Physics-based enzyme design: Predicting binding affinity and catalytic activity

Proteins: Structure, Function and Bioinformatics

Volumn 82, Issue 12, 2014, Pages 3397-3409

  Sirin, Sarah ^a   Pearlman, David A ^b   Sherman, Woody ^b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b SCHRÖDINGER INC   (United States)

Author keywords

Automated workflow; Binding optimization; Computational enzyme design; DIG binder protein; Kemp eliminase (KE07); Ranking; Structure based design; Transition state optimization; gliadin peptidase

Indexed keywords

ALPHA GLIADIN PEPTIDASE; BACTERIAL PROTEIN; ENZYME VARIANT; KEMP ELIMINASE; LYASE; PEPTIDASE; PROTEIN PRECURSOR; STEROID BINDING PROTEIN; UNCLASSIFIED DRUG; GLIADIN; ISOXAZOLE DERIVATIVE; MUTANT PROTEIN; SERINE PROTEINASE; SEX HORMONE BINDING GLOBULIN; SOLVENT;

ARTICLE; BINDING AFFINITY; CATALYSIS; CATALYTIC EFFICIENCY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME CONFORMATION; ENZYME METABOLISM; ENZYME STABILITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; MOLECULAR DYNAMICS; PHYSICS; PRIORITY JOURNAL; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; DIRECTED MOLECULAR EVOLUTION; ENERGY TRANSFER; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; LABORATORY AUTOMATION; METABOLISM; PROCEDURES; PROTEIN DATABASE; PROTEIN ENGINEERING; PSEUDOMONAS AERUGINOSA; SURFACE PROPERTY;

AUTOMATION, LABORATORY; BACTERIAL PROTEINS; BINDING SITES; CATALYTIC DOMAIN; DATABASES, PROTEIN; DIRECTED MOLECULAR EVOLUTION; ENERGY TRANSFER; GLIADIN; ISOXAZOLES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; MUTANT PROTEINS; PHYSICS; PROTEIN ENGINEERING; PSEUDOMONAS AERUGINOSA; SERINE ENDOPEPTIDASES; SEX HORMONE-BINDING GLOBULIN; SOFTWARE VALIDATION; SOLVENTS; SUBSTRATE SPECIFICITY; SURFACE PROPERTIES;

EID: 84937486849     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24694     Document Type: Article

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