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Items: 42

1.

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.

2.

Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery.

Heifetz A, Southey M, Morao I, Townsend-Nicholson A, Bodkin MJ.

Methods Mol Biol. 2018;1705:375-394. doi: 10.1007/978-1-4939-7465-8_19.

PMID:
29188574
3.

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
4.

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.

5.

Rapid and accurate assessment of GPCR-ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method.

Morao I, Fedorov DG, Robinson R, Southey M, Townsend-Nicholson A, Bodkin MJ, Heifetz A.

J Comput Chem. 2017 Sep 5;38(23):1987-1990. doi: 10.1002/jcc.24850. Epub 2017 Jul 4.

6.

Polypharmacological in Silico Bioactivity Profiling and Experimental Validation Uncovers Sedative-Hypnotic Effects of Approved and Experimental Drugs in Rat.

Drakakis G, Wafford KA, Brewerton SC, Bodkin MJ, Evans DA, Bender A.

ACS Chem Biol. 2017 Jun 16;12(6):1593-1602. doi: 10.1021/acschembio.7b00209. Epub 2017 May 1.

PMID:
28414209
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.

Guiding lead optimization with GPCR structure modeling and molecular dynamics.

Heifetz A, James T, Morao I, Bodkin MJ, Biggin PC.

Curr Opin Pharmacol. 2016 Oct;30:14-21. doi: 10.1016/j.coph.2016.06.004. Epub 2016 Jul 13. Review.

PMID:
27419904
9.

Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory.

Gerogiokas G, Southey MW, Mazanetz MP, Heifetz A, Bodkin M, Law RJ, Henchman RH, Michel J.

J Phys Chem B. 2016 Oct 13;120(40):10442-10452. Epub 2016 Sep 29.

PMID:
27645529
10.

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
11.

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.

12.

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
13.

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
14.

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.

15.

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
16.

Discovery of the First Selective, Nonpeptidic Orexin 2 Receptor Agonists.

Heifetz A, Bodkin MJ, Biggin PC.

J Med Chem. 2015 Oct 22;58(20):7928-30. doi: 10.1021/acs.jmedchem.5b01394. Epub 2015 Sep 16.

PMID:
26375584
17.

Correction: Evaluation of water displacement energetics in protein binding sites with grid cell theory.

Gerogiokas G, Southey MW, Mazanetz MP, Hefeitz A, Bodkin M, Law RJ, Michel J.

Phys Chem Chem Phys. 2015 Jun 28;17(24):16213. doi: 10.1039/c5cp90084k. Epub 2015 May 29. No abstract available.

PMID:
26023833
18.

GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1-2 September 2014.

Heifetz A, Schertler GF, Seifert R, Tate CG, Sexton PM, Gurevich VV, Fourmy D, Cherezov V, Marshall FH, Storer RI, Moraes I, Tikhonova IG, Tautermann CS, Hunt P, Ceska T, Hodgson S, Bodkin MJ, Singh S, Law RJ, Biggin PC.

Naunyn Schmiedebergs Arch Pharmacol. 2015 Aug;388(8):883-903. doi: 10.1007/s00210-015-1111-8. Epub 2015 Mar 14.

19.

Comparing global and local likelihood score thresholds in multiclass laplacian-modified Naive Bayes protein target prediction.

Drakakis G, Koutsoukas A, Brewerton SC, Bodkin MJ, Evans DA, Bender A.

Comb Chem High Throughput Screen. 2015;18(3):323-30.

PMID:
25747441
20.

Evaluation of water displacement energetics in protein binding sites with grid cell theory.

Gerogiokas G, Southey MW, Mazanetz MP, Heifetz A, Bodkin M, Law RJ, Michel J.

Phys Chem Chem Phys. 2015 Apr 7;17(13):8416-26. doi: 10.1039/c4cp05572a. Epub 2015 Jan 20. Erratum in: Phys Chem Chem Phys. 2015 Jun 28;17(24):16213. Hefeitz, A [corrected to Heifetz, A].

PMID:
25600031
21.

Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts.

Liggi S, Drakakis G, Koutsoukas A, Cortes-Ciriano I, Martínez-Alonso P, Malliavin TE, Velazquez-Campoy A, Brewerton SC, Bodkin MJ, Evans DA, Glen RC, Carrodeguas JA, Bender A.

Future Med Chem. 2014;6(18):2029-56. doi: 10.4155/fmc.14.137.

22.

Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis.

Ravindranath AC, Perualila-Tan N, Kasim A, Drakakis G, Liggi S, Brewerton SC, Mason D, Bodkin MJ, Evans DA, Bhagwat A, Talloen W, Göhlmann HW, Shkedy Z, Bender A; QSTAR Consortium.

Mol Biosyst. 2015 Jan;11(1):86-96. doi: 10.1039/c4mb00328d. Epub 2014 Sep 25.

PMID:
25254964
23.

Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus laevis Phenotypic Readouts.

Liggi S, Drakakis G, Hendry AE, Hanson KM, Brewerton SC, Wheeler GN, Bodkin MJ, Evans DA, Bender A.

