河北精品网站建设,国外特效网站,网站常用布局方法,wordpress添加视频相册机器学习的打分方程集合 受到机器学习#xff08;Machine Learning#xff09;和深度学习#xff08;Deep Learning#xff09;等算法模型的创新性冲击#xff0c;其应用范围涵盖了自然语言处理#xff08;Natural Language Processing#xff09;、自动驾驶#xff08…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 RD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
ModelAlgorithmRpRMSEReferenceAGL-ScoreGBT0.831.27[13]ECIFGBT0.871.17[14]AEScoreMLP0.831.22[15]OnionNet-2CNN0.861.16[16]graphDeltaGNN0.871.05[17]PointTransformerCNNATT0.851.19[18]
2. 机器学习打分方程
Scoring FunctionAlgorithmDescription of protein–ligand complexesReferenceRF-ScoreRFProtein−ligand atom-type pair countsBallester et al. (2010)NN-Score 2.0ANNAutodock Vina interaction terms, protein−ligand atom-type pair counts and electrostatic terms (BINANA)Durrant and McCammon (2011)ID-ScoreSVMNine categories of descriptors related to protein–ligand interactionsLi et al. (2013)SFCscore R F ^{RF} RFRFSFCscore interaction termsZilian and Sotriffer (2013)ΔVinaRF 20 _{20} 20RFAutodock Vina interaction terms and additional molecular descriptorsWang and Zhang (2017)RI-ScoreRFRigidity index descriptorsNguyen et al. (2017)TNet-BPCNNAlgebraic topologyCang and Wei (2017)K D E E P _{DEEP} DEEPCNNMolecular descriptors embedded into a 3D gridJiménez et al. (2018)TopBP-MLGBTAlgebraic topologyCang et al. (2018)TopBP-DLCNNAlgebraic topologyCang et al. (2018)PafnucyCNNMolecular descriptors embedded into a 3D gridStepniewska-Dziubinska et al. (2018)PLEC-nnDNNHashed fingerprint constructed by pairing ligand and protein atoms according to its environmentWójcikowski et al. (2019)EIC-ScoreGBTDifferential geometry representationsNguyen and Wei (2019b)AGL-ScoreGBTStatistical features of the adjacency and Laplacian matrices of multiscale weighted labeled algebraic subgraphsNguyen and Wei (2019a)OnionNetCNNRotation-free element pair-specific contacts between ligands and protein atoms, grouped into different distance rangesZheng et al. (2019)ΔVinaXGBXGBTAutodock Vina score and molecular descriptors, including water moleculesLu et al. (2019)NNScore::LDFFNNNNScore 2.0 features and RDKit ligand descriptorsBoyles et al. (2020)RosENetCNNMolecular mechanics energies from Rosetta force field and molecular descriptors embedded onto a 3D gridHassan-Harrirou et al. (2020)ECIF-GBTGBTProtein−ligand atom-type pair counts considering each atoms connectivityNorberto et al. (2021)ECIF::LD-GBTGBTProtein−ligand atom-type pair counts considering each atoms connectivity and RDKit ligand descriptorsNorberto et al. (2021)
