Lee, Seho Seok, Chaok Park, Hahnbeom 2024-01-19T09:33:31Z 2024-01-19T09:33:31Z 2023-03-23 2023-05 0192-8651 https://pubs.kist.re.kr/handle/201004/113780 Cryo-electron microscopy (cryo-EM) is gaining large attention for high-resolution protein structure determination in solutions. However, a very high percentage of cryo-EM structures correspond to resolutions of 3-5 & Aring;, making the structures difficult to be used in in silico drug design. In this study, we analyze how useful cryo-EM protein structures are for in silico drug design by evaluating ligand docking accuracy. From realistic cross-docking scenarios using medium resolution (3-5 & Aring;) cryo-EM structures and a popular docking tool Autodock-Vina, only 20% of docking succeeded, when the success rate doubles in the same kind of cross-docking but using high-resolution (< 2 & Aring;) crystal structures instead. We decipher the reason for failures by decomposing the contribution from resolution-dependent and independent factors. The heterogeneity in the protein side-chain and backbone conformations is identified as the major resolution-dependent factor causing docking difficulty from our analysis, while intrinsic receptor flexibility mainly comprises the resolution independent factor. We demonstrate the flexibility implementation in current ligand docking tools is able to rescue only a portion of failures (10%), and the limited performance was majorly due to potential structural errors than conformational changes. Our work suggests the strong necessity of more robust method developments on ligand docking and EM modeling techniques in order to fully utilize cryo-EM structures for in silico drug design. English John Wiley & Sons Inc. Benchmarking applicability of medium-resolution cryo-EM protein structures for structure-based drug design Article 10.1002/jcc.27091 1 Journal of Computational Chemistry, v.44, no.14, pp.1360 - 1364 Journal of Computational Chemistry 44 14 1360 1364 N scie scopus 000940818400001 2-s2.0-85149898037 Chemistry, Multidisciplinary Chemistry Article; Early Access FIT ATOMIC STRUCTURES MOLPROBITY DOCKING structure-based drug design computer-aided drug design cryo-EM structure ligand docking protein structure prediction