Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT

Methods in Enzymology

Volumn 553, Issue , 2015, Pages 215-234

  Kirmizialtin, Serdal ^a,b   Hennelly, Scott P ^a,b   Schug, Alexander ^c   Onuchic, Jose N ^d   Sanbonmatsu, Karissa Y ^a,b  

^a NEW MEXICO CONSORTIUM   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^d RICE UNIVERSITY   (United States)

Author keywords

Modeling; Molecular dynamics simulation; Riboswitch; RNA; SHAPE

Indexed keywords

APTAMER; BACTERIAL RNA; RNA 16S; S ADENOSYLMETHIONINE; HYDROXYL RADICAL; LIGAND; RNA;

ACYLATION; ANALYTIC METHOD; ARTICLE; AUTOMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; LIGAND BINDING; MECHANICAL TORSION; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; RIBOSWITCH; RNA ANALYSIS; RNA CONFORMATION; RNA PROBE; RNA STRUCTURE; SELECTIVE 2' HYDROXYL ACYLATION BY PRIMER EXTENSION; STRUCTURE ANALYSIS; THERMOANAEROBACTER; THERMOANAEROBACTER TENGCONGENSIS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; PROCEDURES;

ACYLATION; COMPUTATIONAL BIOLOGY; HYDROXYL RADICAL; LIGANDS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; RNA;

EID: 84923574631     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/bs.mie.2014.10.061     Document Type: Chapter

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