Gaudreault, F.; Sulea, T.; Corbeil, C. R. AI-Augmented Physics-Based Docking for Antibody-Antigen Complex Prediction. bioRxiv (2024). doi: 10.1101/2024.11.06.622293

Wei, W.; Sulea, T. Sequence-based engineering of pH-sensitive antibodies for tumor targeting or endosomal recycling applications. MAbs (2024). 16:2404064. doi: 10.1080/19420862.2024.2404064

Martina, M.; Banderali, U.; Yogi, A.; Arbabi Ghahroudi, M.; Liu, H.; Sulea, T.; Durocher, Y.; Hussack, G.; van Faassen, H.; Chakravarty, B.; Liu, Q. Y.; Iqbal, U.; Ling, B.; Lessard, E.; Sheff, J.; Robotham, A.; Callaghan, D.; Moreno, M.; Comas, T.; Ly, D.; Stanimirovic, D. A Novel Antigen Design Strategy to Isolate Single-Domain Antibodies that Target Human Nav1.7 and Reduce Pain in Animal Models. Advanced Science (Weinh) (2024). 11:e2405432. doi: 10.1002/advs.202405432

Peters, D. L.; Gaudreault, F.; Wangxue, C. Functional domains of Acinetobacter bacteriophage tail fibers. Frontiers in Microbiology (2024). 15:1230997. doi: 10.3389/fmicb.2024.1230997

Sulea, T.; Kumar, S.; Kuroda, D. Editorial: Editorial: Progress and challenges in computational structure-based design and development of biologic drugs. Frontiers in Molecular Biosciences (2024). 11:1360267. doi: 10.3389/fmolb.2024.1360267

Trentin-Sonoda, M.; Zimpelmann, J.; Tailor, K.; Gillard, J. W.; Yoganathan, N.; Sulea, T.; Burns, K. D. Effects of Two Soluble ACE2-Fc Variants on Blood Pressure and Albuminuria in Hypertensive Mice: Research Letter. Canadian Journal of Kidney Health and Disease (2023). 10:20543581231207146. doi: 10.1177/20543581231207146

Gaudreault, F.; Corbeil, C. R.; Sulea, T. Enhanced antibody-antigen structure prediction from molecular docking using AlphaFold2. Scientific Reports (2023). 13:15107. doi: 10.1038/s41598-023-42090-5

Gaudreault, F.; Baardsnes, J.; Martynova, Y.; Dachon, A.; Hogues, H.; Corbeil, C. R.; Purisima, E. O.; Arbour, M.; Sulea, T. Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold. Frontiers in Molecular Biosciences (2023). 10:1253689. doi: 10.3389/fmolb.2023.1253689

Wei, W.; Hogues, H.; Sulea, T. Comparative Performance of High-Throughput Methods for Protein pKa Predictions. Journal of Chemical Information and Modeling (2023). 63:5169-5181. doi: 10.1021/acs.jcim.3c00165

Purisima, E. O.; Corbeil, C. R.; Gaudreault, F.; Wei, W.; Deprez, C.; Sulea, T. Solvated interaction energy: from small-molecule to antibody drug design. Frontiers in Molecular Biosciences (2023). 10:1210576. doi: 10.3389/fmolb.2023.1210576

Sulea, T.; Deprez, C.; Corbeil, C. R.; Purisima, E. O. Optimizing Antibody-Antigen Binding Affinities with the ADAPT Platform. Methods in Molecular Biology (2023). 2552:361-374. doi: 10.1007/978-1-0716-2609-2_20

Jaramillo, M. L.; Sulea, T.; Durocher, Y.; Acchione, M.; Schur, M. J.; Robotham, A.; Kelly, J. F.; Goneau, M. F.; Robert, A.; Cepero-Donates, Y.; Gilbert, M. A glyco-engineering approach for site-specific conjugation to Fab glycans. MAbs (2023). 15:2149057. doi: 10.1080/19420862.2022.2149057

McComb, S.; Nguyen, T.; Shepherd, A.; Henry, K. A.; Bloemberg, D.; Marcil, A.; Maclean, S.; Zafer, A.; Gilbert, R.; Gadoury, C.; Pon, R. A.; Sulea, T.; Zhu, Q.; Weeratna, R. D. Programmable Attenuation of Antigenic Sensitivity for a Nanobody-Based EGFR Chimeric Antigen Receptor Through Hinge Domain Truncation. Frontiers in Immunology (2022). 13:864868. doi: 10.3389/fimmu.2022.864868

Yogi, A.; Hussack, G.; van Faassen, H.; Haqqani, A. S.; Delaney, C. E.; Brunette, E.; Sandhu, J. K.; Hewitt, M.; Sulea, T.; Kemmerich, K.; Stanimirovic, D. B. Brain Delivery of IGF1R5, a Single-Domain Antibody Targeting Insulin-like Growth Factor-1 Receptor. Pharmaceutics (2022). 14. doi: 10.3390/pharmaceutics14071452

Wei, W.; Corbeil, C. R.; Gaudreault, F.; Deprez, C.; Purisima, E. O.; Sulea, T. Antibody mutations favoring pH-dependent binding in solid tumor microenvironments: Insights from large-scale structure-based calculations. Proteins: Structure, Function and Bioinformatics (2022). 90:1538-1546. doi: 10.1002/prot.26340

Sulea, T.; Baardsnes, J.; Stuible, M.; Rohani, N.; Tran, A.; Parat, M.; Donates, Y. C.; Duchesne, M.; Plante, P.; Kour, G.; Durocher, Y. Structure-based dual affinity optimization of a SARS-CoV-1/2 cross-reactive single-domain antibody. PLoS ONE (2022). 17. doi: 10.1371/journal.pone.0266250

Sulea, T. Humanization of Camelid Single-Domain Antibodies. Methods in Molecular Biology (2022). 2446:299-312. doi: 10.1007/978-1-0716-2075-5_14

Gaudreault, F.; Corbeil, C. R.; Purisima, E. O.; Sulea, T. Coevolved Canonical Loops Conformations of Single-Domain Antibodies: A Tale of Three Pockets Playing Musical Chairs. Frontiers in Immunology (2022). 13. doi: 10.3389/fimmu.2022.884132

Abokitse, K.; Grosse, S.; Leisch, H.; Corbeil, C. R.; Perrin-Sarazin, F.; Lau, P. C. K. A Novel Actinobacterial Cutinase Containing a Noncatalytic Polymer-Binding Domain. Applied and Environmental Microbiology (2022). 88. doi: 10.1128/AEM.01522-21

Shrestha, B. R.; Liberelle, B.; Murschel, F.; Purisima, E. O.; Sulea, T.; De Crescenzo, G.; Banquy, X. Binding mechanism of a de novo coiled coil complex elucidated from surface forces measurements. Journal of Colloid and Interface Science (2021). 581:218-225. doi: 10.1016/j.jcis.2020.07.097

Sheff, J. G.; Kelly, J. F.; Robotham, A.; Sulea, T.; Malenfant, F.; L’Abbé, D.; Duchesne, M.; Pelletier, A.; Lefebvre, J.; Acel, A.; Parat, M.; Gosselin, M.; Wu, C.; Fortin, Y.; Baardsnes, J.; Van Faassen, H.; Awrey, S.; Chafe, S. C.; McDonald, P. C.; Dedhar, S.; Lenferink, A. E. G. Hydrogen-deuterium exchange mass spectrometry reveals three unique binding responses of mAbs directed to the catalytic domain of hCAIX. mAbs (2021). 13. doi: 10.1080/19420862.2021.1997072

