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Items: 1 to 50 of 69

1.

Application of Assisted Design of Antibody and Protein Therapeutics (ADAPT) improves efficacy of a Clostridium difficile toxin A single-domain antibody.

Sulea T, Hussack G, Ryan S, Tanha J, Purisima EO.

Sci Rep. 2018 Feb 2;8(1):2260. doi: 10.1038/s41598-018-20599-4.

2.

Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method.

Hogues H, Sulea T, Gaudreault F, Corbeil CR, Purisima EO.

J Comput Aided Mol Des. 2018 Jan;32(1):143-150. doi: 10.1007/s10822-017-0071-0. Epub 2017 Oct 5.

PMID:
28983727
3.

Assisted Design of Antibody and Protein Therapeutics (ADAPT).

Vivcharuk V, Baardsnes J, Deprez C, Sulea T, Jaramillo M, Corbeil CR, Mullick A, Magoon J, Marcil A, Durocher Y, O'Connor-McCourt MD, Purisima EO.

PLoS One. 2017 Jul 27;12(7):e0181490. doi: 10.1371/journal.pone.0181490. eCollection 2017.

4.

A Rational Engineering Strategy for Designing Protein A-Binding Camelid Single-Domain Antibodies.

Henry KA, Sulea T, van Faassen H, Hussack G, Purisima EO, MacKenzie CR, Arbabi-Ghahroudi M.

PLoS One. 2016 Sep 15;11(9):e0163113. doi: 10.1371/journal.pone.0163113. eCollection 2016.

5.

Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities.

Sulea T, Vivcharuk V, Corbeil CR, Deprez C, Purisima EO.

J Chem Inf Model. 2016 Jul 25;56(7):1292-303. doi: 10.1021/acs.jcim.6b00043. Epub 2016 Jul 14.

PMID:
27367467
6.

Structural Studies of Trypanosoma brucei RNA Editing Ligases and Their Binding Partner Proteins.

Shaneh A, Purisima EO, Salavati R, Sulea T.

Biochemistry. 2016 Apr 26;55(16):2319-31. doi: 10.1021/acs.biochem.5b01257. Epub 2016 Apr 13.

PMID:
27031688
7.

Evaluation of the Wilma-SIE Virtual Screening Method in Community Structure-Activity Resource 2013 and 2014 Blind Challenges.

Hogues H, Sulea T, Purisima EO.

J Chem Inf Model. 2016 Jun 27;56(6):955-64. doi: 10.1021/acs.jcim.5b00278. Epub 2015 Aug 24.

PMID:
26282162
8.

Small-molecule inhibitors of the pseudaminic acid biosynthetic pathway: targeting motility as a key bacterial virulence factor.

Ménard R, Schoenhofen IC, Tao L, Aubry A, Bouchard P, Reid CW, Lachance P, Twine SM, Fulton KM, Cui Q, Hogues H, Purisima EO, Sulea T, Logan SM.

Antimicrob Agents Chemother. 2014 Dec;58(12):7430-40. doi: 10.1128/AAC.03858-14. Epub 2014 Sep 29.

9.

Shuttle-cargo fusion molecules of transport peptides and the hD2/3 receptor antagonist fallypride: a feasible approach to preserve ligand-receptor binding?

Wängler C, Chowdhury S, Höfner G, Djurova P, Purisima EO, Bartenstein P, Wängler B, Fricker G, Wanner KT, Schirrmacher R.

J Med Chem. 2014 May 22;57(10):4368-81. doi: 10.1021/jm5004123. Epub 2014 May 8.

PMID:
24779610
10.

Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge.

Hogues H, Sulea T, Purisima EO.

J Comput Aided Mol Des. 2014 Apr;28(4):417-27. doi: 10.1007/s10822-014-9715-5. Epub 2014 Jan 29.

PMID:
24474162
11.

Solvation models: theory and validation.

Purisima EO, Sulea T.

Curr Pharm Des. 2014;20(20):3266-80. Review.

