publications

 

2017


46. Najmanovich RJ. Evolutionary studies of ligand binding sites in proteins. Curr Opin Struct Biol. 2017;45: 85–90. PubMed | Journal | PDF

45. Chénard T, Guénard F, Vohl M-C, Carpentier A, Tchernof A, Najmanovich RJ. Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes. BMC Systems Biology. 2017;11: 615. PubMed | Journal | PDF

44. Chartier M, Morency L-P, Zylber MI, Najmanovich RJ. Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects. BMC Pharmacol Toxicol. 2017;18: 1046. PubMed | Journal | PDF

43. St-Georges C, Désilets A, Béliveau F, Ghinet M, Dion SP, Colombo E, Boudreault P-L, Najmanovich RJ, Leduc R & Marsault E. Modulating the selectivity of matriptase-2 inhibitors with unnatural amino acids. European Journal of Medicinal Chemistry. 2017;129: 110–123. PubMed | Journal | PDF

42. Frappier V, Chartier M, Najmanovich R. Applications of Normal Mode Analysis Methods in Computational Protein Design. Methods Mol Biol. 2017;1529: 203–214. PubMed | Journal | PDF


2016


41. Belloli L, Wainer G, Najmanovich RJ. Parsing and model generation for biological processes. TMS-DEVS 16 Proceedings of the Symposium on Theory of Modelling & Simulation. 2016. PubMed | Journal | PDF


2015


40. Gaudreault F, Morency L-P, Najmanovich RJ. NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID. Bioinformatics. 2015;31: 3856–3858. PubMed | Journal | PDF

39. Chartier M, Adriansen E, Najmanovich R. IsoMIF Finder: online detection of binding site molecular interaction field similarities. Bioinformatics. 2015;32: btv616–623. PubMed | Journal | PDF

38. Chartier M, Najmanovich R. Detection of Binding Site Molecular Interaction Field Similarities. J Chem Inf Model. 2015;55: 1600–1615. PubMed | Journal | PDF

37. Frappier V, Chartier M, Najmanovich RJ. ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability. Nucleic Acids Res. 2015;43: W395–400. PubMed | Journal | PDF

36. Gaudreault F, Najmanovich RJ. FlexAID: Revisiting Docking on Non-Native-Complex Structures. J Chem Inf Model. 2015;55: 1323–1336. PubMed | Journal | PDF

35. Frappier V, Najmanovich RJ. Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering. Protein Science. 2015;24: 474–483. PubMed | Journal | PDF

34. Samish I, Bourne PE, Najmanovich RJ. Achievements and challenges in structural bioinformatics and computational biophysics. Bioinformatics. 2015;31: 146–150. PubMed | Journal | PDF


2014


33. Duchêne D, Colombo E, Désilets A, Boudreault P-L, Leduc R, Marsault E, Najmanovich RJ. Analysis of subpocket selectivity and identification of potent selective inhibitors for matriptase and matriptase-2. J Med Chem. 2014;57: 10198–10204. PubMed | Journal | PDF

32. Larocque M, Chénard T, Najmanovich RJ. A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors. BMC Systems Biology. BioMed Central Ltd; 2014;8: 117. PubMed | Journal | PDF

31. Frappier V, Najmanovich RJ. A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations. MacKerell AD, editor. PLoS Comput Biol. 2014;10: e1003569. PubMed | Journal | PDF

30. Glouzon J-PS, Bolduc F, Wang S, Najmanovich RJ, Perreault J-P. Deep-sequencing of the peach latent mosaic viroid reveals new aspects of population heterogeneity. PLoS ONE. 2014;9: e87297. PubMed | Journal | PDF


2013


29. Kurbatova N, Chartier M, Zylber MI, Najmanovich RJ. IsoCleft Finder - a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities. F1000Res. 2013;2: 117. PubMed | Journal | PDF

28. Chartier M, Chénard T, Barker J, Najmanovich RJ. Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree. PeerJ. PeerJ Inc; 2013;1: e126. PubMed | Journal | PDF

27. Rosado LA, Vasconcelos IB, Palma MS, Frappier V, Najmanovich RJ, Santos DS, Basso LA. The Mode of Action of Recombinant Mycobacterium tuberculosis Shikimate Kinase: Kinetics and Thermodynamics Analyses. PLoS ONE. 2013;8: e61918. PubMed | Journal | PDF


2012


26. Letourneau D, Lorin A, Lefebvre A, Frappier V, Gaudreault F, Najmanovich R, Lavigne P, Lehoux J-G. StAR-related lipid transfer domain protein 5 binds primary bile acids. J Lipid Res. 2012;53: 2677–2689. PubMed | Journal | PDF

25. Gaudreault F, Chartier M, Najmanovich RJ. Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding. Bioinformatics. 2012;28: i423–i430. PubMed | Journal | PDF

24. Colombo E, Désilets A, Duchêne D, Chagnon F, Najmanovich RJ, Leduc R, Marsault E. Design and synthesis of potent, selective inhibitors of matriptase. ACS Med Chem Lett. 2012;3: 530–534. PubMed | Journal | PDF

23. Chartier M, Gaudreault F, Najmanovich R. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. Bioinformatics. 2012;28: 1438–1445. PubMed | Journal | PDF


2011


22. Campagna-Slater V, Mok MW, Nguyen KT, Feher M, Najmanovich R, Schapira M. Structural chemistry of the histone methyltransferases cofactor binding site. J Chem Inf Model. 2011;51: 612–623. PubMed | Journal | PDF