Corbeil, C. R.; Manenda, M. S.; Sulea, T.; Baardsnes, J.; Picard, M. È.; Hogues, H.; Gaudreault, F.; Deprez, C.; Shi, R.; Purisima, E. O. Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences. Scientific Reports (2021). 11. doi: 10.1038/s41598-021-00669-w

Akache, B.; Renner, T. M.; Tran, A.; Deschatelets, L.; Dudani, R.; Harrison, B. A.; Duque, D.; Haukenfrers, J.; Rossotti, M. A.; Gaudreault, F.; Hemraz, U. D.; Lam, E.; Régnier, S.; Chen, W.; Gervais, C.; Stuible, M.; Krishnan, L.; Durocher, Y.; McCluskie, M. J. Immunogenic and efficacious SARS-CoV-2 vaccine based on resistin-trimerized spike antigen SmT1 and SLA archaeosome adjuvant. Scientific Reports (2021). 11. doi: 10.1038/s41598-021-01363-7

van Faassen, H.; Ryan, S.; Henry, K. A.; Raphael, S.; Yang, Q.; Rossotti, M. A.; Brunette, E.; Jiang, S.; Haqqani, A. S.; Sulea, T.; MacKenzie, C. R.; Tanha, J.; Hussack, G. Serum albumin-binding VHHs with variable pH sensitivities enable tailored half-life extension of biologics. FASEB Journal (2020). 34:8155-8171. doi: 10.1096/fj.201903231R

Sulea, T.; Rohani, N.; Baardsnes, J.; Corbeil, C. R.; Deprez, C.; Cepero-Donates, Y.; Robert, A.; Schrag, J. D.; Parat, M.; Duchesne, M.; Jaramillo, M. L.; Purisima, E. O.; Zwaagstra, J. C. Structure-based engineering of pH-dependent antibody binding for selective targeting of solid-tumor microenvironment. mAbs (2020). 12. doi: 10.1080/19420862.2019.1682866

Zwaagstra, J. C.; Sulea, T.; Baardsnes, J.; Radinovic, S.; Cepero-Donates, Y.; Robert, A.; O'Connor-McCourt, M. D.; Tikhomirov, I. A.; Jaramillo, M. L. Binding and functional profiling of antibody mutants guides selection of optimal candidates as antibody drug conjugates. PLoS ONE (2019). 14. doi: 10.1371/journal.pone.0226593

Sharmeen, N.; Sulea, T.; Whiteway, M.; Wu, C. The adaptor protein Ste50 directly modulates yeast MAPK signaling specificity through differential connections of its RA domain. Molecular Biology of the Cell (2019). 30:794-807. doi: 10.1091/mbc.E18-11-0708

Schrag, J. D.; Picard, M. È.; Gaudreault, F.; Gagnon, L. P.; Baardsnes, J.; Manenda, M. S.; Sheff, J.; Deprez, C.; Baptista, C.; Hogues, H.; Kelly, J. F.; Purisima, E. O.; Shi, R.; Sulea, T. Binding symmetry and surface flexibility mediate antibody self-association. mAbs (2019). 11:1300-1318. doi: 10.1080/19420862.2019.1632114

Henry, K. A.; Hussack, G.; Kumaran, J.; Gilbert, M.; MacKenzie, C. R.; Sulea, T.; Arbabi-Ghahroudi, M. Role of the non-hypervariable FR3 D-E loop in single-domain antibody recognition of haptens and carbohydrates. Journal of Molecular Recognition (2019). 32. doi: 10.1002/jmr.2805

Chowdhury, S.; Beitel, L. K.; Lumbroso, R.; Purisima, E. O.; Paliouras, M.; Trifiro, M. A Targeted Bivalent Androgen Receptor Binding Compound for Prostate Cancer Therapy. Hormones and Cancer (2019). 10:24-35. doi: 10.1007/s12672-018-0353-6

Vaniotis, G.; Moffett, S.; Sulea, T.; Wang, N.; Elahi, S. M.; Lessard, E.; Baardsnes, J.; Perrino, S.; Durocher, Y.; Frystyk, J.; Massie, B.; Brodt, P. Enhanced anti-metastatic bioactivity of an IGF-TRAP re-engineered to improve physicochemical properties. Scientific Reports (2018). 8. doi: 10.1038/s41598-018-35407-2

Sulea, T.; Hussack, G.; Ryan, S.; Tanha, J.; Purisima, E. O. Application of Assisted Design of Antibody and Protein Therapeutics (ADAPT) improves efficacy of a Clostridium difficile toxin A single-domain antibody. Scientific Reports (2018). 8. doi: 10.1038/s41598-018-20599-4

Hogues, H.; Sulea, T.; Gaudreault, F.; Corbeil, C. R.; Purisima, E. O. Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method. Journal of Computer-Aided Molecular Design (2018). 32:143-150. doi: 10.1007/s10822-017-0071-0

Hogues, H.; Gaudreault, F.; Corbeil, C. R.; Deprez, C.; Sulea, T.; Purisima, E. O. ProPOSE: Direct Exhaustive Protein-Protein Docking with Side Chain Flexibility. Journal of Chemical Theory and Computation (2018). 14:4938-4947. doi: 10.1021/acs.jctc.8b00225

Hill, J. J.; Tremblay, T. L.; Corbeil, C. R.; Purisima, E. O.; Sulea, T. An accurate TMT-based approach to quantify and model lysine susceptibility to conjugation via N-hydroxysuccinimide esters in a monoclonal antibody. Scientific Reports (2018). 8. doi: 10.1038/s41598-018-35924-0

Vivcharuk, V.; Baardsnes, J.; Deprez, C.; Sulea, T.; Jaramillo, M.; Corbeil, C. R.; Mullick, A.; Magoon, J.; Marcil, A.; Durocher, Y.; O’Connor-McCourt, M. D.; Purisima, E. O. Assisted Design of Antibody and Protein Therapeutics (ADAPT). PLoS ONE (2017). 12. doi: 10.1371/journal.pone.0181490

Kim, S. K.; Barron, L.; Hinck, C. S.; Petrunak, E. M.; Cano, K. E.; Thangirala, A.; Iskra, B.; Brothers, M.; Vonberg, M.; Leal, B.; Richter, B.; Kodali, R.; Taylor, A. B.; Du, S.; Barnes, C. O.; Sulea, T.; Calero, G.; Hart, P. J.; Hart, M. J.; Demeler, B.; Hinck, A. P. An engineered transforming growth factor β (TGF-β) monomer that functions as a dominant negative to block TGF-β signaling. Journal of Biological Chemistry (2017). 292:7173-7188. doi: 10.1074/jbc.M116.768754

Sulea, T.; Vivcharuk, V.; Corbeil, C. R.; Deprez, C.; Purisima, E. O. Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities. Journal of Chemical Information and Modeling (2016). 56:1292-1303. doi: 10.1021/acs.jcim.6b00043