PMID:
23947651
12.

Protein-ligand binding free energies from exhaustive docking.

Purisima EO, Hogues H.

J Phys Chem B. 2012 Jun 14;116(23):6872-9. doi: 10.1021/jp212646s. Epub 2012 Apr 2.

PMID:
22432509
13.

Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction.

Sulea T, Hogues H, Purisima EO.

J Comput Aided Mol Des. 2012 May;26(5):617-33. doi: 10.1007/s10822-011-9529-7. Epub 2011 Dec 25.

PMID:
22198519
14.

Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models.

Sulea T, Purisima EO.

J Comput Aided Mol Des. 2012 May;26(5):661-7. doi: 10.1007/s10822-011-9522-1. Epub 2011 Dec 22.

PMID:
22190141
15.

The solvated interaction energy method for scoring binding affinities.

Sulea T, Purisima EO.

Methods Mol Biol. 2012;819:295-303. doi: 10.1007/978-1-61779-465-0_19.

PMID:
22183544
16.

Molecular dynamics study of small molecule inhibitors of the Bcl-2 family.

Acoca S, Cui Q, Shore GC, Purisima EO.

Proteins. 2011 Sep;79(9):2624-36. doi: 10.1002/prot.23083. Epub 2011 Jun 30.

PMID:
21721047
17.

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise.

Sulea T, Cui Q, Purisima EO.

J Chem Inf Model. 2011 Sep 26;51(9):2066-81. doi: 10.1021/ci2000242. Epub 2011 Jul 13.

PMID:
21714553
18.

Contribution of active site residues to substrate hydrolysis by USP2: insights into catalysis by ubiquitin specific proteases.

Zhang W, Sulea T, Tao L, Cui Q, Purisima EO, Vongsamphanh R, Lachance P, Lytvyn V, Qi H, Li Y, Ménard R.

Biochemistry. 2011 May 31;50(21):4775-85. doi: 10.1021/bi101958h. Epub 2011 May 4.

PMID:
21542621
19.

Identification of high-quality cancer prognostic markers and metastasis network modules.

Li J, Lenferink AE, Deng Y, Collins C, Cui Q, Purisima EO, O'Connor-McCourt MD, Wang E.

Nat Commun. 2010 Jul 13;1:34. doi: 10.1038/ncomms1033. Erratum in: Nat Commun. 2012;3. doi:10.1038/ncomms1033.

20.

A monovalent agonist of TrkA tyrosine kinase receptors can be converted into a bivalent antagonist.

Brahimi F, Liu J, Malakhov A, Chowdhury S, Purisima EO, Ivanisevic L, Caron A, Burgess K, Saragovi HU.

Biochim Biophys Acta. 2010 Sep;1800(9):1018-26. doi: 10.1016/j.bbagen.2010.06.007. Epub 2010 Jun 19.

21.

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model.

Corbeil CR, Sulea T, Purisima EO.

J Chem Theory Comput. 2010 May 11;6(5):1622-37. doi: 10.1021/ct9006037. Epub 2010 Apr 2.

PMID:
26615695
22.

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE).

Sulea T, Corbeil CR, Purisima EO.

J Chem Theory Comput. 2010 May 11;6(5):1608-21. doi: 10.1021/ct9006025.

PMID:
26615694
23.

Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge.

Purisima EO, Corbeil CR, Sulea T.

J Comput Aided Mol Des. 2010 Apr;24(4):373-83. doi: 10.1007/s10822-010-9341-9. Epub 2010 Apr 6.

PMID:
20414699
24.

Small-molecule ligands of GD2 ganglioside, designed from NMR studies, exhibit induced-fit binding and bioactivity.

Tong W, Gagnon M, Sprules T, Gilbert M, Chowdhury S, Meerovitch K, Hansford K, Purisima EO, Blankenship JW, Cheung NK, Gehring K, Lubell WD, Saragovi HU.

Chem Biol. 2010 Feb 26;17(2):183-94. doi: 10.1016/j.chembiol.2010.01.012.