Mol Inform. 2013 Dec;32(11-12):1009-24. doi: 10.1002/minf.201300102. Epub 2013 Oct 18.

PMID:
27481146
24.

ChEMBLSpace--a graphical explorer of the chemogenomic space covered by the ChEMBL database.

Fechner N, Papadatos G, Evans D, Morphy JR, Brewerton SC, Thorner D, Bodkin M.

Bioinformatics. 2013 Feb 15;29(4):523-4. doi: 10.1093/bioinformatics/bts711. Epub 2012 Dec 20.

PMID:
23257198
25.

Why don't we see a greater uptake of computational chemistry approaches by the medicinal chemistry community?

Bodkin MJ.

Future Med Chem. 2012 Oct;4(15):1889-91. doi: 10.4155/fmc.12.154. No abstract available.

PMID:
23088270
26.

Knowledge-based approach to de novo design using reaction vectors.

Patel H, Bodkin MJ, Chen B, Gillet VJ.

J Chem Inf Model. 2009 May;49(5):1163-84. doi: 10.1021/ci800413m.

PMID:
19382767
27.

Janocchio--a Java applet for viewing 3D structures and calculating NMR couplings and NOEs.

Evans DA, Bodkin MJ, Baker SR, Sharman GJ.

Magn Reson Chem. 2007 Jul;45(7):595-600.

PMID:
17534870
28.

3D QSAR methods: Phase and Catalyst compared.

Evans DA, Doman TN, Thorner DA, Bodkin MJ.

J Chem Inf Model. 2007 May-Jun;47(3):1248-57. Epub 2007 May 4.

PMID:
17477520
29.

Species selectivity of a nicotinic acetylcholine receptor agonist is conferred by two adjacent extracellular beta4 amino acids that are implicated in the coupling of binding to channel gating.

Young GT, Broad LM, Zwart R, Astles PC, Bodkin M, Sher E, Millar NS.

Mol Pharmacol. 2007 Feb;71(2):389-97. Epub 2006 Oct 25.

PMID:
17065235
30.

Clinical correlation of asbestos bodies in BAL fluid.

Vathesatogkit P, Harkin TJ, Addrizzo-Harris DJ, Bodkin M, Crane M, Rom WN.

Chest. 2004 Sep;126(3):966-71.

PMID:
15364780
31.

GM-CSF gene expression is normal but protein release is absent in a patient with pulmonary alveolar proteinosis.

Tchou-Wong KM, Harkin TJ, Chi C, Bodkin M, Rom WN.

Am J Respir Crit Care Med. 1997 Dec;156(6):1999-2002. Erratum in: Am J Respir Crit Care Med 1998 Apr;157(4 Pt 1):1353.

PMID:
9412586
32.

Hydrophobic solvation in aqueous trifluoroethanol solution.

Bodkin MJ, Goodfellow JM.

Biopolymers. 1996 Jul;39(1):43-50.

PMID:
8924626
33.

Tuberculosis in HIV-positive patients: cellular response and immune activation in the lung.

Law KF, Jagirdar J, Weiden MD, Bodkin M, Rom WN.

Am J Respir Crit Care Med. 1996 Apr;153(4 Pt 1):1377-84.

PMID:
8616569
35.
36.

Enhanced interleukin-8 release and gene expression in macrophages after exposure to Mycobacterium tuberculosis and its components.

Zhang Y, Broser M, Cohen H, Bodkin M, Law K, Reibman J, Rom WN.

J Clin Invest. 1995 Feb;95(2):586-92.

37.

A new class of non-peptidic cholecystokinin-B/gastrin receptor antagonists based on dibenzobicyclo[2.2.2]octane.

Kalindjian SB, Bodkin MJ, Buck IM, Dunstone DJ, Low CM, McDonald IM, Pether MJ, Steel KI.

J Med Chem. 1994 Oct 28;37(22):3671-3. No abstract available.

PMID:
7966125
38.

NF-kappa B-dependent and -independent pathways of HIV activation in a chronically infected T cell line.

Antoni BA, Rabson AB, Kinter A, Bodkin M, Poli G.

Virology. 1994 Aug 1;202(2):684-94.

PMID:
7913275
39.

Identification of a missense mutation in an adult-onset patient with glycogenosis type II expressing only one allele.

Martiniuk F, Mehler M, Bodkin M, Tzall S, Hirschhorn K, Zhong N, Hirschhorn R.

DNA Cell Biol. 1991 Nov;10(9):681-7.

PMID:
1684505
40.

Isolation and partial characterization of the structural gene for human acid alpha glucosidase.

Martiniuk F, Bodkin M, Tzall S, Hirschhorn R.

DNA Cell Biol. 1991 May;10(4):283-92.

PMID:
1674202
42.

The intactness and orientation of acetylcholine receptor-rich membrane from Torpedo californica electric tissue.

Czajkowski C, DiPaola M, Bodkin M, Salazar-Jimenez G, Holtzman E, Karlin A.

Arch Biochem Biophys. 1989 Aug 1;272(2):412-20.

PMID:
2751309

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