Mondal A - Search Results

1

Revolutionizing Peptide-Based Drug Discovery: Advances in the Post-AlphaFold Era.

Chang L, Mondal A, Singh B, Martínez-Noa Y, Perez A. Chang L, et al. Among authors: mondal a. Wiley Interdiscip Rev Comput Mol Sci. 2024 Jan-Feb;14(1):e1693. doi: 10.1002/wcms.1693. Epub 2023 Nov 12. Wiley Interdiscip Rev Comput Mol Sci. 2024. PMID: 38680429

2

Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets.

Mondal A, Perez A. Mondal A, et al. Front Mol Biosci. 2021 Nov 24;8:774394. doi: 10.3389/fmolb.2021.774394. eCollection 2021. Front Mol Biosci. 2021. PMID: 34912846 Free PMC article.

3

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.

4

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.

5

Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations.

Mondal A, Swapna GVT, Lopez MM, Klang L, Hao J, Ma L, Roth MJ, Montelione GT, Perez A. Mondal A, et al. J Chem Inf Model. 2023 Apr 10;63(7):2058-2072. doi: 10.1021/acs.jcim.2c01595. Epub 2023 Mar 29. J Chem Inf Model. 2023. PMID: 36988562 Free PMC article.

6

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

7

Hybrid computational methods combining experimental information with molecular dynamics.

Mondal A, Lenz S, MacCallum JL, Perez A. Mondal A, et al. Curr Opin Struct Biol. 2023 Aug;81:102609. doi: 10.1016/j.sbi.2023.102609. Epub 2023 May 22. Curr Opin Struct Biol. 2023. PMID: 37224642 Review.

8

Modelling peptide-protein complexes: docking, simulations and machine learning.

Mondal A, Chang L, Perez A. Mondal A, et al. QRB Discov. 2022 Sep 19;3:e17. doi: 10.1017/qrd.2022.14. eCollection 2022. QRB Discov. 2022. PMID: 37529282 Free PMC article.

9

GENERALIST: A latent space based generative model for protein sequence families.

Akl H, Emison B, Zhao X, Mondal A, Perez A, Dixit PD. Akl H, et al. Among authors: mondal a. PLoS Comput Biol. 2023 Nov 27;19(11):e1011655. doi: 10.1371/journal.pcbi.1011655. eCollection 2023 Nov. PLoS Comput Biol. 2023. PMID: 38011273 Free PMC article.

10

Sifting Through the Noise: A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries.

Mondal A, Singh B, Felkner RH, De Falco A, Swapna G, Montelione GT, Roth MJ, Perez A. Mondal A, et al. bioRxiv [Preprint]. 2024 Jan 23:2024.01.20.576374. doi: 10.1101/2024.01.20.576374. bioRxiv. 2024. PMID: 38328039 Free PMC article. Updated. Preprint.

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