Shaneh, A.; Purisima, E. O.; Salavati, R.; Sulea, T. Structural Studies of Trypanosoma brucei RNA Editing Ligases and Their Binding Partner Proteins. Biochemistry (2016). 55:2319-2331. doi: 10.1021/acs.biochem.5b01257

Hogues, H.; Sulea, T.; Purisima, E. O. Evaluation of the Wilma-SIE Virtual Screening Method in Community Structure-Activity Resource 2013 and 2014 Blind Challenges. Journal of Chemical Information and Modeling (2016). 56:955-964. doi: 10.1021/acs.jcim.5b00278

Henry, K. A.; Sulea, T.; Van Faassen, H.; Hussack, G.; Purisima, E. O.; Roger MacKenzie, C.; Arbabi-Ghahroudi, M. A rational engineering strategy for designing protein a-binding camelid single-domain antibodies. PLoS ONE (2016). 11. doi: 10.1371/journal.pone.0163113

Wängler, C.; Chowdhury, S.; Höfner, G.; Djurova, P.; Purisima, E. O.; Bartenstein, P.; Wängler, B.; Fricker, G.; Wanner, K. T.; Schirrmacher, R. Shuttle-Cargo fusion molecules of transport peptides and the hD 2/3 receptor antagonist fallypride: A feasible approach to preserve ligand-receptor binding. Journal of Medicinal Chemistry (2014). 57:4368-4381. doi: 10.1021/jm5004123

Purisima, E. O.; Sulea, T. Solvation models: Theory and validation. Current Pharmaceutical Design (2014). 20:3266-3280. doi: 10.2174/13816128113199990599

Perron, M. D.; Chowdhury, S.; Aubry, I.; Purisima, E.; Tremblay, M. L.; Uri Saragovi, H. Allosteric noncompetitive small molecule selective inhibitors of CD45 tyrosine phosphatase suppress T-cell receptor signals and inflammation in vivo. Molecular Pharmacology (2014). 85:553-563. doi: 10.1124/mol.113.089847

Ménard, R.; Schoenhofen, I. C.; Tao, L.; Aubry, A.; Bouchard, P.; Reid, C. W.; Lachance, P.; Twine, S. M.; Fulton, K. M.; Cui, Q.; Hogues, H.; Purisima, E. O.; Sulea, T.; Logan, S. M. Small-molecule inhibitors of the pseudaminic acid biosynthetic pathway: Targeting motility as a key bacterial virulence factor. Antimicrobial Agents and Chemotherapy (2014). 58:7430-7440. doi: 10.1128/AAC.03858-14

Hogues, H.; Sulea, T.; Purisima, E. O. Exhaustive docking and solvated interaction energy scoring: Lessons learned from the SAMPL4 challenge. Journal of Computer-Aided Molecular Design (2014). 28:417-427. doi: 10.1007/s10822-014-9715-5

Yerko, V.; Sulea, T.; Ekiel, I.; Harcus, D.; Baardsnes, J.; Cyglera, M.; Whiteway, M.; Wu, C. Structurally unique interaction of RBD-like and PH domains is crucial for yeast pheromone signaling. Molecular Biology of the Cell (2013). 24:409-420. doi: 10.1091/mbc.E12-07-0516

Nägler, D. K.; Ménard, R.; Sulea, T. Cathepsin X. Handbook of Proteolytic Enzymes (2013). 2:1839-1844. doi: 10.1016/B978-0-12-382219-2.00415-4

Zwaagstra, J. C.; Sulea, T.; Baardsnes, J.; Lenferink, A. E. G.; Collins, C.; Cantin, C.; Paul-Roc, B.; Grothe, S.; Hossain, S.; Richer, L. P.; L'Abbé, D.; Tom, R.; Cass, B.; Durocher, Y.; O'Connor-McCourt, M. D. Engineering and therapeutic application of single-chain bivalent TGF-β family traps. Molecular Cancer Therapeutics (2012). 11:1477-1487. doi: 10.1158/1535-7163.MCT-12-0060

Sulea, T.; Purisima, E. O. Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models. Journal of Computer-Aided Molecular Design (2012). 26:661-667. doi: 10.1007/s10822-011-9522-1

Sulea, T.; Purisima, E. O. The solvated interaction energy method for scoring binding affinities. Methods in Molecular Biology (2012). 819:295-303. doi: 10.1007/978-1-61779-465-0_19

Sulea, T.; Hogues, H.; Purisima, E. O. Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction. Journal of Computer-Aided Molecular Design (2012). 26:617-633. doi: 10.1007/s10822-011-9529-7

Shi, R.; Munger, C.; Kalan, L.; Sulea, T.; Wright, G. D.; Cygler, M. Sulfonation of glycopeptide antibiotics by sulfotransferase StaL depends on conformational flexibility of aglycone scaffold. Proceedings of the National Academy of Sciences of the United States of America (2012). 109:11824-11829. doi: 10.1073/pnas.1205377109

Purisima, E. O.; Hogues, H. Protein - Ligand binding free energies from exhaustive docking. Journal of Physical Chemistry B (2012). 116:6872-6879. doi: 10.1021/jp212646s

Menard, R.; Sulea, T. Selective inhibition of USP7. Chemistry and Biology (2012). 19:437-438. doi: 10.1016/j.chembiol.2012.04.001

Zhang, W.; Sulea, T.; Tao, L.; Cui, Q.; Purisima, E. O.; Vongsamphanh, R.; Lachance, P.; Lytvyn, V.; Qi, H.; Li, Y.; Ménard, R. Contribution of active site residues to substrate hydrolysis by USP2: Insights into catalysis by ubiquitin specific proteases. Biochemistry (2011). 50:4775-4785. doi: 10.1021/bi101958h

Sulea, T.; Cui, Q.; Purisima, E. O. Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. benchmark in the CSAR-2010 scoring exercise. Journal of Chemical Information and Modeling (2011). 51:2066-2081. doi: 10.1021/ci2000242

Moshiri, H.; Acoca, S.; Kala, S.; Najafabadi, H. S.; Hogues, H.; Purisima, E.; Salavati, R. Naphthalene-based RNA editing inhibitor blocks RNA editing activities and editosome assembly in Trypanosoma brucei. Journal of Biological Chemistry (2011). 286:14178-14189. doi: 10.1074/jbc.M110.199646

Côte, P.; Sulea, T.; Dignard, D.; Wu, C.; Whiteway, M. Evolutionary reshaping of fungal mating pathway scaffold proteins. mBio (2011). 2. doi: 10.1128/mBio.00230-10

Askew, C.; Sellam, A.; Epp, E.; Mallick, J.; Hogues, H.; Mullick, A.; Nantel, A.; Whiteway, M. The zinc cluster transcription factor Ahr1p directs Mcm1p regulation of Candida albicans adhesion. Molecular Microbiology (2011). 79:940-953. doi: 10.1111/j.1365-2958.2010.07504.x

Acoca, S.; Cui, Q.; Shore, G. C.; Purisima, E. O. Molecular dynamics study of small molecule inhibitors of the Bcl-2 family. Proteins: Structure, Function and Bioinformatics (2011). 79:2624-2636. doi: 10.1002/prot.23083

Yergeau, E.; Hogues, H.; Whyte, L. G.; Greer, C. W. The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME Journal (2010). 4:1206-1214. doi: 10.1038/ismej.2010.41

