自然杂志 ›› 2021, Vol. 43 ›› Issue (5): 383-390.doi: 10.3969/j.issn.0253-9608.2021.05.009
所属专题: 人工智能
• 免疫化学专刊 • 上一篇
李风雷,胡乔宇,熊若凡,白芳
收稿日期:2021-05-30
出版日期:2021-10-22
发布日期:2021-10-25
通讯作者:
白芳,通信作者,研究方向:药物设计。
LI Fenglei, HU Qiaoyu, XIONG Ruofan, BAI Fang
Received:2021-05-30
Online:2021-10-22
Published:2021-10-25
摘要: 药物研发是一个长周期、高投入和高风险的过程。随着科学技术的不断革新,生物医学数据呈爆炸式增长,为深度学习技术在生物医药领域的应用带来了契机,同时也为加速新药研发赋予了前所未有的希望。文章围绕药物设计流程,简要介绍深度学习算法在药物靶标发现、分子生成、基于配体的药物设计和基于结构的药物设计4个主要环节中的应用和研究进 展。
李风雷, 胡乔宇, 熊若凡, 白芳. 基于深度学习的药物设计方法[J]. 自然杂志, 2021, 43(5): 383-390.
LI Fenglei, HU Qiaoyu, XIONG Ruofan, BAI Fang. Computational drug design methods by deep learning algorithms [J]. Chinese Journal of Nature, 2021, 43(5): 383-390.
| [1] VASWANI A, SHAZEER N, PARMAR N, et al. Attention is all you need [J]. NIPS, 2017, 17: 6000-6010. [2] DEVLIN J, CHANG M-W, LEE K, et al. BERT: pre-training of deep bidirectional transformers for language understanding [J]. NAACL-HLT, 2019, 1: 4171-4186. [3] RAMSUNDAR B, EASTMAN P, WALTERS P, et al. Deep learning for the life sciences [M]. Sevastopol: O’ Reilly Media, 2019. [4] HUANG K, FU T, GLASS L M, et al. DeepPurpose: a deep learning library for drug-target interaction prediction [J]. Bioinform, 2020, 36: 5545-5547. [5] KORSHUNOVA M, GINSBURG B, TROPSHA A, et al. OpenChem: a deep learning toolkit for computational chemistry and drug design [J]. J Chem Inf Model, 2021, 61: 7-13. [6] WANG J-C, CHU P-Y, CHEN C-M, et al. IdTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach [J]. Nucleic Acids Res, 2012, 40: 393-399. [7] LI H, GAO Z, KANG L, et al. TarFisDock: a web server for identifying drug targets with docking approach [J]. Nucleic Acids Res, 2006, 34: 219-224. [8] GONG J, CAI C, LIU X, et al. ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method [J]. Bioinform, 2013, 29: 1827-1829. [9] LIU X, OUYANG S, YU B, et al. PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach [J]. Nucleic Acids Res, 2010, 38: 609-614. [10] GFELLE R D , GROSDIDE R A , WIRT H M , e t a l . SwissTargetPrediction: a web server for target prediction of bioactive small molecules [J]. Nucleic Acids Res, 2014, 42: 32-38. [11] BAI F, MORCOS F, CHENG R R, et al. Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis [J]. Pro Natl Acad Sci USA, 2016, 113: 8051-8058. [12] ZENG X, ZHU S, LU W, et al. Target identification among known drugs by deep learning from heterogeneous networks [J]. Chem Sci, 2020, 11: 1775-1797. [13] CONG Q, ANISHCHENKO I, OVCHINNIKOV S, et al. Protein interaction networks revealed by proteome coevolution [J]. Science, 2019, 365: 185-189. [14] HASHEMIFAR S, NEYSHABUR B, KHAN A A, et al. Predicting protein-protein interactions through sequence-based deep learning [J]. Bioinform, 2018, 34: 802-810. [15] GAINZA P, SVERRISSON F, MONTI F, et al. Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning [J]. Nat Methods, 2020, 17: 184-192. [16] ALTSCHUL S F, GISH W, MILLER W, et al. Basic local alignment search tool [J]. J Mol Biol, 1990, 215: 403-410. [17] ALTSCHUL S F, MADDEN T L, SCHÄFFER A A, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J]. Nucleic Acids Res, 1997, 25: 3389-3402. [18] FINN R D, CLEMENTS J, EDDY S R. HMMER web server: interactive sequence similarity searching [J]. Nucleic Acids Res, 2011, 39: 29-37. [19] DAMIAN S, ANDREA F, STEFAN W, et al. STRING v10: protein– protein interaction networks, integrated over the tree of life [J]. Nucleic Acids Res, 2015, 43: D1. [20] KULMANOV M, KHAN M A, HOEHNDORF R. DeepGO: Predicting protein functions from sequence and interactions using a deep ontologyaware classifier [J]. Bioinform, 2017, 34(4): 660-668. [21] CAO Y, SHEN Y. TALE: transformer-based protein function annotation with joint sequence-label embedding [J]. Bioinform, 2021, 37(18): 2825-2833. [22] MA J, SHERIDAN R P, LIAW A, et al. Deep neural nets as a method for quantitative structure-activity relationships [J]. J Chem Info Model, 2015, 55: 263-274. [23] XU Y, MA J, LIAW A, et al. Demystifying multitask deep neural networks for quantitative structure-activity relationships [J]. J Chem Info Model, 2017, 57: 2490-2504. [24] SENIOR A W, EVANS R, JUMPER J, et al. Improved protein structure prediction using potentials