Macromolecular modeling and design in Rosetta: recent methods and frameworks JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ... Nature methods 17 (7), 665-680, 2020 | 580 | 2020 |
Protein–peptide docking: opportunities and challenges M Ciemny, M Kurcinski, K Kamel, A Kolinski, N Alam, O Schueler-Furman, ... Drug discovery today 23 (8), 1530-1537, 2018 | 266 | 2018 |
High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock N Alam, O Goldstein, B Xia, KA Porter, D Kozakov, O Schueler-Furman PLoS computational biology 13 (12), e1005905, 2017 | 129 | 2017 |
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT KA Porter, B Xia, D Beglov, T Bohnuud, N Alam, O Schueler-Furman, ... Bioinformatics 33 (20), 3299-3301, 2017 | 104 | 2017 |
Structure-based identification of HDAC8 non-histone substrates N Alam, L Zimmerman, NA Wolfson, CG Joseph, CA Fierke, ... Structure 24 (3), 458-468, 2016 | 57 | 2016 |
Modeling peptide-protein structure and binding using Monte Carlo sampling approaches: Rosetta FlexPepDock and FlexPepBind N Alam, O Schueler-Furman Modeling Peptide-Protein Interactions: Methods and Protocols, 139-169, 2017 | 34 | 2017 |
FlexPepDock lessons from CAPRI peptide–protein rounds and suggested new criteria for assessment of model quality and utility O Marcu, EJ Dodson, N Alam, M Sperber, D Kozakov, MF Lensink, ... Proteins: Structure, Function, and Bioinformatics 85 (3), 445-462, 2017 | 21 | 2017 |
Novel structural mechanism of allosteric regulation of aspartic peptidases via an evolutionarily conserved exosite I Hánová, J Brynda, R Houštecká, N Alam, D Sojka, P Kopáček, ... Cell Chemical Biology 25 (3), 318-329. e4, 2018 | 16 | 2018 |
Escherichia coli Quorum-Sensing EDF, A Peptide Generated by Novel Multiple Distinct Mechanisms and Regulated by trans-Translation S Kumar, I Kolodkin-Gal, O Vesper, N Alam, O Schueler-Furman, I Moll, ... MBio 7 (1), 10.1128/mbio. 02034-15, 2016 | 16 | 2016 |
Host FIH-Mediated Asparaginyl Hydroxylation of Translocated Legionella pneumophila Effectors C Price, M Merchant, S Jones, A Best, J Von Dwingelo, MB Lawrenz, ... Frontiers in cellular and infection microbiology 7, 54, 2017 | 15 | 2017 |
Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45 A Khramushin, O Marcu, N Alam, O Shimony, D Padhorny, E Brini, KA Dill, ... Proteins: Structure, Function, and Bioinformatics 88 (8), 1037-1049, 2020 | 11 | 2020 |
ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking D Padhorny, KA Porter, M Ignatov, A Alekseenko, D Beglov, S Kotelnikov, ... Proteins: Structure, Function, and Bioinformatics 88 (8), 1082-1090, 2020 | 9 | 2020 |
The PfRCR complex bridges malaria parasite and erythrocyte during invasion B Farrell, N Alam, MN Hart, A Jamwal, RJ Ragotte, H Walters-Morgan, ... Nature 625 (7995), 578-584, 2024 | 5 | 2024 |
A spike with which to beat COVID-19? N Alam, MK Higgins Nature Reviews Microbiology, 2020 | 5 | 2020 |
MinD-RNase E interplay controls localization of polar mRNAs in E. coli S Kannaiah, O Goldberger, N Alam, G Barnabas, Y Pozniak, ... The EMBO Journal 43 (4), 637-662, 2024 | 1 | 2024 |
Rational structure-guided design of a blood stage malaria vaccine immunogen presenting a single epitope from PfRH5 T Harrison, N Alam, B Farrell, D Quinkert, A Lias, L King, SJ Draper, ... bioRxiv, 2024.02. 29.582763, 2024 | | 2024 |