Tong, W.; Gagnon, M.; Sprules, T.; Gilbert, M.; Chowdhury, S.; Meerovitch, K.; Hansford, K.; Purisima, E. O.; Blankenship, J. W.; Cheung, N. K. V.; Gehring, K.; Lubell, W. D.; Saragovi, H. U. Small-Molecule Ligands of GD2 Ganglioside, Designed from NMR Studies, Exhibit Induced-Fit Binding and Bioactivity. Chemistry and Biology (2010). 17:183-194. doi: 10.1016/j.chembiol.2010.01.012

Sulea, T.; Corbeil, C. R.; Purisima, E. O. Rapid prediction of solvation free energy. 1. An extensive test of linear interaction energy (LIE). Journal of Chemical Theory and Computation (2010). 6:1608-1621. doi: 10.1021/ct9006025

Shaya, D.; Zhao, W.; Garron, M. L.; Xiao, Z.; Cui, Q.; Zhang, Z.; Sulea, T.; Linhardt, R. J.; Cygler, M. Catalytic mechanism of heparinase II investigated by site-directed mutagenesis and the crystal structure with its substrate. Journal of Biological Chemistry (2010). 285:20051-20061. doi: 10.1074/jbc.M110.101071

Sellam, A.; Hogues, H.; Askew, C.; Tebbji, F.; van het Hoog, M.; Lavoie, H.; Kumamoto, C. A.; Whiteway, M.; Nantel, A. Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays. Genome Biology (2010). 11. doi: 10.1186/gb-2010-11-7-r71

Purisima, E. O.; Corbeil, C. R.; Sulea, T. Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge. Journal of Computer-Aided Molecular Design (2010). 24:373-383. doi: 10.1007/s10822-010-9341-9

Naudin, C.; Lecaille, F.; Chowdhury, S.; Krupa, J. C.; Purisima, E.; Mort, J. S.; Lalmanach, G. The Occluding Loop of Cathepsin B Prevents Its Effective Inhibition by Human Kininogens. Journal of Molecular Biology (2010). 400:1022-1035. doi: 10.1016/j.jmb.2010.06.006

Li, J.; Lenferink, A. E. G.; Deng, Y.; Collins, C.; Cui, Q.; Purisima, E. O.; O'Connor-McCourt, M. D.; Wang, E. Identification of high-quality cancer prognostic markers and metastasis network modules. Nature Communications (2010). 1. doi: 10.1038/ncomms1033

Lavoie, H.; Hogues, H.; Mallick, J.; Sellam, A.; Nantel, A.; Whiteway, M. Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biology (2010). 8. doi: 10.1371/journal.pbio.1000329

Grosse, S.; Bergeron, H.; Imura, A.; Boyd, J.; Wang, S.; Kubota, K.; Miyadera, A.; Sulea, T.; Lau, P. C. K. Nature versus nurture in two highly enantioselective esterases from Bacillus cereus and Thermoanaerobacter tengcongensis. Microbial Biotechnology (2010). 3:65-73. doi: 10.1111/j.1751-7915.2009.00142.x

Corbeil, C. R.; Sulea, T.; Purisima, E. O. Rapid prediction of solvation free energy. 2. the first-shell hydration (FISH) continuum model. Journal of Chemical Theory and Computation (2010). 6:1622-1637. doi: 10.1021/ct9006037

Brahimi, F.; Liu, J.; Malakhov, A.; Chowdhury, S.; Purisima, E. O.; Ivanisevic, L.; Caron, A.; Burgess, K.; Saragovi, H. U. A monovalent agonist of TrkA tyrosine kinase receptors can be converted into a bivalent antagonist. Biochimica et Biophysica Acta - General Subjects (2010). 1800:1018-1026. doi: 10.1016/j.bbagen.2010.06.007

Sulea, T.; Wanapun, D.; Dennis, S.; Purisima, E. O. Prediction of SAMPL-1 hydration free energies using a continuum electrostatics-dispersion model. Journal of Physical Chemistry B (2009). 113:4511-4520. doi: 10.1021/jp8061477

Shi, R.; Proteau, A.; Wagner, J.; Cui, Q.; Purisima, E. O.; Matte, A.; Cygler, M. Trapping open and closed forms of FitE - A group III periplasmic binding protein. Proteins: Structure, Function and Bioinformatics (2009). 75:598-609. doi: 10.1002/prot.22272

Shi, R.; Lamb, S. S.; Zakeri, B.; Proteau, A.; Cui, Q.; Sulea, T.; Matte, A.; Wright, G. D.; Cygler, M. Structure and Function of the Glycopeptide N-methyltransferase MtfA, a Tool for the Biosynthesis of Modified Glycopeptide Antibiotics. Chemistry and Biology (2009). 16:401-410. doi: 10.1016/j.chembiol.2009.02.007

Shenoy, R. T.; Chowdhury, S. F.; Kumar, S.; Joseph, L.; Purisima, E. O.; Sivaraman, J. A combined crystallographic and molecular dynamics study of cathepsin L retrobinding inhibitors. Journal of Medicinal Chemistry (2009). 52:6335-6346. doi: 10.1021/jm900596y

Rangarajan, E. S.; Proteau, A.; Cui, Q.; Logan, S. M.; Potetinova, Z.; Whitfield, D.; Purisima, E. O.; Cygler, M.; Matte, A.; Sulea, T.; Schoenhofen, I. C. Structural and functional analysis of Campylobacter jejuni PseG. A UDP-sugar hydrolase from the pseudaminic acid biosynthetic pathway. Journal of Biological Chemistry (2009). 284:20989-21000. doi: 10.1074/jbc.M109.012351

Purisima, E. O.; Sulea, T. Restoring charge asymmetry in continuum electrostatics calculations of hydration free energies. Journal of Physical Chemistry B (2009). 113:8206-8209. doi: 10.1021/jp9020799

Lavoie, H.; Hogues, H.; Whiteway, M. Rearrangements of the transcriptional regulatory networks of metabolic pathways in fungi. Current Opinion in Microbiology (2009). 12:655-663. doi: 10.1016/j.mib.2009.09.015

Jarussophon, S.; Acoca, S.; Gao, J. M.; Deprez, C.; Kiyota, T.; Draghici, C.; Purisima, E.; Konishi, Y. Automated molecular formula determination by tandem mass spectrometry (MS/MS). Analyst (2009). 134:690-700. doi: 10.1039/b818398h

Ekiel, I.; Sulea, T.; Jansen, G.; Kowalik, M.; Minailiuc, O.; Cheng, J.; Harcus, D.; Cygler, M.; Whiteway, M.; Wu, C. Binding the atypical RA domain of Ste50p to the unfolded Opy2p cytoplasmic tail is essential for the high-osmolarity glycerol pathway. Molecular Biology of the Cell (2009). 20:5117-5126. doi: 10.1091/mbc.E09-07-0645

Cui, Q.; Purisima, E. O.; Wang, E. Protein evolution on a human signaling network. BMC Systems Biology (2009). 3. doi: 10.1186/1752-0509-3-21

Côte, P.; Hogues, H.; Whiteway, M. Transcriptional analysis of the Candida albicans cell cycle. Molecular Biology of the Cell (2009). 20:3363-3373. doi: 10.1091/mbc.E09-03-0210

