The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

Journal of Computational Chemistry

Volumn 29, Issue 10, 2008, Pages 1527-1542

  Georgiev, Ivelin ^a   Lilien, Ryan H ^b   Donald, Bruce R ^a  

^a DUKE UNIVERSITY   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Conformational ensembles; Dead end elimination; Partition functions; Protein design; Provably accurate algorithms; Rotameric energy minimization

Indexed keywords

ALGORITHMS; BIOCHEMISTRY; BOOLEAN FUNCTIONS; CHEMOTHERAPY; COMBINATORIAL MATHEMATICS; CONFORMATIONS; DRUG DELIVERY; DRUG DOSAGE; FORECASTING; FUNCTION EVALUATION; HEURISTIC PROGRAMMING; LEARNING ALGORITHMS; PROCESS DESIGN; PROCESS ENGINEERING;

(ALGORITHMIC) COMPLEXITY; (N-1) CRITERION; AND SEARCH ALGORITHM; BIOLOGICAL ACTIVITIES; COMPUTATIONAL PREDICTIONS; COMPUTER AIDED DRUG DESIGN (CADD); DEAD-END ELIMINATION (DEE); ENERGY MINIMIZATIONS; GLOBAL MINIMUM (GM); LIGAND BINDING; LOW ENERGIES; LOWER ENERGIES; MOLECULAR ENSEMBLES; PARTITION FUNCTIONS; PROTEIN DESIGN; PROTEIN FLEXIBILITY; PROTEIN MUTANTS; ROTAMER; ROTAMERS; SIDE CHAINS;

TELEMETERING SYSTEMS;

ISOMERASE; PHENYLALANINE; PHENYLALANINE RACEMASE (ATP HYDROLYZING); PHENYLALANINE RACEMASE (ATP-HYDROLYZING); PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMISTRY; DRUG DESIGN; PROTEIN CONFORMATION; THERMODYNAMICS;

ALGORITHMS; AMINO ACID ISOMERASES; DRUG DESIGN; MODELS, CHEMICAL; PHENYLALANINE; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 46449106372     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20909     Document Type: Article

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