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Rafael J. Najmanovich - Publications

Affiliations: 
Pharmacology Université de Montréal, Montréal, Canada 
Area:
Computational Pharmacology
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Gonzalez-Orozco M, Tseng HC, Hage A, Xia H, Behera P, Afreen K, Peñaflor-Tellez Y, Giraldo MI, Huante M, Puebla-Clark L, van Tol S, Odle A, Crown M, Teruel N, Shelite TR, ... ... Najmanovich RJ, et al. TRIM7 ubiquitinates SARS-CoV-2 membrane protein to limit apoptosis and viral replication. Biorxiv : the Preprint Server For Biology. PMID 38948778 DOI: 10.1101/2024.06.17.599107  0.621
2022 Mailhot O, Frappier V, Major F, Najmanovich RJ. Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation. Plos Computational Biology. 18: e1010777. PMID 36516216 DOI: 10.1371/journal.pcbi.1010777  0.736
2022 Crown M, Teruel N, Najmanovich R, Bashton M. SPEAR: Systematic ProtEin AnnotatoR. Bioinformatics (Oxford, England). PMID 35695776 DOI: 10.1093/bioinformatics/btac391  0.666
2018 Bernier SC, Morency LP, Najmanovich R, Salesse C. Identification of an alternative translation initiation site in the sequence of the commonly used Glutathione S-Transferase tag. Journal of Biotechnology. PMID 30195923 DOI: 10.1016/J.Jbiotec.2018.09.003  0.378
2018 Morency LP, Gaudreault F, Najmanovich R. Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design. Methods in Molecular Biology (Clifton, N.J.). 1762: 367-388. PMID 29594781 DOI: 10.1007/978-1-4939-7756-7_18  0.751
2018 Briot J, Mailhot O, Bourdin B, Tétreault MP, Najmanovich R, Parent L. A three-way inter-molecular network accounts for the Caα2δ1-induced functional modulation of the pore-forming Ca1.2 subunit. The Journal of Biological Chemistry. 293: 7176-7188. PMID 29588365 DOI: 10.1074/Jbc.Ra118.001902  0.314
2018 Yan LH, Le Roux A, Boyapelly K, Lamontagne AM, Archambault MA, Picard-Jean F, Lalonde-Seguin D, St-Pierre E, Najmanovich RJ, Fortier LC, Lafontaine D, Marsault É. Purine analogs targeting the guanine riboswitch as potential antibiotics against Clostridioides difficile. European Journal of Medicinal Chemistry. 143: 755-768. PMID 29220796 DOI: 10.1016/J.Ejmech.2017.11.079  0.309
2017 Chénard T, Guénard F, Vohl MC, 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. 11: 60. PMID 28606124 DOI: 10.1186/S12918-017-0438-9  0.714
2017 Chartier M, Morency LP, Zylber MI, Najmanovich RJ. Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects. Bmc Pharmacology & Toxicology. 18: 18. PMID 28449705 DOI: 10.1186/S40360-017-0128-7  0.595
2017 Frappier V, Chartier M, Najmanovich R. Applications of Normal Mode Analysis Methods in Computational Protein Design. Methods in Molecular Biology (Clifton, N.J.). 1529: 203-214. PMID 27914052 DOI: 10.1007/978-1-4939-6637-0_9  0.771
2017 Morency L, Najmanovich R. The impact of conformational entropy on the accuracy of the molecular docking software FlexAID in binding mode prediction F1000research. 6. DOI: 10.7490/F1000Research.1114728.1  0.357
2016 Najmanovich RJ. Evolutionary studies of ligand binding sites in proteins. Current Opinion in Structural Biology. 45: 85-90. PMID 27992825 DOI: 10.1016/J.Sbi.2016.11.024  0.383
2016 Chartier M, Adriansen E, Najmanovich R. IsoMIF Finder: online detection of binding site molecular interaction field similarities Bioinformatics. 32: 621-623. PMID 26504139 DOI: 10.1093/Bioinformatics/Btv616  0.348
2015 Gaudreault F, Morency LP, Najmanovich RJ. NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID. Bioinformatics (Oxford, England). PMID 26249810 DOI: 10.1093/Bioinformatics/Btv458  0.752