Askew, C.; Sellam, A.; Epp, E.; Hogues, H.; Mullick, A.; Nantel, A.; Whiteway, M. Transcriptional regulation of carbohydrate metabolism in the human pathogen Candida albicans. PLoS Pathogens (2009). 5. doi: 10.1371/journal.ppat.1000612

Arbour, M.; Epp, E.; Hogues, H.; Sellam, A.; Lacroix, C.; Rauceo, J.; Mitchell, A.; Whiteway, M.; Nantel, A. Widespread occurrence of chromosomal aneuploidy following the routine production of Candida albicans mutants. FEMS Yeast Research (2009). 9:1070-1077. doi: 10.1111/j.1567-1364.2009.00563.x

Xiao, Z.; Bergeron, H.; Grosse, S.; Beauchemin, M.; Garron, M. L.; Shaya, D.; Sulea, T.; Cygler, M.; Lau, P. C. K. Improvement of the thermostability and activity of a pectate lyase by single amino acid substitutions, using a strategy based on melting-temperature- guided sequence alignment. Applied and Environmental Microbiology (2008). 74:1183-1189. doi: 10.1128/AEM.02220-07

Tessier, D. C.; Arbour, M.; Benoit, F.; Hogues, H.; Rigby, T. A DNA Microarray Fabrication Strategy for Research Laboratories. Handbook of Genome Research: Genomics, Proteomics, Metabolomics, Bioinformatics, Ethical and Legal Issues (2008). 223-238. doi: 10.1002/9783527619733.ch9

Southwell, J.; Chowdhury, S. F.; Gottlieb, B.; Beitel, L. K.; Lumbroso, R.; Purisima, E. O.; Trifiro, M. An investigation into CAG repeat length variation and N/C terminal interactions in the T877A mutant androgen receptor found in prostate cancer. Journal of Steroid Biochemistry and Molecular Biology (2008). 111:138-146. doi: 10.1016/j.jsbmb.2008.04.009

Serbielle, C.; Chowdhury, S.; Pichon, S.; Dupas, S.; Lesobre, J.; Purisima, E. O.; Drezen, J. M.; Huguet, E. Viral cystatin evolution and three-dimensional structure modelling: A case of directional selection acting on a viral protein involved in a host-parasitoid interaction. BMC Biology (2008). 6. doi: 10.1186/1741-7007-6-38

Rangarajan, E. S.; Ruane, K. M.; Sulea, T.; Watson, D. C.; Proteau, A.; Leclerc, S.; Cygler, M.; Matte, A.; Young, N. M. Structure and active site residues of PglD, an N-acetyltransferase from the bacillosamine synthetic pathway required for N-glycan synthesis in Campylobacter jejuni. Biochemistry (2008). 47:1827-1836. doi: 10.1021/bi702032r

Lindner, H. A.; Alary, A.; Wilke, M.; Sulea, T. Probing the acy1-binding pocket of aminoacylase-1. Biochemistry (2008). 47:4266-4275. doi: 10.1021/bi702156h

Hogues, H.; Lavoie, H.; Sellam, A.; Mangos, M.; Roemer, T.; Purisima, E.; Nantel, A.; Whiteway, M. Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation. Molecular Cell (2008). 29:552-562. doi: 10.1016/j.molcel.2008.02.006

Cui, Q.; Sulea, T.; Schrag, J. D.; Munger, C.; Hung, M. N.; Naïm, M.; Cygler, M.; Purisima, E. O. Molecular Dynamics-Solvated Interaction Energy Studies of Protein-Protein Interactions: The MP1-p14 Scaffolding Complex. Journal of Molecular Biology (2008). 379:787-802. doi: 10.1016/j.jmb.2008.04.035

Chowdhury, S. F.; Joseph, L.; Kumar, S.; Tulsidas, S. R.; Bhat, S.; Ziomek, E.; Ménard, R.; Sivaraman, J.; Purisima, E. O. Exploring inhibitor binding at the S′ subsites of cathepsin L. Journal of Medicinal Chemistry (2008). 51:1361-1368. doi: 10.1021/jm701190v

Zhu, X.; Ménard, R.; Sulea, T. High incidence of ubiquitin-like domains in human ubiquitin-specific proteases. Proteins: Structure, Function and Genetics (2007). 69:1-7. doi: 10.1002/prot.21546

Yu, Z.; Jian, Z.; Shen, S. H.; Purisima, E.; Wang, E. Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos. Nucleic Acids Research (2007). 35:152-164. doi: 10.1093/nar/gkl1032

Van het Hoog, M.; Rast, T. J.; Martchenko, M.; Grindle, S.; Dignard, D.; Hogues, H.; Cuomo, C.; Berriman, M.; Scherer, S.; Magee, B. B.; Whiteway, M.; Chibana, H.; Nantel, A.; Magee, P. T. Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biology (2007). 8. doi: 10.1186/gb-2007-8-4-r52

Shi, R.; Lamb, S. S.; Bhat, S.; Sulea, T.; Wright, G. D.; Matte, A.; Cygler, M. Crystal structure of StaL, a glycopeptide antibiotic sulfotransferase from Streptomyces toyocaensis. Journal of Biological Chemistry (2007). 282:13073-13086. doi: 10.1074/jbc.M611912200

Reis, F. C. G.; Costa, T. F. R.; Sulea, T.; Mezzetti, A.; Scharfstein, J.; Brömme, D.; Ménard, R.; Lima, A. P. C. A. The propeptide of cruzipain - A potent selective inhibitor of the trypanosomal enzymes cruzipain and brucipain, and of the human enzyme cathepsin F. FEBS Journal (2007). 274:1224-1234. doi: 10.1111/j.1742-4658.2007.05666.x

Prakesch, M.; Arya, P.; Naim, M.; Sulea, T.; Purisima, E.; Denisov, A. Y.; Gehring, K.; Foster, T. L.; Korneluk, R. G. Combinatorial Synthesis of Alkaloid-like Compounds In Search of Chemical Probes of Protein-Protein Interactions. Modern Alkaloids: Structure, Isolation, Synthesis and Biology (2007). 521-540. doi: 10.1002/9783527621071.ch17

Nguyen, M.; Marcellus, R. C.; Roulston, A.; Watson, M.; Serfass, L.; Murthy Madiraju, S. R.; Goulet, D.; Viallet, J.; Bélec, L.; Billot, X.; Acoca, S.; Purisima, E.; Wiegmans, A.; Cluse, L.; Johnstone, R. W.; Beauparlant, P.; Shore, G. C. Small molecule obatoclax (GX15-070) antagonizes MCL-1 and overcomes MCL-1-mediated resistance to apoptosis. Proceedings of the National Academy of Sciences of the United States of America (2007). 104:19512-19517. doi: 10.1073/pnas.0709443104

Nantel, A.; Rigby, T.; Hogues, H.; Whiteway, M. Microarrays for Studying Pathogenicity in Candida Albicans. Medical Mycology: Cellular and Molecular Techniques (2007). 181-209. doi: 10.1002/9780470057414.ch9

Naïm, M.; Bhat, S.; Rankin, K. N.; Dennis, S.; Chowdhury, S. F.; Siddiqi, I.; Drabik, P.; Sulea, T.; Bayly, C. I.; Jakalian, A.; Purisima, E. O. Solvated Interaction Energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space. Journal of Chemical Information and Modeling (2007). 47:122-133. doi: 10.1021/ci600406v

