R35 GM139585/GM/NIGMS NIH HHS/United States[Grants and Funding] - Search Results

Year	Number of Results
2021	1
2023	5
2024	5

1

Specific regulation of BACH1 by the hotspot mutant p53^R175H reveals a distinct gain-of-function mechanism.

Su Z, Kon N, Yi J, Zhao H, Zhang W, Tang Q, Li H, Kobayashi H, Li Z, Duan S, Liu Y, Olive KP, Zhang Z, Honig B, Manfredi JJ, Rustgi AK, Gu W. Su Z, et al. Nat Cancer. 2023 Apr;4(4):564-581. doi: 10.1038/s43018-023-00532-z. Epub 2023 Mar 27. Nat Cancer. 2023. PMID: 36973430 Free PMC article.

2

Integrating 3D structural information into systems biology.

Murray D, Petrey D, Honig B. Murray D, et al. J Biol Chem. 2021 Jan-Jun;296:100562. doi: 10.1016/j.jbc.2021.100562. Epub 2021 Mar 18. J Biol Chem. 2021. PMID: 33744294 Free PMC article. Review.

3

Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.

Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Rosenberger G, et al. Nat Commun. 2024 May 9;15(1):3909. doi: 10.1038/s41467-024-47957-3. Nat Commun. 2024. PMID: 38724493 Free PMC article.

4

Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity.

Sergeeva AP, Katsamba PS, Liao J, Sampson JM, Bahna F, Mannepalli S, Morano NC, Shapiro L, Friesner RA, Honig B. Sergeeva AP, et al. J Mol Biol. 2023 Aug 1;435(15):168187. doi: 10.1016/j.jmb.2023.168187. Epub 2023 Jun 22. J Mol Biol. 2023. PMID: 37355034 Free PMC article.

5

ZEPPI: proteome-scale sequence-based evaluation of protein-protein interaction models.

Zhao H, Murray D, Petrey D, Honig B. Zhao H, et al. Res Sq [Preprint]. 2023 Sep 18:rs.3.rs-3289791. doi: 10.21203/rs.3.rs-3289791/v1. Res Sq. 2023. Update in: Proc Natl Acad Sci U S A. 2024 May 21;121(21):e2400260121. doi: 10.1073/pnas.2400260121. PMID: 37790387 Free PMC article. Updated. Preprint.

6

PrePPI: A Structure Informed Proteome-wide Database of Protein-Protein Interactions.

Petrey D, Zhao H, Trudeau SJ, Murray D, Honig B. Petrey D, et al. J Mol Biol. 2023 Jul 15;435(14):168052. doi: 10.1016/j.jmb.2023.168052. Epub 2023 Mar 17. J Mol Biol. 2023. PMID: 36933822 Free PMC article.

7

PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions.

Trudeau SJ, Hwang H, Mathur D, Begum K, Petrey D, Murray D, Honig B. Trudeau SJ, et al. Protein Sci. 2023 Apr;32(4):e4594. doi: 10.1002/pro.4594. Protein Sci. 2023. PMID: 36776141 Free PMC article.

8

ZEPPI: Proteome-scale sequence-based evaluation of protein-protein interaction models.

Zhao H, Petrey D, Murray D, Honig B. Zhao H, et al. Proc Natl Acad Sci U S A. 2024 May 21;121(21):e2400260121. doi: 10.1073/pnas.2400260121. Epub 2024 May 14. Proc Natl Acad Sci U S A. 2024. PMID: 38743624 Free PMC article.

9

Robust Prediction of Relative Binding Energies for Protein-Protein Complex Mutations Using Free Energy Perturbation Calculations.

Sampson JM, Cannon DA, Duan J, Epstein JCK, Sergeeva AP, Katsamba PS, Mannepalli SM, Bahna FA, Adihou H, Guéret SM, Gopalakrishnan R, Geschwindner S, Rees DG, Sigurdardottir A, Wilkinson T, Dodd RB, De Maria L, Mobarec JC, Shapiro L, Honig B, Buchanan A, Friesner RA, Wang L. Sampson JM, et al. J Mol Biol. 2024 Aug 15;436(16):168640. doi: 10.1016/j.jmb.2024.168640. Epub 2024 Jun 4. J Mol Biol. 2024. PMID: 38844044

10

A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein-Ligand Binding.

Liao J, Sergeeva AP, Harder ED, Wang L, Sampson JM, Honig B, Friesner RA. Liao J, et al. J Chem Theory Comput. 2024 Oct 8;20(19):8609-8623. doi: 10.1021/acs.jctc.4c00954. Epub 2024 Sep 27. J Chem Theory Comput. 2024. PMID: 39331379 Free PMC article.

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