A practical guide to large-scale docking
Abstract Structure-based docking screens of large compound libraries have become
common in early drug and probe discovery. As computer efficiency has improved and …
common in early drug and probe discovery. As computer efficiency has improved and …
Molecular docking: challenges, advances and its use in drug discovery perspective
S Saikia, M Bordoloi - Current drug targets, 2019 - ingentaconnect.com
Molecular docking is a process through which small molecules are docked into the
macromolecular structures for scoring its complementary values at the binding sites. It is a …
macromolecular structures for scoring its complementary values at the binding sites. It is a …
Synthon-based ligand discovery in virtual libraries of over 11 billion compounds
AA Sadybekov, AV Sadybekov, Y Liu… - Nature, 2022 - nature.com
Abstract Structure-based virtual ligand screening is emerging as a key paradigm for early
drug discovery owing to the availability of high-resolution target structures,,–and ultra-large …
drug discovery owing to the availability of high-resolution target structures,,–and ultra-large …
Role of molecular dynamics and related methods in drug discovery
Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …
Methods of protein structure comparison
I Kufareva, R Abagyan - Homology modeling: Methods and protocols, 2012 - Springer
Despite its apparent simplicity, the problem of quantifying the differences between two
structures of the same protein or complex is nontrivial and continues evolving. In this …
structures of the same protein or complex is nontrivial and continues evolving. In this …
Structure-based virtual screening for drug discovery: a problem-centric review
Abstract Structure-based virtual screening (SBVS) has been widely applied in early-stage
drug discovery. From a problem-centric perspective, we reviewed the recent advances and …
drug discovery. From a problem-centric perspective, we reviewed the recent advances and …
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 …
Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins
A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …
Docking and scoring with ICM: the benchmarking results and strategies for improvement
Flexible docking and scoring using the internal coordinate mechanics software (ICM) was
benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the …
benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the …
Challenges and advances in computational docking: 2009 in review
E Yuriev, M Agostino… - Journal of Molecular …, 2011 - Wiley Online Library
Docking is a computational technique that places a small molecule (ligand) in the binding
site of its macromolecular target (receptor) and estimates its binding affinity. This review …
site of its macromolecular target (receptor) and estimates its binding affinity. This review …