A medicinal chemist's guide to molecular interactions
Molecular recognition in biological systems relies on the existence of specific attractive
interactions between two partner molecules. Structure-based drug design seeks to identify …
interactions between two partner molecules. Structure-based drug design seeks to identify …
Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description
F Spyrakis, CN Cavasotto - Archives of biochemistry and biophysics, 2015 - Elsevier
Abstract Structure-based virtual screening is currently an established tool in drug lead
discovery projects. Although in the last years the field saw an impressive progress in terms …
discovery projects. Although in the last years the field saw an impressive progress in terms …
Synopsis of some recent tactical application of bioisosteres in drug design
NA Meanwell - Journal of medicinal chemistry, 2011 - ACS Publications
The concept of isosterism between relatively simple chemical entities was originally
contemplated by James Moir in 1909, a notion further refined by HG Grimm's hydride …
contemplated by James Moir in 1909, a notion further refined by HG Grimm's hydride …
A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking
In modeling ligand–protein interactions, the representation and role of water are of great
importance. We introduce a force field and hydration docking method that enables the …
importance. We introduce a force field and hydration docking method that enables the …
Classification of water molecules in protein binding sites
C Barillari, J Taylor, R Viner… - Journal of the American …, 2007 - ACS Publications
Water molecules play a crucial role in mediating the interaction between a ligand and a
macromolecular receptor. An understanding of the nature and role of each water molecule in …
macromolecular receptor. An understanding of the nature and role of each water molecule in …
Rapid and accurate prediction and scoring of water molecules in protein binding sites
Water plays a critical role in ligand-protein interactions. However, it is still challenging to
predict accurately not only where water molecules prefer to bind, but also which of those …
predict accurately not only where water molecules prefer to bind, but also which of those …
Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST
The expulsion of water from surfaces upon molecular recognition and nonspecific
association makes a major contribution to the free energy changes of these processes. In …
association makes a major contribution to the free energy changes of these processes. In …
Thermodynamics of water in an enzyme active site: grid-based hydration analysis of coagulation factor Xa
Water molecules in the active site of an enzyme occupy a complex, heterogeneous
environment, and the thermodynamic properties of active-site water are functions of position …
environment, and the thermodynamic properties of active-site water are functions of position …
Ligand− protein docking with water molecules
BC Roberts, RL Mancera - Journal of chemical information and …, 2008 - ACS Publications
The presence of water molecules plays an important role in the accuracy of ligand− protein
docking predictions. Comprehensive docking simulations have been performed on a large …
docking predictions. Comprehensive docking simulations have been performed on a large …
Dowser++, a new method of hydrating protein structures
A Morozenko, AA Stuchebrukhov - Proteins: Structure, Function …, 2016 - Wiley Online Library
ABSTRACT A new method of hydrating protein structures, which we call Dowser++, is
presented. The method is based on a semi‐empirical modification of a popular program for …
presented. The method is based on a semi‐empirical modification of a popular program for …