25.

A combined crystallographic and molecular dynamics study of cathepsin L retrobinding inhibitors.

Shenoy RT, Chowdhury SF, Kumar S, Joseph L, Purisima EO, Sivaraman J.

J Med Chem. 2009 Oct 22;52(20):6335-46. doi: 10.1021/jm900596y.

PMID:
19761244
26.

Structural and functional analysis of Campylobacter jejuni PseG: a udp-sugar hydrolase from the pseudaminic acid biosynthetic pathway.

Rangarajan ES, Proteau A, Cui Q, Logan SM, Potetinova Z, Whitfield D, Purisima EO, Cygler M, Matte A, Sulea T, Schoenhofen IC.

J Biol Chem. 2009 Jul 31;284(31):20989-1000. doi: 10.1074/jbc.M109.012351. Epub 2009 May 29.

27.

Restoring charge asymmetry in continuum electrostatics calculations of hydration free energies.

Purisima EO, Sulea T.

J Phys Chem B. 2009 Jun 18;113(24):8206-9. doi: 10.1021/jp9020799.

PMID:
19459599
28.

Prediction of SAMPL-1 hydration free energies using a continuum electrostatics-dispersion model.

Sulea T, Wanapun D, Dennis S, Purisima EO.

J Phys Chem B. 2009 Apr 9;113(14):4511-20. doi: 10.1021/jp8061477.

PMID:
19267492
29.

Protein evolution on a human signaling network.

Cui Q, Purisima EO, Wang E.

BMC Syst Biol. 2009 Feb 18;3:21. doi: 10.1186/1752-0509-3-21.

30.

Trapping open and closed forms of FitE: a group III periplasmic binding protein.

Shi R, Proteau A, Wagner J, Cui Q, Purisima EO, Matte A, Cygler M.

Proteins. 2009 May 15;75(3):598-609. doi: 10.1002/prot.22272.

PMID:
19004000
31.

Viral cystatin evolution and three-dimensional structure modelling: a case of directional selection acting on a viral protein involved in a host-parasitoid interaction.

Serbielle C, Chowdhury S, Pichon S, Dupas S, Lesobre J, Purisima EO, Drezen JM, Huguet E.

BMC Biol. 2008 Sep 10;6:38. doi: 10.1186/1741-7007-6-38.

32.

An investigation into CAG repeat length variation and N/C terminal interactions in the T877A mutant androgen receptor found in prostate cancer.

Southwell J, Chowdhury SF, Gottlieb B, Beitel LK, Lumbroso R, Purisima EO, Trifiro M.

J Steroid Biochem Mol Biol. 2008 Jul;111(1-2):138-46. doi: 10.1016/j.jsbmb.2008.04.009. Epub 2008 Jun 20.

PMID:
18619542
33.

Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex.

Cui Q, Sulea T, Schrag JD, Munger C, Hung MN, Naïm M, Cygler M, Purisima EO.

J Mol Biol. 2008 Jun 13;379(4):787-802. doi: 10.1016/j.jmb.2008.04.035. Epub 2008 Apr 20.

PMID:
18479705
34.

Exploring inhibitor binding at the S' subsites of cathepsin L.

Chowdhury SF, Joseph L, Kumar S, Tulsidas SR, Bhat S, Ziomek E, Ménard R, Sivaraman J, Purisima EO.

J Med Chem. 2008 Mar 13;51(5):1361-8. doi: 10.1021/jm701190v. Epub 2008 Feb 16.

PMID:
18278855
35.

A map of human cancer signaling.

Cui Q, Ma Y, Jaramillo M, Bari H, Awan A, Yang S, Zhang S, Liu L, Lu M, O'Connor-McCourt M, Purisima EO, Wang E.

Mol Syst Biol. 2007;3:152. Epub 2007 Dec 18.

36.

Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network.

Awan A, Bari H, Yan F, Moksong S, Yang S, Chowdhury S, Cui Q, Yu Z, Purisima EO, Wang E.

