Borrelli K - Search Results

1

Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations.

Clark AJ, Tiwary P, Borrelli K, Feng S, Miller EB, Abel R, Friesner RA, Berne BJ. Clark AJ, et al. Among authors: borrelli k. J Chem Theory Comput. 2016 Jun 14;12(6):2990-8. doi: 10.1021/acs.jctc.6b00201. Epub 2016 May 13. J Chem Theory Comput. 2016. PMID: 27145262

2

Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods.

Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Knight JL, et al. J Chem Theory Comput. 2014 Aug 12;10(8):3207-20. doi: 10.1021/ct500189s. J Chem Theory Comput. 2014. PMID: 26588291

3

Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding.

Miller EB, Murphy RB, Sindhikara D, Borrelli KW, Grisewood MJ, Ranalli F, Dixon SL, Jerome S, Boyles NA, Day T, Ghanakota P, Mondal S, Rafi SB, Troast DM, Abel R, Friesner RA. Miller EB, et al. J Chem Theory Comput. 2021 Apr 13;17(4):2630-2639. doi: 10.1021/acs.jctc.1c00136. Epub 2021 Mar 29. J Chem Theory Comput. 2021. PMID: 33779166

4

Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models.

Xu T, Zhu K, Beautrait A, Vendome J, Borrelli KW, Abel R, Friesner RA, Miller EB. Xu T, et al. Among authors: borrelli kw. J Chem Theory Comput. 2022 Sep 13;18(9):5710-5724. doi: 10.1021/acs.jctc.2c00371. Epub 2022 Aug 16. J Chem Theory Comput. 2022. PMID: 35972903

5

Docking covalent inhibitors: a parameter free approach to pose prediction and scoring.

Zhu K, Borrelli KW, Greenwood JR, Day T, Abel R, Farid RS, Harder E. Zhu K, et al. Among authors: borrelli kw. J Chem Inf Model. 2014 Jul 28;54(7):1932-40. doi: 10.1021/ci500118s. Epub 2014 Jun 26. J Chem Inf Model. 2014. PMID: 24916536

6

Structure-based virtual screening approach for discovery of covalently bound ligands.

Toledo Warshaviak D, Golan G, Borrelli KW, Zhu K, Kalid O. Toledo Warshaviak D, et al. Among authors: borrelli kw. J Chem Inf Model. 2014 Jul 28;54(7):1941-50. doi: 10.1021/ci500175r. Epub 2014 Jun 26. J Chem Inf Model. 2014. PMID: 24932913

7

GemSpot: A Pipeline for Robust Modeling of Ligands into Cryo-EM Maps.

Robertson MJ, van Zundert GCP, Borrelli K, Skiniotis G. Robertson MJ, et al. Among authors: borrelli k. Structure. 2020 Jun 2;28(6):707-716.e3. doi: 10.1016/j.str.2020.04.018. Epub 2020 May 14. Structure. 2020. PMID: 32413291 Free PMC article.

8

Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility.

Borrelli KW, Cossins B, Guallar V. Borrelli KW, et al. J Comput Chem. 2010 Apr 30;31(6):1224-35. doi: 10.1002/jcc.21409. J Comput Chem. 2010. PMID: 19885871

9

Water Thermodynamics of Peptide Toxin Binding Sites on Ion Channels.

Shah B, Sindhikara D, Borrelli K, Leffler AE. Shah B, et al. Among authors: borrelli k. Toxins (Basel). 2020 Oct 12;12(10):652. doi: 10.3390/toxins12100652. Toxins (Basel). 2020. PMID: 33053750 Free PMC article.

10

Plasticity in ligand recognition at somatostatin receptors.

Robertson MJ, Meyerowitz JG, Panova O, Borrelli K, Skiniotis G. Robertson MJ, et al. Among authors: borrelli k. Nat Struct Mol Biol. 2022 Mar;29(3):210-217. doi: 10.1038/s41594-022-00727-5. Epub 2022 Feb 24. Nat Struct Mol Biol. 2022. PMID: 35210615 Free PMC article.

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