Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

Biopolymers

Volumn 68, Issue 1, 2003, Pages 16-34

  Gouda, Hiroaki ^a   Kuntz, Irwin D ^b   Case, David A ^b   Kollman, Peter A ^b  

^a KITASATO UNIVERSITY   (Japan)

^b NONE

Author keywords

Molecular mechanics Poisson Boltzmann surface area (MM PBSA); RNA aptamer; Theophylline; Theophylline analogs

Indexed keywords

PROTEINS; RNA; THERMODYNAMICS; VAN DER WAALS FORCES;

MOLECULAR MECHANICS;

FREE ENERGY;

1 METHYLXANTHINE; 3 METHYLXANTHINE; APTAMER; HYPOXANTHINE DERIVATIVE; RNA; THEOPHYLLINE; THEOPHYLLINE DERIVATIVE; XANTHINE;

ANALYTIC METHOD; ARTICLE; BINDING AFFINITY; CELL ENERGY; COMPLEX FORMATION; DRUG BINDING; DRUG STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR MECHANICS POISSON BOLTZMANN SURFACE AREA; PROTEIN INTERACTION; RNA BINDING; SOLVATION; STRUCTURE ANALYSIS; THERMODYNAMICS;

BINDING SITES; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; THEOPHYLLINE; THERMODYNAMICS;

EID: 0037234043     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/bip.10270     Document Type: Article

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