Martchenko, M.; Levitin, A.; Hogues, H.; Nantel, A.; Whiteway, M. Transcriptional Rewiring of Fungal Galactose-Metabolism Circuitry. Current Biology (2007). 17:1007-1013. doi: 10.1016/j.cub.2007.05.017

Lecaille, F.; Chowdhury, S.; Purisima, E.; Brömme, D.; Lalmanach, G. The S2 subsites of cathepsins K and L and their contribution to collagen degradation. Protein Science (2007). 16:662-670. doi: 10.1110/ps.062666607

Konishi, Y.; Kiyota, T.; Draghici, C.; Gao, J. M.; Yeboah, F.; Acoca, S.; Jarussophon, S.; Purisima, E. Molecular formula analysis by an MS/MS/MS technique to expedite dereplication of natural products. Analytical Chemistry (2007). 79:1187-1197. doi: 10.1021/ac061391o

Iwaki, H.; Muraki, T.; Ishihara, S.; Hasegawa, Y.; Rankin, K. N.; Sulea, T.; Boyd, J.; Lau, P. C. K. Characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis. Journal of Bacteriology (2007). 189:3502-3514. doi: 10.1128/JB.01098-06

Cui, Q.; Yu, Z.; Purisima, E. O.; Wang, E. MicroRNA regulation and interspecific variation of gene expression. Trends in Genetics (2007). 23:372-375. doi: 10.1016/j.tig.2007.04.003

Cui, Q.; Yu, Z.; Pan, Y.; Purisima, E. O.; Wang, E. MicroRNAs preferentially target the genes with high transcriptional regulation complexity. Biochemical and Biophysical Research Communications (2007). 352:733-738. doi: 10.1016/j.bbrc.2006.11.080

Cui, Q.; Ma, Y.; Jaramillo, M.; Bari, H.; Awan, A.; Yang, S.; Zhang, S.; Liu, L.; Lu, M.; O'Connor-Mccourt, M.; Purisima, E. O.; Wang, E. A map of human cancer signaling. Molecular Systems Biology (2007). 3. doi: 10.1038/msb4100200

Awan, A.; Bari, H.; Yan, F.; Moksong, S.; Yang, S.; Chowdhury, S.; Cui, Q.; Yu, Z.; Purisima, E. O.; Wang, E. Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network. IET Systems Biology (2007). 1:292-297. doi: 10.1049/iet-syb:20060068

Sulea, T.; Lindner, H. A.; Purisima, E. O.; Ménard, R. Binding site-based classification of coronaviral papain-like proteases. Proteins: Structure, Function and Genetics (2006). 62:760-775. doi: 10.1002/prot.20802

Sulea, T.; Lindner, H. A.; Ménard, R. Structural aspects of recently discovered viral deubiquitinating activities. Biological Chemistry (2006). 387:853-862. doi: 10.1515/BC.2006.108

Hung, M. N.; Rangarajan, E.; Munger, C.; Nadeau, G.; Sulea, T.; Matte, A. Crystal structure of TDP-fucosamine acetyltransferase (WecD) from Escherichia coli, an enzyme required for enterobacterial common antigen synthesis. Journal of Bacteriology (2006). 188:5606-5617. doi: 10.1128/JB.00306-06

Elhaji, Y. A.; Stoica, I.; Dennis, S.; Purisima, E. O.; Trifiro, M. A. Impaired helix 12 dynamics due to proline 892 substitutions in the androgen receptor are associated with complete androgen insensitivity. Human Molecular Genetics (2006). 15:921-931. doi: 10.1093/hmg/ddl009

Cui, Q.; Yu, Z.; Purisima, E. O.; Wang, E. Principles of microRNA regulation of a human cellular signaling network. Molecular Systems Biology (2006). 2. doi: 10.1038/msb4100089

Bhat, S.; Sulea, T.; Purisima, E. O. Coupled atomic charge selectivity for optimal ligand-charge distributions at protein binding sites. Journal of Computational Chemistry (2006). 27:1899-1907. doi: 10.1002/jcc.20481

Bhat, S.; Purisima, E. O. Molecular surface generation using a variable-radius solvent probe. Proteins: Structure, Function and Genetics (2006). 62:244-261. doi: 10.1002/prot.20682

Wang, E.; Purisima, E. Network motifs are enriched with transcription factors whose transcripts have short half-lives. Trends in Genetics (2005). 21:492-495. doi: 10.1016/j.tig.2005.06.013

Sulea, T.; Lindner, H. A.; Purisima, E. O.; Ménard, R. Deubiquitination, a new function of the severe acute respiratory syndrome coronavirus papain-like protease. Journal of Virology (2005). 79:4550-4551. doi: 10.1128/JVI.79.7.4550-4551.2005

Sivaraman, J.; Myers, R. S.; Boju, L.; Sulea, T.; Cygler, M.; Davisson, V. J.; Schrag, J. D. Crystal structure of Methanobacterium thermoautotrophicum phosphoribosyl-AMP cyclohydrolase hisI. Biochemistry (2005). 44:10071-10080. doi: 10.1021/bi050472w

Segall, L.; Mezzetti, A.; Scanzano, R.; Gargus, J. J.; Purisima, E.; Blostein, R. Alterations in the α2 isoform of Na, K-ATPase associated with familial hemiplegic migraine type 2. Proceedings of the National Academy of Sciences of the United States of America (2005). 102:11106-11111. doi: 10.1073/pnas.0504323102

Lindner, H. A.; Fotouhi-Ardakani, N.; Lytvyn, V.; Lachance, P.; Sulea, T.; Ménard, R. The papain-like protease from the severe acute respiratory syndrome coronavirus is a deubiquitinating enzyme. Journal of Virology (2005). 79:15199-15208. doi: 10.1128/JVI.79.24.15199-15208.2005

Lindner, H. A.; Alary, A.; Boju, L. I.; Sulea, T.; Ménard, R. Roles of dimerization domain residues in binding and catalysis by aminoacylase-1. Biochemistry (2005). 44:15645-15651. doi: 10.1021/bi051180y

Godat, E.; Chowdhury, S.; Lecaille, F.; Belghazi, M.; Purisima, E. O.; Lalmanach, G. Inhibition of a cathepsin L-like cysteine protease by a chimeric propeptide-derived inhibitor. Biochemistry (2005). 44:10486-10493. doi: 10.1021/bi047590o

Devanathan, G.; Turnbull, J. L.; Ziomek, E.; Purisima, E. O.; Ménard, R.; Sulea, T. Carboxy-monopeptidase substrate specificity of human cathepsin X. Biochemical and Biophysical Research Communications (2005). 329:445-452. doi: 10.1016/j.bbrc.2005.01.150