from deep learning [J]. Nature, 2020, 577: 706-710. [25] ROHL C A, STRAUSS C E M, MISURA K M S, et al. Protein structure prediction using rosetta [J]. Meth Enzymol, 2004, 383: 66-93. [26] YANG J, ANISHCHENKO I, PARK H, et al. Improved protein structure prediction using predicted interresidue orientations [J]. Pro Natl Acad Sci USA, 2020, 117: 1496-1503. [27] CALLAWAY E. ‘It will change everything’: deepmind’s AI makes gigantic leap in solving protein structures [J]. Nature, 2020, 588: 203-204. [28] SATO K, AKIYAMA M, SAKAKIBARA Y. RNA secondary structure prediction using deep learning with thermodynamic integration [J]. Nature Comm, 2021, 12: 941. [29] SINGH J, HANSON J, PALIWAL K, et al. RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning [J]. Nature Comm, 2019, 10: 5407. [30] ZHANG H, ZHANG L, MATHEWS D H, et al. LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities [J]. Bioinform, 2020, 36: 258-267. [31] ZHANG T, SINGH J, LITFIN T, et al. RNAcmap: a fully automatic method for predicting contact maps of RNAs by evolutionary coupling analysis [J]. Bioinform, 2021. DOI: 10.1093/bioinformatics/ btab391. [32] LI J, ZHU W, WANG J, et al. RNA3DCNN: local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks [J]. PLoS Comp Biol, 2018, 14: e1006514. [33] NGAN C H, BOHNUUD T, MOTTARELLA S E, et al. FTMAP: extended protein mapping with user-selected probe molecules [J]. Nucleic Acids Res, 2012, 40: W271-W275. [34] KOZLOVSKII I, POPOV P. Spatiotemporal identification of druggable binding sites using deep learning [J]. Commun Biol, 2020, 3: 1-12. [35] LI Z, YAN X, WEI Q, et al. PointSite: a point cloud segmentation tool for identification of protein ligand binding atoms [J]. BioRxiv, 2019: 831131. DOI: 10.1101/83.1131. [36] ÖZTÜRK H, ÖZGÜR A, OZKIRIMLI E. DeepDTA: deep drugtarget binding affinity prediction [J]. Bioinform, 2018, 34: 821-829. [37] ZHENG L, FAN J, MU Y. OnionNet: a multiple-layer intermolecular-contact-based convolutional neural network for protein-ligand binding affinity prediction [J]. ACS Omega, 2019, 4: 15956-15965. [38] JIMÉNEZ J, ŠKALIČ M, MARTÍNEZ-ROSELL G, et al. KDEEP: protein-ligand absolute binding affinity prediction via 3D-convolutional neural networks [J]. J Chem Info Model, 2018, 58: 287-296. [39] HASSAN-HARRIROU H, ZHANG C, LEMMIN T. RosENet: improving binding affinity prediction by leveraging molecular mechanics energies with an ensemble of 3D convolutional neural networks [J]. J Chem Info Model, 2020, 60: 2791-2802. [40] LIN X, ZHAO K, XIAO T, et al. DeepGS: deep representation learning of graphs and sequences for drug-target binding affinity prediction [J]. ECAI, 2020: 1301-1308. [41] MÉNDEZ-LUCIO O, BAILLIF B, CLEVERT D-A, et al. De novo generation of hit-like molecules from gene expression signatures using artificial intelligence [J]. Nature Comm, 2020, 11: 10. [42] GOODFELLOW I J, POUGET-ABADIE J, MIRZA M, et al. Generative adversarial networks [J]. Commun ACM, 2020, 63: 139-144. [43] POPOVA M, ISAYEV O, TROPSHA A. Deep reinforcement learning for de novo drug design [J]. Sci Adv, 2018, 4: eaap7885. [44] KHEMCHANDANI Y, O’HAGAN S, SAMANTA S, et al. DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach [J]. J Chem , 2020, 12: 53. [45] LIU B, RAMSUNDAR B, KAWTHEKAR P, et al. Retrosynthetic reaction prediction using neural sequence-to-sequence models [J]. ACS Cent Sci, 2017, 3: 1103-1113. [46] SHI C, XU M, GUO H, et al. A graph to graphs framework for retrosynthesis prediction [J]. ICML, 2020,119: 8818-8827. [47] CHENG F, LI W, ZHOU Y, et al. AdmetSAR: A comprehensive source and free tool for assessment of chemical admet properties [J]. J Chem Info Model, 2012, 52: 3099-3105. [48] YANG H, LOU C, SUN L, et al. admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties [J]. Bioinform, 2019, 35: 1067-1069. [49] LIU K, SUN X, JIA L, et al. Chemi-net: a graph convolutional network for accurate drug property prediction [J]. Int J Mol Sci, 2019, 20: 3389. [50] WENZEL J, MATTER H, SCHMIDT F. Predictive multitask deep neural network models for adme-tox properties: learning from large data sets [J]. J Chem Info Model, 2019, 59: 1253-1268.
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