA
    Nat Struct Biol 2:790-6. 1995
    ..Dimerization is mediated by hydrophobic contacts from several highly conserved residues, which suggests that the dimer fold identified for calcyclin will serve as a structural paradigm for the S100 subfamily of calcium-binding proteins...
  26. ncbi Generalized born models of macromolecular solvation effects
    D Bashford
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Phys Chem 51:129-52. 2000
    ..We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations...
  27. ncbi The implementation of a fast and accurate QM/MM potential method in Amber
    Ross C Walker
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Comput Chem 29:1019-31. 2008
    ....
  28. ncbi Effective Born radii in the generalized Born approximation: the importance of being perfect
    Alexey Onufriev
    Department of Molecular Biology, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, California 92037, USA
    J Comput Chem 23:1297-304. 2002
    ....
  29. ncbi Three-dimensional solution structure of the reduced form of Escherichia coli thioredoxin determined by nuclear magnetic resonance spectroscopy
    H J Dyson
    Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, California 92037
    Biochemistry 29:4129-36. 1990
    ..This conformational change has important implications for the mechanism of thioredoxin as a protein disulfide oxidoreductase...
  30. ncbi A comparison of quantum chemical models for calculating NMR shielding parameters in peptides: mixed basis set and ONIOM methods combined with a complete basis set extrapolation
    Seongho Moon
    Department of Molecular Biology, Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, California 92037
    J Comput Chem 27:825-36. 2006
    ..The information studied here will be useful in guiding the selection of proper quantum chemical models, which are in a tradeoff between accuracy and cost, for shielding studies of peptides and proteins...
  31. ncbi O-glycoside orientation is an essential aspect of base J recognition by the kinetoplastid DNA-binding protein JBP1
    Rajesh K Grover
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Angew Chem Int Ed Engl 46:2839-43. 2007
  32. ncbi A new model for chemical shifts of amide hydrogens in proteins
    Seongho Moon
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Biomol NMR 38:139-50. 2007
    ..Comparison to observed shifts for 15 proteins shows a significant improvement over existing structure-shift correlations. These additions are incorporated in a new version of the SHIFTS program...
  33. ncbi Constant pH molecular dynamics in generalized Born implicit solvent
    John Mongan
    The Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Dr, La Jolla, California 92093 0365, USA
    J Comput Chem 25:2038-48. 2004
    ..A strong correlation between conformation and protonation state is noted and quantitatively analyzed, emphasizing the importance of sampling protonation states in conjunction with dynamics...
  34. ncbi Extended sugar-assisted glycopeptide ligations: development, scope, and applications
    Richard J Payne
    Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Am Chem Soc 129:13527-36. 2007
    ..To demonstrate the applicability of the method, extended SAL was successfully implemented in the synthesis of the starting unit of the cancer-associated MUC1 glycoprotein...
  35. ncbi Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
    Holger Gohlke
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 330:891-913. 2003
    ..This explains the finding of a conformational change in this region upon complex formation with Ras, and it may trigger a larger structural change in Raf, which is considered to be necessary for activation of the effector by Ras...
  36. ncbi Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
    Michael Feig
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Comput Chem 25:265-84. 2004
    ..25% between each other for both native and nonnative structures. The performance of the best GB methods is discussed in more detail for the application for force field-based minimizations or molecular dynamics simulations...
  37. ncbi Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
    Holger Gohlke
    Department of Molecular Biology, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, California 92037, USA
    J Comput Chem 25:238-50. 2004
    ..3 kcal mol(-1) is in good agreement with the experimental result of -9.6 kcal mol(-1), however, further probing the transferability of the applied protocol that led to this result is necessary...
  38. pmc A novel method for finding tRNA genes
    Vickie Tsui
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    RNA 9:507-17. 2003
    ..Prospects for using this general approach to find other RNA structural motifs are discussed...
  39. ncbi Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water
    Bin Xia
    Department of Molecular Biology and Skaggs Intitute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92122, USA
    J Biomol NMR 22:317-31. 2002
    ..Some improvement for phi and psi angle distribution and hydrogen bond pattern can also be achieved by energy minimizing the vacuum structures with the GB model, which takes a much shorter time than MD simulations with the GB model...