2015 Gaudreault F, Najmanovich RJ. FlexAID: Revisiting Docking on Non-Native-Complex Structures. Journal of Chemical Information and Modeling. PMID 26076070 DOI: 10.1021/Acs.Jcim.5B00078  0.771
2015 Frappier V, Chartier M, Najmanovich RJ. ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability. Nucleic Acids Research. PMID 25883149 DOI: 10.1093/Nar/Gkv343  0.776
2015 Frappier V, Najmanovich R. Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering. Protein Science : a Publication of the Protein Society. 24: 474-83. PMID 25367089 DOI: 10.1002/Pro.2592  0.783
2015 Chartier M, Najmanovich R. Detection of Binding Site Molecular Interaction Field Similarities Journal of Chemical Information and Modeling. 55: 1600-1615. DOI: 10.1021/Acs.Jcim.5B00333  0.401
2015 Frappier V, Najmanovich R. Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering Protein Science. 24: 474-483. DOI: 10.1002/pro.2592  0.752
2014 Larocque M, Chénard T, Najmanovich R. A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors. Bmc Systems Biology. 8: 117. PMID 25315994 DOI: 10.1186/S12918-014-0117-Z  0.722
2014 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. Plos Computational Biology. 10: e1003569. PMID 24762569 DOI: 10.1371/Journal.Pcbi.1003569  0.781
2013 Kurbatova N, Chartier M, Zylber MI, Najmanovich R. IsoCleft Finder - a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities. F1000research. 2: 117. PMID 24555058 DOI: 10.12688/f1000research.2-117.v2  0.305
2013 Chartier M, Chénard T, Barker J, Najmanovich R. Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree. Peerj. 1: e126. PMID 23940838 DOI: 10.7717/Peerj.126  0.751
2013 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. 8: e61918. PMID 23671579 DOI: 10.1371/Journal.Pone.0061918  0.756
2013 Najmanovich R, Kurbatova N, Chartier M, Zylber MI. IsoCleft Finder - a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities F1000research. 2. DOI: 10.12688/F1000Research.2-117.V2  0.418
2012 Let́ourneau D, Lorin A, Lefebvre A, Frappier V, Gaudreault F, Najmanovich R, Lavigne P, LeHoux JG. StAR-related lipid transfer domain protein 5 binds primary bile acids Journal of Lipid Research. 53: 2677-2689. PMID 23018617 DOI: 10.1194/Jlr.M031245  0.746
2012 Gaudreault F, Chartier M, Najmanovich R. Side-chain rotamer changes upon ligand binding: Common, crucial, correlate with entropy and rearrange hydrogen bonding Bioinformatics. 28: i423-i430. PMID 22962462 DOI: 10.1093/Bioinformatics/Bts395  0.754
2012 Chartier M, Gaudreault F, Najmanovich R. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events Bioinformatics. 28: 1438-1445. PMID 22467916 DOI: 10.1093/Bioinformatics/Bts149  0.745
2011 Campagna-Slater V, Mok MW, Nguyen KT, Feher M, Najmanovich R, Schapira M. Structural chemistry of the histone methyltransferases cofactor binding site. Journal of Chemical Information and Modeling. 51: 612-23. PMID 21366357 DOI: 10.1021/Ci100479Z  0.332
2010 Han GW, Bakolitsa C, Miller MD, Kumar A, Carlton D, Najmanovich RJ, Abdubek P, Astakhova T, Axelrod HL, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, et al. 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 Crystallographica. Section F, Structural Biology and Crystallization Communications. 66: 1218-25. PMID 20944214 DOI: 10.1107/S1744309109050416  0.343
2010 Bakolitsa C, Kumar A, McMullan D, Krishna SS, Miller MD, Carlton D, Najmanovich R, Abdubek P, Astakhova T, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Feuerhelm J, et al. The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 66: 1211-7. PMID 20944213 DOI: 10.1107/S1744309109022684  0.357
