机器学习的打分方程集合

  受到机器学习（Machine Learning）和深度学习（Deep Learning）等算法模型的创新性冲击，其应用范围涵盖了自然语言处理（Natural Language Processing）、自动驾驶（Autopilot）、金融分析（Financial analysis）和生物医药研发（Biopharmaceutical R&D）等多个领域。其中，应用深度学习算法在预测小分子药物与疾病靶点蛋白之间的结合亲和力方面的设计和应用变得日益重要。分子对接(Molecular Docking)计算中打分方程(Scoring Function)算法通常用于对药物活性数据进行评估、分类、排名或预测，其结果对于决策制定候选药物分子而言至关重要。因此，本文将介绍一些基于机器学习和深度学习的打分方程。

1. 亲和力预测模型

Model	Algorithm	Rp	RMSE	Reference
AGL-Score	GBT	0.83	1.27	[13]
ECIF	GBT	0.87	1.17	[14]
AEScore	MLP	0.83	1.22	[15]
OnionNet-2	CNN	0.86	1.16	[16]
graphDelta	GNN	0.87	1.05	[17]
PointTransformer	CNN+ATT	0.85	1.19	[18]

2. 机器学习打分方程

Scoring Function	Algorithm	Description of protein–ligand complexes	Reference
RF-Score	RF	Protein−ligand atom-type pair counts	Ballester et al. (2010)
NN-Score 2.0	ANN	Autodock Vina interaction terms, protein−ligand atom-type pair counts and electrostatic terms (BINANA)	Durrant and McCammon (2011)
ID-Score	SVM	Nine categories of descriptors related to protein–ligand interactions	Li et al. (2013)
SFCscore${}^{RF}$	RF	SFCscore interaction terms	Zilian and Sotriffer (2013)
ΔVinaRF${}_{20}$	RF	Autodock Vina interaction terms and additional molecular descriptors	Wang and Zhang (2017)
RI-Score	RF	Rigidity index descriptors	Nguyen et al. (2017)
TNet-BP	CNN	Algebraic topology	Cang and Wei (2017)
K${}_{DEEP}$	CNN	Molecular descriptors embedded into a 3D grid	Jiménez et al. (2018)
TopBP-ML	GBT	Algebraic topology	Cang et al. (2018)
TopBP-DL	CNN	Algebraic topology	Cang et al. (2018)
Pafnucy	CNN	Molecular descriptors embedded into a 3D grid	Stepniewska-Dziubinska et al. (2018)
PLEC-nn	DNN	Hashed fingerprint constructed by pairing ligand and protein atoms according to its environment	Wójcikowski et al. (2019)
EIC-Score	GBT	Differential geometry representations	Nguyen and Wei (2019b)
AGL-Score	GBT	Statistical features of the adjacency and Laplacian matrices of multiscale weighted labeled algebraic subgraphs	Nguyen and Wei (2019a)
OnionNet	CNN	Rotation-free element pair-specific contacts between ligands and protein atoms, grouped into different distance ranges	Zheng et al. (2019)
ΔVinaXGB	XGBT	Autodock Vina score and molecular descriptors, including water molecules	Lu et al. (2019)
NNScore::LD	FFNN	NNScore 2.0 features and RDKit ligand descriptors	Boyles et al. (2020)
RosENet	CNN	Molecular mechanics energies from Rosetta force field and molecular descriptors embedded onto a 3D grid	Hassan-Harrirou et al. (2020)
ECIF-GBT	GBT	Protein−ligand atom-type pair counts considering each atoms connectivity	Norberto et al. (2021)
ECIF::LD-GBT	GBT	Protein−ligand atom-type pair counts considering each atoms connectivity and RDKit ligand descriptors	Norberto et al. (2021)