Braun, B. R.; van het Hoog, M.; d'Enfert, C.; Martchenko, M.; Dungan, J.; Kuo, A.; Inglis, D. O.; Uhl, M. A.; Hogues, H.; Berriman, M.; Lorenz, M.; Levitin, A.; Oberholzer, U.; Bachewich, C.; Harcus, D.; Marcil, A.; Dignard, D.; Iouk, T.; Zito, R.; Frangeul, L.; Tekaia, F.; Rutherford, K.; Wang, E.; Munro, C. A.; Bates, S.; Gow, N. A.; Hoyer, L. L.; Köhler, G.; Morschhäuser, J.; Newport, G.; Znaidi, S.; Raymond, M.; Turcotte, B.; Sherlock, G.; Costanzo, M.; Ihmels, J.; Berman, J.; Sanglard, D.; Agabian, N.; Mitchell, A. P.; Johnson, A. D.; Whiteway, M.; Nantel, A. A human-curated annotation of the Candida albicans genome. PLoS Genetics (2005). 1:0036-0057. doi: 10.1371/journal.pgen.0010001

Zhao, H. F.; Kiyota, T.; Chowdhury, S.; Purisima, E.; Banville, D.; Konishi, Y.; Shen, S. H. A mammalian genetic system to screen for small molecules capable of disrupting protein-protein interactions. Analytical Chemistry (2004). 76:2922-2927. doi: 10.1021/ac035396m

Yeboah, F. K.; Alli, I.; Yaylayan, V. A.; Yasuo, K.; Chowdhury, S. F.; Purisima, E. O. Effect of Limited Solid-State Glycation on the Conformation of Lysozyme by ESI-MSMS Peptide Mapping and Molecular Modeling. Bioconjugate Chemistry (2004). 15:27-34. doi: 10.1021/bc034083v

Mouchantaf, R.; Watt, H. L.; Sulea, T.; Seidah, N. G.; Alturaihi, H.; Patel, Y. C.; Kumar, U. Prosomatostatin is proteolytically processed at the amino terminal segment by subtilase SKI-1. Regulatory Peptides (2004). 120:133-140. doi: 10.1016/j.regpep.2004.02.022

Michel, G.; Pojasek, K.; Li, Y.; Sulea, T.; Linhardt, R. J.; Raman, R.; Prabhakar, V.; Sasisekharan, R.; Cygler, M. The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery. Journal of Biological Chemistry (2004). 279:32882-32896. doi: 10.1074/jbc.M403421200

Zhou, N. E.; Guo, D.; Thomas, G.; Reddy, A. V. N.; Kaleta, J.; Purisima, E.; Menard, R.; Micetich, R. G.; Singh, R. 3-Acylamino-azetidin-2-one as a novel class of cysteine proteases inhibitors. Bioorganic and Medicinal Chemistry Letters (2003). 13:139-141. doi: 10.1016/S0960-894X(02)00831-4

Wu, J. H.; Gottlieb, B.; Batist, G.; Sulea, T.; Purisima, E. O.; Beitel, L. K.; Trifiro, M. 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. Human Mutation (2003). 22:465-475. doi: 10.1002/humu.10279

Sulea, T.; Purisima, E. O. Profiling charge complementarity and selectivity for binding at the protein surface. Biophysical Journal (2003). 84:2883-2896. doi: 10.1016/S0006-3495(03)70016-2

Rankin, K. N.; Sulea, T.; Purisima, E. O. On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations. Journal of Computational Chemistry (2003). 24:954-962. doi: 10.1002/jcc.10261

Pauly, T. A.; Sulea, T.; Ammirati, M.; Sivaraman, J.; Danley, D. E.; Griffor, M. C.; Kamath, A. V.; Wang, I. K.; Laird, E. R.; Seddon, A. P.; Ménard, R.; Cygler, M.; Rath, V. L. Specificity determinants of human cathepsin S revealed by crystal structures of complexes. Biochemistry (2003). 42:3203-3213. doi: 10.1021/bi027308i

Zhou, N. E.; Kaleta, J.; Purisima, E.; Menard, R.; Micetich, R. G.; Singh, R. 6-Acylamino-penam derivatives: Synthesis and inhibition of cathepsins B, L, K, and S. Bioorganic and Medicinal Chemistry Letters (2002). 12:3417-3419. doi: 10.1016/S0960-894X(02)00766-7

Zhou, N. E.; Guo, D.; Kaleta, J.; Purisima, E.; Menard, R.; Micetich, R. G.; Singh, R. Design and synthesis of 6-substituted amino-4-oxa-1-azabicyclo[3,2,0]heptan-7-one derivatives as cysteine proteases inhibitors. Bioorganic and Medicinal Chemistry Letters (2002). 12:3413-3415. doi: 10.1016/S0960-894X(02)00765-5

Vasilyev, V.; Purisima, E. O. A fast pairwise evaluation of molecular surface area. Journal of Computational Chemistry (2002). 23:737-745. doi: 10.1002/jcc.10035

Vasilyev, V. Determination of the effective dielectric constant from the accurate solution of the Poisson equation. Journal of Computational Chemistry (2002). 23:1254-1265. doi: 10.1002/jcc.10131

Nantel, A.; Dignard, D.; Bachewich, C.; Harcus, D.; Marcil, A.; Bouin, A. P.; Sensen, C. W.; Hogues, H.; Van het Hoog, M.; Gordon, P.; Rigby, T.; Benoit, F.; Tessier, D. C.; Thomas, D. Y.; Whiteway, M. Transcription profiling of Candida albicans cells undergoing the yeast-to-hyphal transition. Molecular Biology of the Cell (2002). 13:3452-3465. doi: 10.1091/mbc.E02-05-0272

Lin, L. Y. C.; Sulea, T.; Szittner, R.; Kor, C.; Purisima, E. O.; Meighen, E. A. Implications of the reactive thiol and the proximal non-proline cis-peptide bond in the structure and function of Vibrio harveyi luciferase. Biochemistry (2002). 41:9938-9945. doi: 10.1021/bi020295o

Guimond, A.; Sulea, T.; Zwaagstra, J. C.; Ekiel, I.; O'Connor-McCourt, M. D. Identification of a functional site on the type I TGF-β receptor by mutational analysis of its ectodomain. FEBS Letters (2002). 513:147-152. doi: 10.1016/S0014-5793(01)03231-8

Guimond, A.; Sulea, T.; Pen, A.; Ear, P.; O'Connor-McCourt, M. D. Site-directed mutagenesis of the type II TGF-β receptor indicates a ligand-binding site distinct from that of the type II activin receptor. FEBS Letters (2002). 515:13-19. doi: 10.1016/S0014-5793(02)02378-5

Chowdhury, S. F.; Sivaraman, J.; Wang, J.; Devanathan, G.; Lachance, P.; Qi, H.; Ménard, R.; Lefebvre, J.; Konishi, Y.; Cygler, M.; Sulea, T.; Purisima, E. O. Design of noncovalent inhibitors of human cathepsin L. from the 96-residue proregion to optimized tripeptides. Journal of Medicinal Chemistry (2002). 45:5321-5329. doi: 10.1021/jm020238t

Therrien, C.; Lachance, P.; Sulea, T.; Purisima, E. O.; Qi, H.; Ziomek, E.; Alvarez-Hernandez, A.; Roush, W. R.; Ménard, R. Cathepsins X and B can be differentiated through their respective mono- and dipeptidyl carboxypeptidase activities. Biochemistry (2001). 40:2702-2711. doi: 10.1021/bi002460a

Sulea, T.; Purisima, E. O. Optimizing Ligand Charges for Maximum Binding Affinity. A Solvated Interaction Energy Approach. Journal of Physical Chemistry B (2001). 105:889-899. doi: 10.1021/jp0038714

