ReviewCurrent protein & peptide science2009
Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.
Review in Current protein & peptide science, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Structural basis for selective and potent degradation of IRAK4 by KT-474.Nature communications · 2026Article
- Kinetics-Based State Definitions for Discrete Binding Conformations of T4 L99A in MD via Markov State Modeling.Journal of chemical information and modeling · 2024Article
- Total free energy analysis of fully hydrated proteins.Proteins · 2023Article
- Article
- Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface.Entropy (Basel, Switzerland) · 2022Article
- Vibrational Entropy of Crystalline Solids from Covariance of Atomic Displacements.Entropy (Basel, Switzerland) · 2022Article
- Bridging solvent molecules mediate RNase A - Ligand binding.PloS one · 2019Article
- Determinants of human glucokinase activation and implications for small molecule allosteric control.Biochimica et biophysica acta. General subjects · 2018Article
- Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aβ) Antibodies.The journal of physical chemistry. B · 2018Article
- Calculating free energies of organic molecules on insulating substrates.Beilstein journal of nanotechnology · 2017Article
- Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads.Scientific reports · 2015Article
- Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.The Journal of chemical physics · 2014Article
- A simplified confinement method for calculating absolute free energies and free energy and entropy differences.The journal of physical chemistry. B · 2013Article
- Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space.Journal of computational chemistry · 2011Article
- Exploring the free-energy landscapes of biological systems with steered molecular dynamics.Physical chemistry chemical physics : PCCP · 2011Article
- Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors.Journal of molecular modeling · 2011Article
- T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles.Journal of computer-aided molecular design · 2010Article
- Thermal nanostructure: an order parameter multiscale ensemble approach.The Journal of chemical physics · 2010Article
- Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties.Journal of chemical theory and computation · 2009Article
- Article
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Authors and funding
3 authors.
Funding
Abstract
The Helmholtz free energy, F and the entropy, S are related thermodynamic quantities with a special importance in structural biology. We describe the difficulties in calculating these quantities and review recent methodological developments. Because protein flexibility is essential for function and ligand binding, we discuss the related problems involved in the definition, simulation, and free energy calculation of microstates (such as the alpha-helical region of a peptide). While the review is broad, a special emphasize is given to methods for calculating the absolute F (S), where our HSMC(D) method is described in some detail.
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Registered trials
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