Computational challenges in structural and functional genomics

IBM Systems Journal

Volumn 40, Issue 2, 2001, Pages 265-296

  Head Gordon, T ^a   Wooley, J C ^a  

^a University of California at Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTATION THEORY; DNA; PROTEINS;

COMPUTATIONAL BIOLOGY;

GENES;

EID: 0034963883     PISSN: 00188670     EISSN: None     Source Type: Journal    
DOI: 10.1147/sj.402.0265     Document Type: Article

References (122)

1. Computational molecular biophysics today: A confluence of methodological advances and complex biomolecular applications
2. Identification of common molecular subsequences
3. Hidden Markov models in computational biology: Applications to protein modeling
4. An approximation algorithm for alignment of multiple sequences using motif discovery
5. Stochastic context-free grammars for T-RNA modeling
6. Bayesian inference on biopolymer models
7. RNA modeling using gibbs sampling and stochastic context-free grammars
8. Assigning amino acid sequences to 3-dimensional protein folds
9. A method to identify protein sequences that fold into a known three-dimensional structure
10. Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins
11. Fast protein fold recognition via sequence to structure alignment and contact capacity potentials
12. Profile hidden Markov models
13. Definition of general topological equivalence in protein structures: A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming
14. Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology
15. Assessment of comparative modelling in CASP2
16. Fast and simple Monte Carlo algorithm for side chain optimization in proteins: Application to model building by homology
17. Comparison of systematic search and database methods for constructing segments of protein structure
18. Determinants of side chain conformational preferences in protein structures
19. Comparative protein structure modeling of genes and genomes
20. A branch and bound algorithm for local multiple alignment
21. Global optimum protein threading with gapped alignment and empirical pair potentials
22. The protein threading problem with sequence amino acid interaction preferences is NP-complete
23. Progress in fold recognition
24. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
25. First-principles calculation of the folding free energy of a three-helix bundle protein
26. Simulations of protein folding and unfolding
27. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
28. CHARMM: The energy function and its parameterization with an overview of the program
29. Energy parameters in polypeptides, 9. Updating of geometrical parameters, non-bonding interactions and hydrogen bonding interactions for naturally occurring amino acids
30. Atomic-level accuracy in simulations of large protein crystals
31. A very fast molecular dynamics method to simulate biomolecular systems with realistic electrostatic interactions
32. Protein folding/unfolding dynamics
33. Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: Comparison to X-ray crystallographic and NMR data
34. Comparison of database potentials and molecular mechanics force fields
35. Some factors in the interpretation of protein denaturation
36. Atomic solvation parameters applied to molecular dynamics of proteins in solution
37. Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor
38. Semianalytical treatment of solvation for molecular mechanics and dynamics
39. Macroscopic models of aqueous solutions: Biological and chemical applications
40. Determining the role of hydration forces in protein folding
41. Improved simulation of liquid water by molecular dynamics
42. What can X-ray scattering tell us about the radial distribution functions of water?
43. Interaction models for water in relation to protein hydration
44. Comparison of simple potential functions for simulating liquid water
45. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
46. Constructing Ab Initio force fields for molecular dynamics simulations
47. Engineering a simple polarizable model for the molecular simulation of water applicable over wide ranges of state conditions
48. Liquid water with an Ab Initio potential-X-ray and neutron scattering from 238k to 368k
49. Polarizable point-charge model for water-results under normal and extreme conditions
50. Development of polarizable water force fields for phase equilibrium calculations
51. Fine- and coarse-grain parallel AMBER and particle mesh ewald on MPP's
52. Recent advances in molecular dynamics simulation towards realistic representation of biomolecules in solution
53. Dielectric theory for polar molecules with fluctuating polarizability
54. Effective field of a dipole in non-polar polarizable fluids
55. Theory and simulation of polar and nonpolar polarizable fluids
56. Effects of polarizability on the hydration of the chloride ion