Mouchantaf, R.; Kumar, U.; Sulea, T.; Patel, Y. C. A Conserved α-Helix at the Amino Terminus of Prosomatostatin Serves as a Sorting Signal for the Regulated Secretory Pathway. Journal of Biological Chemistry (2001). 276:26308-26316. doi: 10.1074/jbc.M102514200

Ménard, R.; Therrien, C.; Lachance, P.; Sulea, T.; Qi, H.; Alvarez-Hernandez, A.; Roush, W. R. Cathepsins X and B display distinct activity profiles that can be exploited for inhibitor design. Biological Chemistry (2001). 382:839-845. doi: 10.1515/BC.2001.102

Lin, L. Y. C.; Sulea, T.; Szittner, R.; Vassilyev, V.; Purisima, E. O.; Meighen, E. A. Modeling of the bacterial luciferase-flavin mononucleotide complex combining flexible docking with structure-activity data. Protein Science (2001). 10:1563-1571. doi: 10.1110/ps.7201

Ménard, R.; Nägler, D. K.; Zhang, R.; Tam, W.; Sulea, T.; Purisima, E. O. Human cathepsin X: A novel cysteine protease with unique specificity. Advances in Experimental Medicine and Biology (2000). 477:317-322.

Kohls, D.; Sulea, T.; Purisima, E. O.; MacKenzie, R. E.; Vrielink, A. The crystal structure of the formiminotransferase domain of formiminotransferase-cyclodeaminase: Implications for substrate channeling in a bifunctional enzyme. Structure (2000). 8:35-46. doi: 10.1016/S0969-2126(00)00078-2

Sulea, T.; Purisima, E. O. Desolvation free energy field derived from boundary element continuum dielectric calculations. Quantitative Structure-Activity Relationships (1999). 18:154-158. doi: 10.1002/(SICI)1521-3838(199906)18:2<154::AID-QSAR154>3.0.CO:2-W

Schleiff, E.; Sulea, T. Structure determination and prediction: A study on human Tom20. Journal of Molecular Structure: THEOCHEM (1999). 468:127-134. doi: 10.1016/S0166-1280(98)00504-1

Nägler, D. K.; Zhang, R.; Tam, W.; Sulea, T.; Purisima, E. O.; Ménard, R. Human cathepsin X: A cysteine protease with unique carboxypeptidase activity. Biochemistry (1999). 38:12648-12654. doi: 10.1021/bi991371z

Nägler, D. K.; Sulea, T.; Ménard, R. Full-length cDNA of human cathepsin F predicts the presence of a cystatin domain at the N-terminus of the cysteine protease zymogen. Biochemical and Biophysical Research Communications (1999). 257:313-318. doi: 10.1006/bbrc.1999.0461

Guimond, A.; Sulea, T.; Pepin, M. C.; O'Connor-Mccourt, M. D. Mapping of putative binding sites on the ectodomain of the type II TGF-β receptor by scanning-deletion mutagenesis and knowledge-based modeling. FEBS Letters (1999). 456:79-84. doi: 10.1016/S0014-5793(99)00869-8

Sulea, T.; Purisima, E. O. Comparative molecular field analysis of protein tyrosine phosphatase low-molecular-weight substrates. Journal of Molecular Structure: THEOCHEM (1998). 434:139-153. doi: 10.1016/S0166-1280(98)00082-7

Purisima, E. O. Fast summation boundary element method for calculating solvation free energies of macromolecules. Journal of Computational Chemistry (1998). 19:1494-1504. doi: 10.1002/(SICI)1096-987X(199810)19:13<1494::AID-JCC6>3.0.CO:2-L

Chan, S. L.; Purisima, E. O. Molecular surface generation using marching tetrahedra. Journal of Computational Chemistry (1998). 19:1268-1277. doi: 10.1002/(SICI)1096-987X(199808)19:11<1268::AID-JCC6>3.0.CO:2-I

Chan, S. L.; Purisima, E. O. A new tetrahedral tesselation scheme for isosurface generation. Computers and Graphics (Pergamon) (1998). 22:83-90. doi: 10.1016/S0097-8493(97)00085-X

Sulea, T.; Oprea, T. I.; Muresan, S.; Chan, S. L. A different method for steric field evaluation in CoMFA improves model robustness. Journal of Chemical Information and Computer Sciences (1997). 37:1162-1170. doi: 10.1021/ci9704221

Slon-Usakiewicz, J. J.; Purisima, E.; Tsuda, Y.; Sulea, T.; Pedyczak, A.; Féthière, J.; Cygler, M.; Konishi, Y. Nonpolar interactions of thrombin S' subsites with its bivalent inhibitor: Methyl scan of the inhibitor linker. Biochemistry (1997). 36:13494-13502. doi: 10.1021/bi970857h

Illy, C.; Quraishi, O.; Wang, J.; Purisima, E.; Vernet, T.; Mort, J. S. Role of the occluding loop in cathepsin B activity. Journal of Biological Chemistry (1997). 272:1197-1202. doi: 10.1074/jbc.272.2.1197

Cheng, Y.; Slon-Usakiewicz, J.; Wang, J.; Purisima, E. O.; Konishi, Y. Thermodynamic investigation of enzyme and inhibitor interactions with high affinity. Techniques in Protein Chemistry (1997). 8:513-521. doi: 10.1016/S1080-8914(97)80051-8

Wang, J.; Purisima, E. O. Analysis of thermodynamic determinants in helix propensities of nonpolar amino acids through a novel free energy calculation. Journal of the American Chemical Society (1996). 118:995-1001. doi: 10.1021/ja953347o

Cheng, Y.; Slon-Usakiewicz, J. J.; Wang, J.; Purisima, E. O.; Konishi, Y. Nonpolar interactions of thrombin and its inhibitors at the fibrinogen recognition exosite: Thermodynamic analysis. Biochemistry (1996). 35:13021-13029. doi: 10.1021/bi961039c

Brömme, D.; Bonneau, P. R.; Purisima, E.; Lachance, P.; Hajnik, S.; Thomas, D. Y.; Storer, A. C. Contribution to activity of histidine-aromatic, amide-aromatic, and aromatic-aromatic interactions in the extended catalytic site of cysteine proteinases. Biochemistry (1996). 35:3970-3979. doi: 10.1021/bi9523015

Wang, J.; Szewczuk, Z.; Yue, S. Y.; Tsuda, Y.; Konishi, Y.; Purisima, E. O. Calculation of relative binding free energies and configurational entropies: A structural and thermodynamic analysis of the nature of non-polar binding of thrombin inhibitors based on hirudin55-65. Journal of Molecular Biology (1995). 253:473-492. doi: 10.1006/jmbi.1995.0567

Tsuda, Y.; Szewczuk, Z.; Wang, J.; Yue, S. Y.; Purisima, E.; Konishi, Y. Interactions of Hirudin-Based Inhibitor with Thrombin: Critical Role of the IleH59 Side Chain of the Inhibitor. Biochemistry (1995). 34:8708-8714. doi: 10.1021/bi00027a021

Purisima, E. O.; Nilar, S. H. A simple yet accurate boundary element method for continuum dielectric calculations. Journal of Computational Chemistry (1995). 16:681-689. doi: 10.1002/jcc.540160604

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