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Overview of the SAMPL5 host-guest challenge: Are we doing better?
Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. Yin J, et al. J Comput Aided Mol Des. 2017 Jan;31(1):1-19. doi: 10.1007/s10822-016-9974-4. Epub 2016 Sep 22. J Comput Aided Mol Des. 2017. PMID: 27658802 Free PMC article. Review.
D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings.
Gaieb Z, Parks CD, Chiu M, Yang H, Shao C, Walters WP, Lambert MH, Nevins N, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK. Gaieb Z, et al. J Comput Aided Mol Des. 2019 Jan;33(1):1-18. doi: 10.1007/s10822-018-0180-4. Epub 2019 Jan 10. J Comput Aided Mol Des. 2019. PMID: 30632055 Free PMC article.
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Parks CD, Gaieb Z, Chiu M, Yang H, Shao C, Walters WP, Jansen JM, McGaughey G, Lewis RA, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK. Parks CD, et al. J Comput Aided Mol Des. 2020 Feb;34(2):99-119. doi: 10.1007/s10822-020-00289-y. Epub 2020 Jan 23. J Comput Aided Mol Des. 2020. PMID: 31974851 Free PMC article.
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB Jr, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK. Gathiaka S, et al. J Comput Aided Mol Des. 2016 Sep;30(9):651-668. doi: 10.1007/s10822-016-9946-8. Epub 2016 Sep 30. J Comput Aided Mol Des. 2016. PMID: 27696240 Free PMC article.
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. Adams PD, et al. Structure. 2016 Apr 5;24(4):502-508. doi: 10.1016/j.str.2016.02.017. Structure. 2016. PMID: 27050687 Free PMC article.
Overview of the SAMPL6 host-guest binding affinity prediction challenge.
Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Rizzi A, et al. J Comput Aided Mol Des. 2018 Oct;32(10):937-963. doi: 10.1007/s10822-018-0170-6. Epub 2018 Nov 10. J Comput Aided Mol Des. 2018. PMID: 30415285 Free PMC article.
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