Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation: Protein-ligand interactions in the light of the alanine scanning and free energy decomposition methods

Journal of Molecular Graphics and Modelling

Volumn 29, Issue 5, 2011, Pages 726-739

  Saíz Urra, Liane ^a,b   Cabrera, Miguel Angel ^a   Froeyen, Matheus ^b  

^a CENTRAL UNIVERSITY OF LAS VILLAS   (Cuba)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

Author keywords

Computational alanine scanning; Free energy decomposition; Inhibitors of GyrB; MM PBSA MM GBSA; Molecular dynamics

Indexed keywords

ANTI-MICROBIAL AGENT; ATP BINDING POCKETS; ATP-BINDING SITE; BACTERIAL DISEASE; BINDING MODES; CLOROBIOCIN; CLUSTERING DATA; COMPUTATIONAL ALANINE SCANNING; CONFORMATIONAL CHANGE; CONFORMATIONAL SPACE; DEATH TOLLS; DESIGN PROCESS; DNA GYRASES; ENERGY DECOMPOSITION; FREE ENERGY DECOMPOSITION; HETERODIMERS; INHIBITORS OF GYRB; INITIAL STRUCTURES; MD SIMULATION; MM-PBSA/MM-GBSA; MOLECULAR DYNAMICS SIMULATIONS; NOVOBIOCIN; PROTEIN-LIGAND INTERACTIONS; ROOT MEAN SQUARES; TEMPERATURE FACTOR; TIME DEPENDENT;

AMINO ACIDS; BINDING ENERGY; COMPUTATIONAL CHEMISTRY; DATA MINING; DYNAMICS; ESCHERICHIA COLI; FREE ENERGY; LIGANDS; MOLECULAR MECHANICS; NUCLEIC ACIDS; SCANNING;

MOLECULAR DYNAMICS;

ADENOSINE TRIPHOSPHATE; ALANINE; DNA TOPOISOMERASE (ATP HYDROLYSING) B;

ALGORITHM; ARTICLE; BINDING AFFINITY; BINDING SITE; DECOMPOSITION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION; SOLVATION; STRUCTURE ANALYSIS; TEMPERATURE MEASUREMENT;

ADENOSINE TRIPHOSPHATE; ALANINE; BACTERIAL PROTEINS; BINDING SITES; CLUSTER ANALYSIS; DNA GYRASE; ESCHERICHIA COLI; HUMANS; LIGANDS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 79751536124     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2010.12.005     Document Type: Article

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