[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 …
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 …
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 …
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 …
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 …
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
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 …
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 …
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 …
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 …
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 …
target of the sulfonamide class of antibacterials. Resistance and toxicities associated with …