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Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.
Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant M, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Lawson CL, et al. Among authors: mondal a. Res Sq [Preprint]. 2024 Jan 25:rs.3.rs-3864137. doi: 10.21203/rs.3.rs-3864137/v1. Res Sq. 2024. PMID: 38343795 Free PMC article. Preprint.
CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps.
Shekhar M, Terashi G, Gupta C, Sarkar D, Debussche G, Sisco NJ, Nguyen J, Mondal A, Vant J, Fromme P, Van Horn WD, Tajkhorshid E, Kihara D, Dill K, Perez A, Singharoy A. Shekhar M, et al. Among authors: mondal a. Matter. 2021 Oct 6;4(10):3195-3216. doi: 10.1016/j.matt.2021.09.004. Epub 2021 Sep 22. Matter. 2021. PMID: 35874311 Free PMC article.
Towards rational computational peptide design.
Chang L, Mondal A, Perez A. Chang L, et al. Among authors: mondal a. Front Bioinform. 2022 Oct 21;2:1046493. doi: 10.3389/fbinf.2022.1046493. eCollection 2022. Front Bioinform. 2022. PMID: 36338806 Free PMC article.
CryoFold 2.0: Cryo-EM Structure Determination with MELD.
Chang L, Mondal A, MacCallum JL, Perez A. Chang L, et al. Among authors: mondal a. J Phys Chem A. 2023 May 4;127(17):3906-3913. doi: 10.1021/acs.jpca.3c01731. Epub 2023 Apr 21. J Phys Chem A. 2023. PMID: 37084537
1,405 results