Unknown

Dataset Information

0

Efficient incorporation of protein flexibility and dynamics into molecular docking simulations.

ABSTRACT: Flexibility and dynamics are protein characteristics that are essential for the process of molecular recognition. Conformational changes in the protein that are coupled to ligand binding are described by the biophysical models of induced fit and conformational selection. Different concepts that incorporate protein flexibility into protein-ligand docking within the context of these two models are reviewed. Several computational studies that discuss the validity and possible limitations of such approaches will be presented. Finally, different approaches that incorporate protein dynamics, e.g., configurational entropy, and solvation effects into docking will be highlighted.

SUBMITTER: Lill MA 

PROVIDER: S-EPMC3172316 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

Efficient incorporation of protein flexibility and dynamics into molecular docking simulations.

Lill Markus A MA  

Biochemistry 20110622 28

Flexibility and dynamics are protein characteristics that are essential for the process of molecular recognition. Conformational changes in the protein that are coupled to ligand binding are described by the biophysical models of induced fit and conformational selection. Different concepts that incorporate protein flexibility into protein-ligand docking within the context of these two models are reviewed. Several computational studies that discuss the validity and possible limitations of such ap  ...[more]

Similar Datasets

Unknown BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from brownian dynamics simulations.
| S-EPMC3477184 | biostudies-other
Unknown Flexibility in a drug transport accessory protein: molecular dynamics simulations of MexA.
| S-EPMC1483075 | biostudies-literature
Unknown Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations.
| S-EPMC7534544 | biostudies-literature
Unknown Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations.
| S-EPMC6835073 | biostudies-literature
Unknown Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.
| S-EPMC8306105 | biostudies-literature
Unknown An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.
| S-EPMC2772076 | biostudies-literature
Unknown Homology modeling, molecular docking, and molecular dynamics simulations elucidated ?-fetoprotein binding modes.
| S-EPMC3851483 | biostudies-literature
Unknown Germacrone derivatives: synthesis, biological activity, molecular docking studies and molecular dynamics simulations.
| S-EPMC5362474 | biostudies-literature
Unknown Targeting N-Terminal Human Maltase-Glucoamylase to Unravel Possible Inhibitors Using Molecular Docking, Molecular Dynamics Simulations, and Adaptive Steered Molecular Dynamics Simulations.
| S-EPMC8435576 | biostudies-literature
Unknown Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.
| S-EPMC4144196 | biostudies-literature