Molecular docking: a powerful approach for structure-based drug discovery
Molecular docking has become an increasingly important tool for drug discovery. In this
review, we present a brief introduction of the available molecular docking methods, and their …
review, we present a brief introduction of the available molecular docking methods, and their …
Principles of docking: An overview of search algorithms and a guide to scoring functions
The docking field has come of age. The time is ripe to present the principles of docking,
reviewing the current state of the field. Two reasons are largely responsible for the maturity …
reviewing the current state of the field. Two reasons are largely responsible for the maturity …
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
This paper describes the development of a simple empirical scoringfunction designed to
estimate the free energy of binding for aprotein–ligand complex when the 3D structure of the …
estimate the free energy of binding for aprotein–ligand complex when the 3D structure of the …
Knowledge-based scoring function to predict protein-ligand interactions
The development and validation of a new knowledge-based scoring function (DrugScore) to
describe the binding geometry of ligands in proteins is presented. It discriminates efficiently …
describe the binding geometry of ligands in proteins is presented. It discriminates efficiently …
A general and fast scoring function for protein− ligand interactions: a simplified potential approach
A fast, simplified potential-based approach is presented that estimates the protein− ligand
binding affinity based on the given 3D structure of a protein− ligand complex. This general …
binding affinity based on the given 3D structure of a protein− ligand complex. This general …
Approaches to the description and prediction of the binding affinity of small‐molecule ligands to macromolecular receptors
The influence of a xenobiotic compound on an organism is usually summarized by the
expression biological activity. If a controlled, therapeutically relevant, and regulatory action …
expression biological activity. If a controlled, therapeutically relevant, and regulatory action …
Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction
The distance‐dependent structure‐derived potentials developed so far all employed a
reference state that can be characterized as a residue (atom)‐averaged state. Here, we …
reference state that can be characterized as a residue (atom)‐averaged state. Here, we …
Inhibitors of HIV-1 protease: a major success of structure-assisted drug design
▪ Abstract Retroviral protease (PR) from the human immunodeficiency virus type 1 (HIV-1)
was identified over a decade ago as a potential target for structure-based drug design. This …
was identified over a decade ago as a potential target for structure-based drug design. This …
[HTML][HTML] Determination of atomic desolvation energies from the structures of crystallized proteins
We estimated effective atomic contact energies (ACE), the desolvation free energies
required to transfer atoms from water to a protein's interior, using an adaptation of a method …
required to transfer atoms from water to a protein's interior, using an adaptation of a method …
Thermodynamics of protein–ligand interactions: history, presence, and future aspects
R Perozzo, G Folkers, L Scapozza - Journal of Receptors and …, 2004 - Taylor & Francis
The understanding of molecular recognition processes of small ligands and biological
macromolecules requires a complete characterization of the binding energetics and …
macromolecules requires a complete characterization of the binding energetics and …