Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

By Shengyou Huang, S. Grinter, Xiaoqin Zou. 2010

453 citations recorded by the source corpus.

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 interactions is still a challenge in molecular docking. In this perspective, we have reviewed three basic types of scoring functions (force-field, empirical, and knowledge-based) and the consensus scoring technique used in protein-ligand docking. The commonly-used criteria/methods and publicly available protein-ligand databases that are used to evaluate the performance of scoring functions are also depicted and discussed. We end with a discussion of the challenges faced by existing scoring functions and possible future directions for developing improved scoring functions.

Subfields: Computational Theory and Mathematics, Molecular Biology, Organic Chemistry, Computational Chemistry & Drug Discovery

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

In Molecular Biology

In Organic Chemistry

In Computational Chemistry & Drug Discovery

Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, background): “Scoring functions are categorized in the three following groups: force-field-based, empirical, and knowledge-based functions [56].”
Score_set: A CAPRI benchmark for scoring protein complexes (2014, background): “9 The energy terms may represent physics-based residue or atom pair potentials,10,11 or a statistical simplification thereof.”
Virtual screening strategies in drug discovery: a critical review. (2013, background): “Scoring functions developed during the last few years have been reviewed in other works [67, 68].”
Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, methodology): “Since empirical scoring functions comprise many energy terms, another challenge is how to avoid double-counting problems (over-fitting) [183].”
Role of computer-aided drug design in modern drug discovery (2015, background): “Frequently used scoring functions, as reported in several papers (Huang et al. 2010; Cheng et al. 2012; Lavecchia and Di Giovanni 2013; Liu and Wang 2015), are divided into three categories: (a) Force ﬁeld - based functions calculate binding afﬁnity derived from physical atomic contacts in the…”
Structure-Based Virtual Screening: From Classical to Artificial Intelligence (2020, methodology): “A linear regression is then performed as a way of predicting the values of some variables (Huang et al., 2010).”