2010


21. Han GW, Bakolitsa C, Miller MD, Kumar A, Carlton D, Najmanovich RJ, Abdubek P, Astakhova T, Axelrod HL, Chen C, Chiu H-J, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Krishna SS, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sfcovic N, Tien HJ, Trame CB, van de Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger M-A, Deacon AM, Godzik A, Lesley SA & Wilson IA. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66: 1218–1225. PubMed | Journal | PDF

20. Bakolitsa C, Kumar A, McMullan D, Krishna SS, Miller MD, Carlton D, Najmanovich RJ, Abdubek, P, Astakhova T, Chiu H-J, Clayton T, Deller MC, Duan L, Elias Y, Feuerhelm J, Grant JC, Grzechnik SK, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Trout CV, van de Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger M-A, Deacon AM, Godzik A, Lesley SA & Wilson IA. The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66: 1211–1217. PubMed | Journal | PDF

19. Lavigne P, Najmanovich RJ, Lehoux J-G. Mammalian StAR-related lipid transfer (START) domains with specificity for cholesterol: structural conservation and mechanism of reversible binding. Subcell Biochem. 2010;51: 425–437. PubMed | Journal | PDF


2009


18. Herrera JL, Gonzalez-Rey E, Fernandez-Montesinos R, Quintana FJ, Najmanovich R, Pozo D. Toll-like receptor stimulation differentially regulates vasoactive intestinal peptide type 2 receptor in macrophages. J Cell Mol Med. 2009;13: 3209–3217. PubMed | Journal | PDF

17. Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM. Structural analysis of metal sites in proteins: non-heme iron sites as a case study. J Mol Biol. 2009;388: 356–380. PubMed | Journal | PDF


2008


16. Najmanovich R, Kurbatova N, Thornton J. Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. Bioinformatics. 2008;24: i105–11. PubMed | Journal | PDF

15. Eswaran J, Bernad A, Ligos JM, Guinea B, Debreczeni JE, Sobott F, Parker SA, Najmanovich RJ, Turk BE, Knapp S. Structure of the human protein kinase MPSK1 reveals an atypical activation loop architecture. Structure. 2008;16: 115–124. PubMed | Journal | PDF


2007


14. Allali-Hassani A*, Pan PW*, Dombrovski L*, Najmanovich R*, Tempel W, Dong A, Loppnau P, Martin F, Thornton JM, Edwards AM, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH. Structural and chemical profiling of the human cytosolic sulfotransferases. PLoS Biol. 2007;5: e97. (* Equal contributing authors) PubMed | Journal | PDF

13. Najmanovich RJ, Allali-Hassani A, Morris RJ, Dombrovsky L, Pan PW, Vedadi M, Plotnikov AN, Edwards A, Arrowsmith C & Thornton JM. Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family. Bioinformatics. 2007;23: e104–9. PubMed | Journal | PDF


2006


12. Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM. A method for localizing ligand binding pockets in protein structures. Proteins. 2006;62: 479–488. PubMed | Journal | PDF


2005


11. Najmanovich RJ, Torrance JW, Thornton JM. Prediction of protein function from structure: insights from methods for the detection of local structural similarities. BioTechniques. 2005;38: 847, 849, 851. PubMed | Journal | PDF

10. Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics. 2005;21: 2347–2355. PubMed | Journal | PDF

9. Funkhouser, T., Glaser, F., Laskowski, R., Morris, R., Najmanovich, R., Stockwell, G., & Thornton, J. Shape-based classification of bound ligands. In S Barber, PD Baxter, KVMardia, & RE Walls (Eds), Quantitative Biology, Shape Analysis, and Wavelets. 2005; 39–42. PubMed | Journal | PDF

8. Morris RJ, Kahraman A, Funkhauser T, Najmanovich RJ, Stockwell G, Glaser F, Laskowski, R., Binding pocket shape analysis for protein function prediction. In S Barber, PD Baxter, KVMardia, & RE Walls (Eds), Quantitative Biology, Shape Analysis, and Wavelets. 2005; 91–94. PubMed | Journal | PDF


2004


7. Eyal E, Najmanovich R, McConkey BJ, Edelman M, Sobolev V. Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins. J Comput Chem. 2004;25: 712–724. doi:10.1002/jcc.10420 PubMed | Journal | PDF

Najmanovich RJ. Side chain flexibility upon ligand binding: Docking predictions and statistical analysis. PhD Thesis (Feinberg Graduate School, Weizmann Institute of Sciences) arXiv:13014564. 2004. arXiv | PDF


2003


6. Eyal E, Najmanovich R, Edelman M, Sobolev V. Protein side-chain rearrangement in regions of point mutations. Proteins. 2003;50: 272–282. doi:10.1002/prot.10276 PubMed | Journal | PDF


2001


5. Eyal E, Najmanovich RJ, Sobolev V, Edelman M. MutaProt: a web interface for structural analysis of point mutations. Bioinformatics. 2001;17: 381–382. PubMed | Journal | PDF


2000


4. Najmanovich RJ, Kuttner J, Sobolev V, Edelman M. Side-chain flexibility in proteins upon ligand binding. PROTEINS: Structure, Function and Genetics. 2000;39: 261–268. PubMed | Journal | PDF

3. Vendruscolo M, Najmanovich RJ, Domany E. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? PROTEINS: Structure, Function and Genetics. 2000;38: 134–148. PubMed | Journal | PDF


1999


2. Vendruscolo M, Najmanovich RJ, Domany E. Protein folding in contact map space. Phys Rev Lett. 1999;82: 656–659. PubMed | Journal | PDF


1998


1. Najmanovich RJ, deLyra J, Henriques V. The collapse transition in the HP model. Physica A. 1998;249: 374–379. PubMed | Journal | PDF