2009 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. Journal of Molecular Biology. 388: 356-80. PMID 19265704 DOI: 10.1016/J.Jmb.2009.02.052  0.529
2008 Najmanovich R, Kurbatova N, Thornton J. Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites Bioinformatics. 24: i105-i111. PMID 18689810 DOI: 10.1093/bioinformatics/btn263  0.506
2008 Eswaran J, Bernad A, Ligos JM, Guinea B, Debreczeni JE, Sobott F, Parker SA, Najmanovich R, Turk BE, Knapp S. Structure of the human protein kinase MPSK1 reveals an atypical activation loop architecture. Structure (London, England : 1993). 16: 115-24. PMID 18184589 DOI: 10.1016/J.Str.2007.10.026  0.306
2007 Allali-Hassani A, Pan PW, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Thonton J, Edwards AM, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH. Structural and chemical profiling of the human cytosolic sulfotransferases. Plos Biology. 5: e97. PMID 17425406 DOI: 10.1371/journal.pbio.0050097  0.434
2007 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 (Oxford, England). 23: e104-9. PMID 17237076 DOI: 10.1093/Bioinformatics/Btl292  0.617
2007 Allali-Hassani A, Pan PW, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thonton J, Edwards AM, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH. Structural and chemical profiling of the human cytosolic sulfotransferases Plos Biology. 5: 1063-1078. DOI: 10.1371/Journal.Pbio.0050097  0.333
2006 Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM. A method for localizing ligand binding pockets in protein structures. Proteins. 62: 479-88. PMID 16304646 DOI: 10.1002/Prot.20769  0.634
2005 Najmanovich RJ, Torrance JW, Thornton JM. Prediction of protein function from structure: insights from methods for the detection of local structural similarities. Biotechniques. 38: 847, 849, 851. PMID 16018542 DOI: 10.2144/05386Te01  0.639
2005 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 (Oxford, England). 21: 2347-55. PMID 15728116 DOI: 10.1093/Bioinformatics/Bti337  0.727
2004 Eyal E, Najmanovich R, Mcconkey BJ, Edelman M, Sobolev V. Importance of Solvent Accessibility and Contact Surfaces in Modeling Side-Chain Conformations in Proteins Journal of Computational Chemistry. 25: 712-724. PMID 14978714 DOI: 10.1002/Jcc.10420  0.6
2003 Eyal E, Najmanovich R, Edelman M, Sobolev V. Protein side-chain rearrangement in regions of point mutations Proteins: Structure, Function and Genetics. 50: 272-282. PMID 12486721 DOI: 10.1002/Prot.10276  0.642
2001 Eyal E, Najmanovich R, Sobolev V, Edelman M. MutaProt: A web interface for structural analysis of point mutations Bioinformatics. 17: 381-382. PMID 11301313 DOI: 10.1093/Bioinformatics/17.4.381  0.598
2000 Najmanovich R, Kuttner J, Sobolev V, Edelman M. Side-chain flexibility in proteins upon ligand binding Proteins: Structure, Function and Genetics. 39: 261-268. PMID 10737948 DOI: 10.1002/(Sici)1097-0134(20000515)39:3<261::Aid-Prot90>3.0.Co;2-4  0.65
2000 Vendruscolo M, Najmanovich R, Domany E. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? Proteins: Structure, Function and Genetics. 38: 134-148. PMID 10656261 DOI: 10.1002/(Sici)1097-0134(20000201)38:2<134::Aid-Prot3>3.0.Co;2-A  0.561
1999 Vendruscolo M, Najmanovich R, Domany E. Protein Folding in Contact Map Space Physical Review Letters. 82: 656-659. DOI: 10.1103/Physrevlett.82.656  0.535
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