IET Syst Biol. 2007 Sep;1(5):292-7.

PMID:
17907678
37.

MicroRNA regulation and interspecific variation of gene expression.

Cui Q, Yu Z, Purisima EO, Wang E.

Trends Genet. 2007 Aug;23(8):372-5. Epub 2007 May 4.

PMID:
17482307
38.

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.

Naïm M, Bhat S, Rankin KN, Dennis S, Chowdhury SF, Siddiqi I, Drabik P, Sulea T, Bayly CI, Jakalian A, Purisima EO.

J Chem Inf Model. 2007 Jan-Feb;47(1):122-33.

PMID:
17238257
39.

MicroRNAs preferentially target the genes with high transcriptional regulation complexity.

Cui Q, Yu Z, Pan Y, Purisima EO, Wang E.

Biochem Biophys Res Commun. 2007 Jan 19;352(3):733-8. Epub 2006 Nov 27.

PMID:
17141185
40.

Coupled atomic charge selectivity for optimal ligand-charge distributions at protein binding sites.

Bhat S, Sulea T, Purisima EO.

J Comput Chem. 2006 Dec;27(16):1899-907.

PMID:
16988958
41.

Principles of microRNA regulation of a human cellular signaling network.

Cui Q, Yu Z, Purisima EO, Wang E.

Mol Syst Biol. 2006;2:46. Epub 2006 Sep 12.

42.

Impaired helix 12 dynamics due to proline 892 substitutions in the androgen receptor are associated with complete androgen insensitivity.

Elhaji YA, Stoica I, Dennis S, Purisima EO, Lumbroso R, Beitel LK, Trifiro MA.

Hum Mol Genet. 2006 Mar 15;15(6):921-31. Epub 2006 Jan 31. Erratum in: Hum Mol Genet. 2006 May 1;15(9):1561. Lumbroso, Rose [added]; Beitel, Lenore K [added].

PMID:
16449235
43.

Binding site-based classification of coronaviral papain-like proteases.

Sulea T, Lindner HA, Purisima EO, Ménard R.

Proteins. 2006 Mar 15;62(3):760-75.

PMID:
16358325
44.

Molecular surface generation using a variable-radius solvent probe.

Bhat S, Purisima EO.

Proteins. 2006 Jan 1;62(1):244-61.

PMID:
16287115
45.

Inhibition of a cathepsin L-like cysteine protease by a chimeric propeptide-derived inhibitor.

Godat E, Chowdhury S, Lecaille F, Belghazi M, Purisima EO, Lalmanach G.

Biochemistry. 2005 Aug 9;44(31):10486-93.

PMID:
16060657
46.

Deubiquitination, a new function of the severe acute respiratory syndrome coronavirus papain-like protease?

Sulea T, Lindner HA, Purisima EO, Ménard R.

J Virol. 2005 Apr;79(7):4550-1. No abstract available.

47.

Carboxy-monopeptidase substrate specificity of human cathepsin X.

Devanathan G, Turnbull JL, Ziomek E, Purisima EO, Ménard R, Sulea T.

Biochem Biophys Res Commun. 2005 Apr 8;329(2):445-52.

PMID:
15737607
48.

Effect of limited solid-state glycation on the conformation of lysozyme by ESI-MSMS peptide mapping and molecular modeling.

Yeboah FK, Alli I, Yaylayan VA, Yasuo K, Chowdhury SF, Purisima EO.

Bioconjug Chem. 2004 Jan-Feb;15(1):27-34.

PMID:
14733580
49.

Bridging structural biology and genetics by computational methods: an investigation into how the R774C mutation in the AR gene can result in complete androgen insensitivity syndrome.

Wu JH, Gottlieb B, Batist G, Sulea T, Purisima EO, Beitel LK, Trifiro M.

Hum Mutat. 2003 Dec;22(6):465-75. Erratum in: Hum Mutat. 2004 Apr;23(4):394.

PMID:
14635106
50.

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