标题/作者	年份
Protein Data Bank: the single global archive for 3D macromolecular structure data Nucleic acids research 47 (D1), D520-D528	2019
Comparative assessment of scoring functions: the CASF-2016 update M Su, Q Yang, Y Du, G Feng, Z Liu, Y Li, R Wang Journal of chemical information and modeling 59 (2), 895-913	2018
Key topics in molecular docking for drug design PHM Torres, ACR Sodero, P Jofily, FP Silva-Jr International journal of molecular sciences 20 (18), 4574	2019
Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges IA Guedes, FSS Pereira, LE Dardenne Frontiers in pharmacology 9, 1089	2018
In need of bias control: evaluating chemical data for machine learning in structure-based virtual screening J Sieg, F Flachsenberg, M Rarey Journal of chemical information and modeling 59 (3), 947-961	2019
From machine learning to deep learning: Advances in scoring functions for protein–ligand docking C Shen, J Ding, Z Wang, D Cao, X Ding, T Hou Wiley Interdisciplinary Reviews: Computational Molecular Science 10 (1), e1429	2020
Best practices for alchemical free energy calculations [article v1. 0] ASJS Mey, BK Allen, HEB Macdonald, JD Chodera, DF Hahn, M Kuhn, ... Living journal of computational molecular science 2 (1)	2020
Multiscale methods in drug design bridge chemical and biological complexity in the search for cures RE Amaro, AJ Mulholland Nature Reviews Chemistry 2 (4), 0148	2018
Decision making in structure-based drug discovery: visual inspection of docking results A Fischer, M Smiesko, M Sellner, MA Lill Journal of Medicinal Chemistry 64 (5), 2489-2500	2021
D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings Z Gaieb, CD Parks, M Chiu, H Yang, C Shao, WP Walters, MH Lambert, ... Journal of computer-aided molecular design 33, 1-18	2019
Large-scale prediction of binding affinity in protein–small ligand complexes: The PRODIGY-LIG web server A Vangone, J Schaarschmidt, P Koukos, C Geng, N Citro, ME Trellet, ... Bioinformatics 35 (9), 1585-1587	2019
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations A Rizzi, T Jensen, DR Slochower, M Aldeghi, V Gapsys, D Ntekoumes, ... Journal of computer-aided molecular design 34 (5), 601-633	2020
Machine‐learning scoring functions for structure‐based drug lead optimization H Li, KH Sze, G Lu, PJ Ballester Wiley Interdisciplinary Reviews: Computational Molecular Science 10 (5), e1465	2020
The Groebke‐Blackburn‐Bienaymé Reaction A Boltjes, A Dömling European Journal of Organic Chemistry 2019 (42), 7007-7049	2019
Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it? C Geng, LC Xue, J Roel‐Touris, AMJJ Bonvin Wiley Interdisciplinary Reviews: Computational Molecular Science 9 (5), e1410	2019
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies CD Parks, Z Gaieb, M Chiu, H Yang, C Shao, WP Walters, JM Jansen, ... Journal of computer-aided molecular design 34, 99-119	2020
Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics Y Miao, A Bhattarai, J Wang Journal of chemical theory and computation 16 (9), 5526-5547	2020
Merging ligand-based and structure-based methods in drug discovery: An overview of combined virtual screening approaches J Vázquez, M López, E Gibert, E Herrero, FJ Luque Molecules 25 (20), 4723	2020
MathDL: mathematical deep learning for D3R Grand Challenge 4 DD Nguyen, K Gao, M Wang, GW Wei Journal of computer-aided molecular design 34, 131-147	2020
Are 2D fingerprints still valuable for drug discovery? K Gao, DD Nguyen, V Sresht, AM Mathiowetz, M Tu, GW Wei Physical chemistry chemical physics 22 (16), 8373-8390	2020

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