  40. ncbi Evaluating rotational diffusion from protein MD simulations
    Vance Wong
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    J Phys Chem B 112:6013-24. 2008
    ..A number of residues exhibit internal motions on the nanosecond time scale, but in all cases examined here, a product of internal and overall time-correlation functions matches the total time-correlation function well...
  41. pmc Carbon-deuterium bonds as probes of dihydrofolate reductase
    Megan C Thielges
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
    J Am Chem Soc 130:6597-603. 2008
    ....
  42. doi Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain
    Tingjun Hou
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
    J Mol Biol 376:1201-14. 2008
    ....
  43. pmc Multiscale modeling of nucleic acids: insights into DNA flexibility
    Yannick J Bomble
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92122, USA
    Biopolymers 89:722-31. 2008
    ..The results suggest that current all-atom potentials, which were parameterized on small molecules and short oligonucleotides, also provide a useful description of duplex DNA at much longer length scales...
  44. ncbi Molecular dynamics and NMR spin relaxation in proteins
    David A Case
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Acc Chem Res 35:325-31. 2002
    ..Such information could provide a sound foundation for a new generation of detailed interpretation of NMR spin-relaxation results...
  45. pmc Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains
    Tingjun Hou
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 8:639-49. 2009
    ..The success of our framework on SH3 domains suggests that it is possible to establish a theoretical model to decipher the protein recognition code of any modular domain...
  46. pmc Direct simulation of electron transfer reactions in DNA radical cations
    Thomas Steinbrecher
    The Scripps Research Institute, 10550 North Torrey Pines Road, San Diego, CA 92037, USA
    J Phys Chem B 112:16935-44. 2008
    ..The reorganization energy lambda for hopping between neighboring bases was found to be ca. 25 kcal/mol and charge transfer rates of 4.1 x 10(9) s(-1) for AA hopping and 1.3 x 10(9) s(-1) for GG hopping were obtained...
  47. ncbi Structural details, pathways, and energetics of unfolding apomyoglobin
    Alexey Onufriev
    Department of Molecular Biology, The Scripps Research Institute, TPC15, 10550 N Torrey Pines Road, La Jolla, CA 93027, USA
    J Mol Biol 325:555-67. 2003
    ..Electrostatic interactions are found to disfavor folding...
  48. pmc Evaluating beta-turn mimics as beta-sheet folding nucleators
    Amelia A Fuller
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 106:11067-72. 2009
    ..These beta-turn mimics can now be used to interrogate protein folding transition state structures and the 2 kinetic analyses presented can be used to assess the nucleation capacity of other beta-turn mimics...
  49. ncbi Probing multiple effects on 15N, 13C alpha, 13C beta, and 13C' chemical shifts in peptides using density functional theory
    Xiao Ping Xu
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
    Biopolymers 65:408-23. 2002
    ..71, 1.22, 1.31, and 1.28 ppm for N, C alpha, C beta, and C', respectively. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement...
  50. ncbi Induced fit and "lock and key" recognition of 5S RNA by zinc fingers of transcription factor IIIA
    Brian M Lee
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 357:275-91. 2006
    ....
  51. ncbi Pseudo-atomic models of swollen CCMV from cryo-electron microscopy data
    Hongjun Liu
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Struct Biol 142:356-63. 2003
    ..Because the hexamers and pentamers were incrementally translated and rotated in a screw motion, with energy minimization at each of 28 steps, a path for the expansion is also implied...
  52. ncbi Differential solvation and tautomer stability of a model base pair within the minor and major grooves of DNA
    Francois Yves Dupradeau
    Faculté de Pharmacie and DMAG EA 3901, Universite de Picardie Jules Verne, Amiens, France
    J Am Chem Soc 127:15612-7. 2005
    ..The differential stabilization of the enol and keto tautomers in the major and minor grooves may reflect the functions for which these environments evolved, including duplex replication, stability, and recognition...
