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 …
End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
Molecular dynamics simulations and novel drug discovery
X Liu, D Shi, S Zhou, H Liu, H Liu… - Expert opinion on drug …, 2018 - Taylor & Francis
Introduction: Molecular dynamics (MD) simulations can provide not only plentiful dynamical
structural information on biomacromolecules but also a wealth of energetic information …
structural information on biomacromolecules but also a wealth of energetic information …
Forging the basis for developing protein–ligand interaction scoring functions
Z Liu, M Su, L Han, J Liu, Q Yang, Y Li… - Accounts of chemical …, 2017 - ACS Publications
Conspectus In structure-based drug design, scoring functions are widely used for fast
evaluation of protein–ligand interactions. They are often applied in combination with …
evaluation of protein–ligand interactions. They are often applied in combination with …
Rigorous free energy simulations in virtual screening
Virtual high throughput screening (vHTS) in drug discovery is a powerful approach to identify
hits: when applied successfully, it can be much faster and cheaper than experimental high …
hits: when applied successfully, it can be much faster and cheaper than experimental high …
Virtual screening and molecular dynamics simulations provide insight into repurposing drugs against SARS-CoV-2 variants Spike protein/ACE2 interface
After over two years of living with Covid-19 and hundreds of million cases worldwide there is
still an unmet need to find proper treatments for the novel coronavirus, due also to the rapid …
still an unmet need to find proper treatments for the novel coronavirus, due also to the rapid …
[HTML][HTML] Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2
JF Fatriansyah, RK Rizqillah, MY Yandi… - Journal of King Saud …, 2022 - Elsevier
Molecular docking and dynamics simulations were conducted to investigate the antiviral
activity of Propolis Sulabiroin-A to inhibit the SARS-CoV-2 virus with quercetin, hesperidin …
activity of Propolis Sulabiroin-A to inhibit the SARS-CoV-2 virus with quercetin, hesperidin …
The performance of several docking programs at reproducing protein–macrolide-like crystal structures
A Castro-Alvarez, AM Costa, J Vilarrasa - Molecules, 2017 - mdpi.com
The accuracy of five docking programs at reproducing crystallographic structures of
complexes of 8 macrolides and 12 related macrocyclic structures, all with their …
complexes of 8 macrolides and 12 related macrocyclic structures, all with their …
Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations
K Liu, E Watanabe, H Kokubo - Journal of computer-aided molecular …, 2017 - Springer
The binding mode prediction is of great importance to structure-based drug design. The
discrimination of various binding poses of ligand generated by docking is a great challenge …
discrimination of various binding poses of ligand generated by docking is a great challenge …
Predicting protein–peptide interactions: benchmarking deep learning techniques and a comparison with focused docking
The accurate prediction of protein structures achieved by deep learning (DL) methods is a
significant milestone and has deeply impacted structural biology. Shortly after its release …
significant milestone and has deeply impacted structural biology. Shortly after its release …