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 …

Comparative assessment of scoring functions on a diverse test set

T Cheng, X Li, Y Li, Z Liu, R Wang - Journal of chemical …, 2009 - ACS Publications
Scoring functions are widely applied to the evaluation of protein− ligand binding in structure-
based drug design. We have conducted a comparative assessment of 16 popular scoring …

Comparative assessment of scoring functions on an updated benchmark: 1. Compilation of the test set

Y Li, Z Liu, J Li, L Han, J Liu, Z Zhao… - Journal of chemical …, 2014 - ACS Publications
Scoring functions are often applied in combination with molecular docking methods to
predict ligand binding poses and ligand binding affinities or to identify active compounds …

Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results

Y Li, L Han, Z Liu, R Wang - Journal of chemical information and …, 2014 - ACS Publications
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 …

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 …

Scoring functions for protein–ligand interactions: a critical perspective

T Schulz-Gasch, M Stahl - Drug Discovery Today: Technologies, 2004 - Elsevier
Scoring functions play an essential role in structure-based virtual screening. They are
required to guide the docking of candidate compounds to structures of receptor binding …

Comparative assessment of scoring functions: the CASF-2016 update

M Su, Q Yang, Y Du, G Feng, Z Liu, Y Li… - Journal of chemical …, 2018 - ACS Publications
In structure-based drug design, scoring functions are often employed to evaluate protein–
ligand interactions. A variety of scoring functions have been developed so far, and thus …

Ligand− protein database: Linking protein− ligand complex structures to binding data

O Roche, R Kiyama, CL Brooks - Journal of medicinal chemistry, 2001 - ACS Publications
In computational structure-based drug design, the scoring functions are the cornerstones to
the success of design/discovery. Many approaches have been explored to improve their …

Assessing protein–ligand interaction scoring functions with the CASF-2013 benchmark

Y Li, M Su, Z Liu, J Li, J Liu, L Han, R Wang - Nature protocols, 2018 - nature.com
Scoring functions are a group of computational methods widely applied in structure-based
drug design for fast evaluation of protein–ligand interactions. To date, a whole spectrum of …

Tapping on the black box: how is the scoring power of a machine-learning scoring function dependent on the training set?

M Su, G Feng, Z Liu, Y Li, R Wang - Journal of chemical …, 2020 - ACS Publications
In recent years, protein–ligand interaction scoring functions derived through machine-
learning are repeatedly reported to outperform conventional scoring functions. However …