  53. ncbi High-resolution field-cycling NMR studies of a DNA octamer as a probe of phosphodiester dynamics and comparison with computer simulation
    Mary F Roberts
    Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
    Biochemistry 43:3637-50. 2004
    ..High-resolution field cycling opens up the possibility of monitoring residue-specific dipolar interactions and dynamics for the phosphorus nuclei of diverse oligonucleotides...
  54. ncbi Testing if the interstitial atom, X, of the nitrogenase molybdenum-iron cofactor is N or C: ENDOR, ESEEM, and DFT studies of the S = 3/2 resting state in multiple environments
    Dmitriy Lukoyanov
    Department of Chemistry, Northwestern University, Evanston, Il 60208 3113, USA
    Inorg Chem 46:11437-49. 2007
    ..3/0.4 MHz and aiso(13CX) = 1 MHz. However, the DFT uncertainties are large enough that the very small hyperfine couplings required by experiment do not necessarily rule out X = N/C...
  55. 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
  56. pmc Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps
    David L Beveridge
    Chemistry Department, Molecular Biology and Biochemistry Department, and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA
    Biophys J 87:3799-813. 2004
    ....
  57. pmc Rescoring docking hit lists for model cavity sites: predictions and experimental testing
    Alan P Graves
    Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158 2330, USA
    J Mol Biol 377:914-34. 2008
    ..We consider the origins of the successes and failures in MM-GBSA rescoring in these model cavity sites and the prospects for rescoring in biologically relevant targets...
  58. pmc Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS)
    YiSong Guo
    Department of Applied Science, University of California, Davis, California 95616, USA
    Inorg Chem 47:3969-77. 2008
    ..A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site...
  59. ncbi NMR structure of a cyclic polyamide-DNA complex
    Qing Zhang
    Department of Chemistry, University of California, Berkeley, California 94720 1460, USA
    J Am Chem Soc 126:7958-66. 2004
    ....
  60. ncbi Development and testing of a general amber force field
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, Texas 77030, USA
    J Comput Chem 25:1157-74. 2004
    ..The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching...
  61. ncbi Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum
    Luc Moulinier
    Département de Biologie et Génomique Structurales, Institut de Génétique et Biologie Moléculaire et Cellulaire CNRS, 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
    Acta Crystallogr D Biol Crystallogr 59:2094-103. 2003
    ..As GB parameterization continues to improve, we expect that this approach will become increasingly useful...
  62. ncbi Exploring protein native states and large-scale conformational changes with a modified generalized born model
    Alexey Onufriev
    Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
    Proteins 55:383-94. 2004
    ..5 A after 6 ns of simulation time. The structure of Barnase/Barstar complex is regenerated, starting from an unbound state, to within 1.9 A relative to the crystal structure of the complex...
  63. ncbi Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods
    Hiroaki Gouda
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
    Biopolymers 68:16-34. 2003
    ..The comparison of MM-PBSA with TI suggests that the MM-PBSA method has some difficulties with the first-solvation-shell energetics...
  64. ncbi Second derivatives in generalized Born theory
    Russell A Brown
    Sun Microsystems, Inc, Menlo Park, California 94025, USA
    J Comput Chem 27:1662-75. 2006
    ..The code has been implemented for parallel computers using both the OpenMP and MPI environments, and good parallel scaling is seen with as many as 144 OpenMP processing threads or MPI processing tasks...
  65. ncbi Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models
    Thomas Simonson
    Laboratoire de Biochimie UMR7654 du CNRS, Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
    J Am Chem Soc 126:4167-80. 2004
    ....
  66. ncbi A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase
    Thomas Steinbrecher
    Institut fur Physikalische Chemie, Albert Ludwigs Universitat Freiburg, Albertstrasse 23a, 79104 Freiburg, Germany
    J Med Chem 49:1837-44. 2006
    ....
  67. ncbi Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair
    David H Mathews
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA
    J Mol Biol 357:1683-93. 2006
    ....
  68. ncbi Automatic atom type and bond type perception in molecular mechanical calculations
    Junmei Wang
    College of Chemistry, Peking University, Beijing 100871, China
    J Mol Graph Model 25:247-60. 2006
    ..for most organic molecules. The algorithms behind the manipulations may be useful for other molecular mechanical packages as well as applications that need to designate atom types and bond types...
