In this revised application of his competitive renewal, Dr. Moult proposes to understand the relationship between protein structure and sequence by extending present computational search algorithms and analyzing free energy functions, as well as investigating potentials based on alternative physical methods. Dr. Moult will test and extend Monte Carlo, genetic algorithm and other co-operative algorithmic conformational search methods, test and improve potentials, use folding simulation methods to probe the extent of context independent conformational choice in fragments of protein structures and to investigate the folding of protein domains by propagation methods.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM041034-10
Application #
6164576
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Edmonds, Charles G
Project Start
1988-12-05
Project End
2002-02-28
Budget Start
2000-03-01
Budget End
2002-02-28
Support Year
10
Fiscal Year
2000
Total Cost
$139,881
Indirect Cost
Name
University of MD Biotechnology Institute
Department
Type
Organized Research Units
DUNS #
603819210
City
Baltimore
State
MD
Country
United States
Zip Code
21202
DeWeese-Scott, Carol; Moult, John (2004) Molecular modeling of protein function regions. Proteins 55:942-61
Oliva, M T; Moult, J (1999) Local electrostatic optimization in proteins. Protein Eng 12:727-35
Samudrala, R; Moult, J (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275:895-916
Samudrala, R; Moult, J (1998) Determinants of side chain conformational preferences in protein structures. Protein Eng 11:991-7
Samudrala, R; Moult, J (1998) A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol 279:287-302
Braxenthaler, M; Unger, R; Auerbach, D et al. (1997) Chaos in protein dynamics. Proteins 29:417-25
Samudrala, R; Moult, J (1997) Handling context-sensitivity in protein structures using graph theory: bona fide prediction. Proteins Suppl 1:43-9
Pedersen, J T; Moult, J (1997) Ab initio protein folding simulations with genetic algorithms: simulations on the complete sequence of small proteins. Proteins Suppl 1:179-84
Pedersen, J T; Moult, J (1995) Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms. Proteins 23:454-60
Braxenthaler, M; Avbelj, F; Moult, J (1995) Structure, dynamics and energetics of initiation sites in protein folding: I. Analysis of a 1 ns molecular dynamics trajectory of an early folding unit in water: the helix I/loop I-fragment of barnase. J Mol Biol 250:239-57

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