Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power
Z Wang, H Sun, X Yao, D Li, L Xu, Y Li… - Physical Chemistry …, 2016 - pubs.rsc.org
As one of the most popular computational approaches in modern structure-based drug
design, molecular docking can be used not only to identify the correct conformation of a …
design, molecular docking can be used not only to identify the correct conformation of a …
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 …
VoteDock: consensus docking method for prediction of protein–ligand interactions
D Plewczynski, M Łażniewski… - Journal of …, 2011 - Wiley Online Library
Molecular recognition plays a fundamental role in all biological processes, and that is why
great efforts have been made to understand and predict protein–ligand interactions. Finding …
great efforts have been made to understand and predict protein–ligand interactions. Finding …
An overview of scoring functions used for protein–ligand interactions in molecular docking
J Li, A Fu, L Zhang - Interdisciplinary Sciences: Computational Life …, 2019 - Springer
Currently, molecular docking is becoming a key tool in drug discovery and molecular
modeling applications. The reliability of molecular docking depends on the accuracy of the …
modeling applications. The reliability of molecular docking depends on the accuracy of the …
PSI‐DOCK: Towards highly efficient and accurate flexible ligand docking
We have developed a new docking method, Pose‐Sensitive Inclined (PSI)‐DOCK, for
flexible ligand docking. An improved SCORE function has been developed and used in PSI …
flexible ligand docking. An improved SCORE function has been developed and used in PSI …
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 …
A new, improved hybrid scoring function for molecular docking and scoring based on AutoDock and AutoDock Vina
VY Tanchuk, VO Tanin, AI Vovk… - Chemical biology & drug …, 2016 - Wiley Online Library
Automated docking is one of the most important tools for structure‐based drug design that
allows prediction of ligand binding poses and also provides an estimate of how well small …
allows prediction of ligand binding poses and also provides an estimate of how well small …
Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results
Our comparative assessment of scoring functions (CASF) benchmark is created to provide
an objective evaluation of current scoring functions. The key idea of CASF is to compare the …
an objective evaluation of current scoring functions. The key idea of CASF is to compare the …
Supervised consensus scoring for docking and virtual screening
R Teramoto, H Fukunishi - Journal of chemical information and …, 2007 - ACS Publications
Docking programs are widely used to discover novel ligands efficiently and can predict
protein− ligand complex structures with reasonable accuracy and speed. However, there is …
protein− ligand complex structures with reasonable accuracy and speed. However, there is …
Are scoring functions in protein− protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark
PL Kastritis, AMJJ Bonvin - Journal of proteome research, 2010 - ACS Publications
The design of an ideal scoring function for protein− protein docking that would also predict
the binding affinity of a complex is one of the challenges in structural proteomics. Such a …
the binding affinity of a complex is one of the challenges in structural proteomics. Such a …
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