57. Adiabatic path integral molecular dynamics methods. I. Theory
58. Adiabatic path integral molecular dynamics methods. II. Algorithms
59. Molecular dynamics simulations at constant pressure and/or temperature
60. Unified approach for molecular dynamics and density-functional theory
61. Constant pressure molecular dynamics algorithms
62. Explicit reversible integrators for extended systems dynamics
63. Modern computational methodology applied to the simulation of blocked trialanine peptide in vacuo, water clusters, and bulk water
64. Reversible multiple time scale molecular dynamics
65. Biomolecular dynamics at long timesteps: Bridging the timescale gap between simulation and experimentation
66. Overcoming stability limitations in biomolecular dynamics: I. Combining force splitting via extrapolation with langevin dynamics in LN
67. Extrapolation versus impulse in multiple-timestepping schemes: II. Linear analysis and applications to newtonian and langevin dynamics
68. Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
69. Two dimensional umbrella sampling techniques for the computer simulation study of helical peptides at thermal equilibrium: The 3k (i) peptide in vacuo and solution
70. Multidimensional free-energy calculations using the weighted histogram analysis method
71. Understanding modern molecular dynamics: Techniques and applications
72. Quantum chemistry and molecular processes
73. Molecular integrals over gaussian basis functions
74. Linear scaling density functional calculations via the continuous fast multipole method
75. A fast algorithm for particle simulations
76. Density-matrix electronic-structure method with linear system-size scaling
77. Large-scale electronic structure calculations
78. Density-functional exchange-energy approximation with correct asymptotic-behavior
79. Atoms, molecules, solids, and surfaces - Applications of the generalized gradient approximation for exchange and correlation
80. Development of the colle-salvetti correlation-energy formula into a functional of the electron density
81. Local treatment of electron correlation
82. Coupled-cluster approach to molecular structure and spectra: A step toward predictive quantum chemistry
83. Unified approach for molecular dynamics and density-functional theory
84. Ab Initio molecular dynamics study of hydrochloric acid in water
85. Ab Initio liquid water
86. Computer modeling of protein folding: Conformational and energetic analysis of reduced and detailed protein models
87. A test of lattice protein folding algorithms
88. Diffusion smoothing
89. Application of the diffusion equation for global optimization to oligopeptides
90. Application of the renormalization group to deterministic global minimization of molecular conformation energy functions
91. Modeling sidechains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
92. A study of simulated annealing protocols for use with molecular dynamics in protein structure prediction
93. The genetic algorithm and the conformational search of polypeptides and proteins
94. Monte-Carlo-minimization approach to the multiple minima problem in protein folding
95. Application of systematic conformational search to protein modeling
96. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
97. A strategy for finding classes of minima on a hypersurface: Implications for approaches to the protein folding problem
98. Predicting polypeptide and protein structures from amino acid sequence: Antlion method applied to melittin
99. A global optimization strategy for predicting α-helical protein tertiary structure
100. A good ligand is hard to find: Automated docking method
101. Structure-based molecular design
102. Ligand-protein docking and rational drug design
103. Flexible protein-ligand docking by global energy optimization in internal coordinates
104. Critical evaluation of search algorithms for automated molecular docking and database screening
105. Flexible ligand docking using conformational ensembles
106. Quantum molecular dynamics on massively parallel computers
107. Efficiency of Ab-Initio total energy calculations for metals and semiconductors using a plane-wave basis set
108. Efficient iterative schemes for Ab Initio total-energy calculations using a plane-wave basis set
109. Stochastic kinetic analysis of developmental pathway bifurcation in phage-infected escherichia coli cells
110. It's a noisy business! genetic regulation at the nanomolar scale
111. Towards a circuit engineering discipline
112. Simulation of prokaryotic genetic circuits
113. Mist: A user-friendly metabolic simulator
114. GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems
115. Circuit simulation of genetic networks
116. Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation
117. Structural genomics: Bioinformatics in the driver's seat