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Items: 15

1.

Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation.

Aldeghi M, Gapsys V, de Groot BL.

ACS Cent Sci. 2018 Dec 26;4(12):1708-1718. doi: 10.1021/acscentsci.8b00717. Epub 2018 Dec 13.

2.

Accurate Calculation of Free Energy Changes upon Amino Acid Mutation.

Aldeghi M, de Groot BL, Gapsys V.

Methods Mol Biol. 2019;1851:19-47. doi: 10.1007/978-1-4939-8736-8_2.

PMID:
30298390
3.

Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo.

Aldeghi M, Ross GA, Bodkin MJ, Essex JW, Knapp S, Biggin PC.

Commun Chem. 2018 Apr 5;1. pii: 19. doi: 10.1038/s42004-018-0019-x.

4.

Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner's Guide.

Aldeghi M, Bluck JP, Biggin PC.

Methods Mol Biol. 2018;1762:199-232. doi: 10.1007/978-1-4939-7756-7_11.

PMID:
29594774
5.

Exploring GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method.

Chudyk EI, Sarrat L, Aldeghi M, Fedorov DG, Bodkin MJ, James T, Southey M, Robinson R, Morao I, Heifetz A.

Methods Mol Biol. 2018;1705:179-195. doi: 10.1007/978-1-4939-7465-8_8.

PMID:
29188563
6.

Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study.

Aldeghi M, Bodkin MJ, Knapp S, Biggin PC.

J Chem Inf Model. 2017 Sep 25;57(9):2203-2221. doi: 10.1021/acs.jcim.7b00347. Epub 2017 Aug 24.

7.

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations.

Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC.

J Am Chem Soc. 2017 Jan 18;139(2):946-957. doi: 10.1021/jacs.6b11467. Epub 2017 Jan 9.

8.

Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties.

Biggin PC, Aldeghi M, Bodkin MJ, Heifetz A.

Adv Exp Med Biol. 2016;922:161-181. doi: 10.1007/978-3-319-35072-1_12.

PMID:
27553242
9.

Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions.

Heifetz A, Aldeghi M, Chudyk EI, Fedorov DG, Bodkin MJ, Biggin PC.

Biochem Soc Trans. 2016 Apr 15;44(2):574-81. doi: 10.1042/BST20150250. Review.

10.

Fragment Molecular Orbital Method Applied to Lead Optimization of Novel Interleukin-2 Inducible T-Cell Kinase (ITK) Inhibitors.

Heifetz A, Trani G, Aldeghi M, MacKinnon CH, McEwan PA, Brookfield FA, Chudyk EI, Bodkin M, Pei Z, Burch JD, Ortwine DF.

J Med Chem. 2016 May 12;59(9):4352-63. doi: 10.1021/acs.jmedchem.6b00045. Epub 2016 Mar 17.

PMID:
26950250
11.

Application of an Integrated GPCR SAR-Modeling Platform To Explain the Activation Selectivity of Human 5-HT2C over 5-HT2B.

Heifetz A, Storer RI, McMurray G, James T, Morao I, Aldeghi M, Bodkin MJ, Biggin PC.

ACS Chem Biol. 2016 May 20;11(5):1372-82. doi: 10.1021/acschembio.5b01045. Epub 2016 Mar 7.

PMID:
26900768
12.

Accurate calculation of the absolute free energy of binding for drug molecules.

Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC.

Chem Sci. 2016 Jan 14;7(1):207-218. Epub 2015 Oct 7.

13.

Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance.

Fedorov O, Castex J, Tallant C, Owen DR, Martin S, Aldeghi M, Monteiro O, Filippakopoulos P, Picaud S, Trzupek JD, Gerstenberger BS, Bountra C, Willmann D, Wells C, Philpott M, Rogers C, Biggin PC, Brennan PE, Bunnage ME, Schüle R, Günther T, Knapp S, Müller S.

Sci Adv. 2015 Nov 13;1(10):e1500723. doi: 10.1126/sciadv.1500723. eCollection 2015 Nov.

14.

The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions.

Heifetz A, Chudyk EI, Gleave L, Aldeghi M, Cherezov V, Fedorov DG, Biggin PC, Bodkin MJ.

J Chem Inf Model. 2016 Jan 25;56(1):159-72. doi: 10.1021/acs.jcim.5b00644. Epub 2015 Dec 24.

PMID:
26642258
15.

Two- and three-dimensional rings in drugs.

Aldeghi M, Malhotra S, Selwood DL, Chan AW.

Chem Biol Drug Des. 2014 Apr;83(4):450-61. doi: 10.1111/cbdd.12260.

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