  69. ncbi Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites
    Jingyang Chen
    Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
    Biochemistry 46:3096-107. 2007
    ..The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed...
  70. pmc Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
    Surjit B Dixit
    Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA
    Biophys J 89:3721-40. 2005
    ..The results in general provide new insight into MD on DNA and the sequence-dependent dynamical structural characteristics of DNA...
  71. pmc Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package
    Gustavo de M Seabra
    Department of Chemistry and Quantum Theory Project, University of Florida, P O Box 118435, Gainesville, Florida 32611 8435, USA
    J Phys Chem A 111:5655-64. 2007
    ..This article shows an implementation of the SCC-DFTB method as part of the new QM/MM support in the AMBER 9 molecular dynamics program suite. Details of the implementation and examples of applications are shown...
  72. pmc How nitrogenase shakes--initial information about P-cluster and FeMo-cofactor normal modes from nuclear resonance vibrational spectroscopy (NRVS)
    Yuming Xiao
    Department of Applied Science, University of California, Davis, California 95616, USA
    J Am Chem Soc 128:7608-12. 2006
    ..A variety of Fe-S stretching modes are also observed between 250 and 400 cm(-)(1). This work is the first spectroscopic information about the vibrational modes of the intact nitrogenase FeMo-cofactor and P-cluster...
  73. ncbi Symmetry and bonding in metalloporphyrins. A modern implementation for the bonding analyses of five- and six-coordinate high-spin iron(III)-porphyrin complexes through density functional calculation and NMR spectroscopy
    Ru Jen Cheng
    Department of Chemistry, National Chung Hsing University, Taichung, Taiwan 402, Republic of China
    J Am Chem Soc 125:6774-83. 2003
    ....
  74. ncbi An accurate and simple quantum model for liquid water
    Francesco Paesani
    Center for Biophysical Modeling and Simulation, University of Utah, Salt Lake City, Utah 84112, USA
    J Chem Phys 125:184507. 2006
    ....
  75. ncbi Homology modeling of NR2B modulatory domain of NMDA receptor and analysis of ifenprodil binding
    Luciana Marinelli
    Dipartimento di Chimica Farmaceutica e Tossicologica, Universita di Napoli Federico II, via D Montesano 49, 80131 Napoli, Italy
    ChemMedChem 2:1498-510. 2007
    ..Thus, for a rational design and/or for virtual screening experiments, the closed conformation of the R1-R2 domain should be taken into account and our 3D model can provide valuable hints for the design of NR2B-selective antagonists...
  76. ncbi Modeling of flap endonuclease interactions with DNA substrate
    Hatim T Allawi
    Third Wave Technologies, Inc, 502 S Rosa Road, Madison, WI 53719, USA
    J Mol Biol 328:537-54. 2003
    ..This model suggests specific interactions between the 3' end of the upstream oligonucleotide and the enzyme. The proposed structure presents the first detailed description of substrate recognition by structure-specific 5' nucleases...
  77. ncbi Design and synthesis of highly constrained factor Xa inhibitors: amidine-substituted bis(benzoyl)--diazepan-2-ones and bis(benzylidene)-bis(gem-dimethyl)cycloketones
    Jian Cui
    Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Avenue, M C 870, Chicago, IL 60607 7173, USA
    Bioorg Med Chem 11:3379-92. 2003
    ..We suggest that this interaction plays an important role in the specificity of these inhibitors against other serine proteases...
  78. ncbi Insights into the mobility of methyl-bearing side chains in proteins from (3)J(CC) and (3)J(CN) couplings
    James J Chou
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Am Chem Soc 125:8959-66. 2003
    ..This indicates that some of the rotameric averaging occurs on a time scale too slow to be observable in traditional relaxation measurements...
  79. pmc DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics
    Jingyang Chen
    Department of Chemistry Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Nucleic Acids Res 36:253-62. 2008
    ..These results provide structural insight into the dynamics of abasic sites that are intrinsically modulated by the bases opposite the abasic site...