An Efficient Computational Method for Calculating Ligand Binding Affinities
نویسندگان
چکیده
منابع مشابه
An Efficient Computational Method for Calculating Ligand Binding Affinities
Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, the docking scores are not sufficiently precise to represent the protein-ligand binding affinity. Here, we developed an efficient computational method for calculating protein-ligand binding affinity, which is based on molecular mechanics generalized Born/surface are...
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Understanding and controlling biological phenomena via structure-based drug screening efforts often critically rely on accurate description of protein-ligand interactions. However, most of the currently available computational techniques are affected by severe deficiencies in both protein and ligand conformational sampling as well as in the scoring of the obtained docking solutions. To overcome...
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The binding energy distribution analysis method (BEDAM) for the computation of receptor-ligand standard binding free energies with implicit solvation is presented. The method is based on a well-established statistical mechanics theory of molecular association. It is shown that, in the context of implicit solvation, the theory is homologous to the test particle method of solvation thermodynamics...
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Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of speci...
متن کاملRecent theoretical and computational advances for modeling protein-ligand binding affinities.
We review recent theoretical and algorithmic advances for the modeling of protein ligand binding free energies. We first describe a statistical mechanics theory of noncovalent association, with particular focus on deriving the fundamental formulas on which computational methods are based. The second part reviews the main computational models and algorithms in current use or development, pointin...
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ژورنال
عنوان ژورنال: PLoS ONE
سال: 2012
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0042846