[HTML][HTML] Advances and challenges in protein-ligand docking

SY Huang, X Zou - International journal of molecular sciences, 2010 - mdpi.com
Molecular docking is a widely-used computational tool for the study of molecular recognition,
which aims to predict the binding mode and binding affinity of a complex formed by two or …

Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions

SY Huang, SZ Grinter, X Zou - Physical Chemistry Chemical Physics, 2010 - pubs.rsc.org
The scoring function is one of the most important components in structure-based drug
design. Despite considerable success, accurate and rapid prediction of protein–ligand …

Rapid context-dependent ligand desolvation in molecular docking

MM Mysinger, BK Shoichet - Journal of chemical information and …, 2010 - ACS Publications
In structure-based screens for new ligands, a molecular docking algorithm must rapidly
score many molecules in multiple configurations, accounting for both the ligand's …

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

S Pérot, O Sperandio, MA Miteva, AC Camproux… - Drug discovery today, 2010 - Elsevier
Detection, comparison and analyses of binding pockets are pivotal to structure-based drug
design endeavors, from hit identification, screening of exosites and de-orphanization of …

DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility

I Antes - Proteins: Structure, Function, and Bioinformatics, 2010 - Wiley Online Library
Molecular docking programs play an important role in drug development and many well‐
established methods exist. However, there are two situations for which the performance of …

Evaluation of the performance of four molecular docking programs on a diverse set of protein‐ligand complexes

X Li, Y Li, T Cheng, Z Liu… - Journal of computational …, 2010 - Wiley Online Library
Many molecular docking programs are available nowadays, and thus it is of great practical
value to evaluate and compare their performance. We have conducted an extensive …

Comparison of structure‐and ligand‐based virtual screening protocols considering hit list complementarity and enrichment factors

DM Krüger, A Evers - ChemMedChem: Chemistry Enabling …, 2010 - Wiley Online Library
Abstract Structure‐and ligand‐based virtual‐screening methods (docking, 2D‐and 3D‐
similarity searching) were analysed for their effectiveness in virtual screening against four …

MolDock applied to structure-based virtual screening

J De Azevedo, F Walter - Current drug targets, 2010 - ingentaconnect.com
Molecular docking is a simulation process where the binding of a small molecule is
identified in the structure of a protein target. There are several different computational …

Cheminformatic tools for medicinal chemists

SW Muchmore, JJ Edmunds, KD Stewart… - Journal of medicinal …, 2010 - ACS Publications
Cheminformatics can be broadly described as any attempt to use chemical information to
infer the relationships between or attributes of chemical structures. From a drug discovery …

Structural studies of pterin-based inhibitors of dihydropteroate synthase

KE Hevener, MK Yun, J Qi, ID Kerr… - Journal of medicinal …, 2010 - ACS Publications
Dihydropteroate synthase (DHPS) is a key enzyme in bacterial folate synthesis and the
target of the sulfonamide class of antibacterials. Resistance and toxicities associated with …