Rafael Najmanovich

Rafael Najmanovich

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Rafael Najmanovich

Rafael Najmanovich

Publications by authors named "Rafael Najmanovich"

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42Publications

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Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design.

Methods Mol Biol 2018 ;1762:367-388

Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.

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http://dx.doi.org/10.1007/978-1-4939-7756-7_18DOI Listing
January 2019

Identification of an alternative translation initiation site in the sequence of the commonly used Glutathione S-Transferase tag.

J Biotechnol 2018 Nov 6;286:14-16. Epub 2018 Sep 6.

CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de médecine, Université Laval, Québec, Québec, Canada; Regroupement stratégique PROTEO, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.jbiotec.2018.09.003DOI Listing
November 2018

Functional diversity of TMPRSS6 isoforms and variants expressed in hepatocellular carcinoma cell lines.

Sci Rep 2018 08 22;8(1):12562. Epub 2018 Aug 22.

Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada.

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http://dx.doi.org/10.1038/s41598-018-30618-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105633PMC
August 2018

Applications of Normal Mode Analysis Methods in Computational Protein Design.

Methods Mol Biol 2017 ;1529:203-214

Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montreal, Montreal, H3C 3J7, QC, Canada.

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http://dx.doi.org/10.1007/978-1-4939-6637-0_9DOI Listing
January 2018

Purine analogs targeting the guanine riboswitch as potential antibiotics against Clostridioides difficile.

Eur J Med Chem 2018 Jan 2;143:755-768. Epub 2017 Dec 2.

Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada; Department of Pharmacology-Physiology, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ejmech.2017.11.079DOI Listing
January 2018

Evolutionary studies of ligand binding sites in proteins.

Curr Opin Struct Biol 2017 08 18;45:85-90. Epub 2016 Dec 18.

Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montreal, Montreal H3T 1J4, Quebec, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2016.11.024DOI Listing
August 2017

Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes.

BMC Syst Biol 2017 Jun 12;11(1):60. Epub 2017 Jun 12.

Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada.

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http://dx.doi.org/10.1186/s12918-017-0438-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468946PMC
June 2017

Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects.

BMC Pharmacol Toxicol 2017 04 28;18(1):18. Epub 2017 Apr 28.

Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Québec, Canada.

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http://dx.doi.org/10.1186/s40360-017-0128-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408384PMC
April 2017

Modulating the selectivity of matriptase-2 inhibitors with unnatural amino acids.

Eur J Med Chem 2017 Mar 11;129:110-123. Epub 2017 Feb 11.

Department of Pharmacology-Physiology, Université de Sherbrooke, 3001 12(e) Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12(e) Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ejmech.2017.02.006DOI Listing
March 2017

IsoMIF Finder: online detection of binding site molecular interaction field similarities.

Bioinformatics 2016 Feb 25;32(4):621-3. Epub 2015 Oct 25.

Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, J1H 5N4 QC, Canada and.

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http://dx.doi.org/10.1093/bioinformatics/btv616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743630PMC
February 2016

NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID.

Bioinformatics 2015 Dec 6;31(23):3856-8. Epub 2015 Aug 6.

Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653388PMC
December 2015

Detection of Binding Site Molecular Interaction Field Similarities.

J Chem Inf Model 2015 Aug 17;55(8):1600-15. Epub 2015 Jul 17.

Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke , 12e Avenue Nord, Sherbrooke, J1H 5N4 Québec, Canada.

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http://dx.doi.org/10.1021/acs.jcim.5b00333DOI Listing
August 2015

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability.

Nucleic Acids Res 2015 Jul 16;43(W1):W395-400. Epub 2015 Apr 16.

Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada

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http://dx.doi.org/10.1093/nar/gkv343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489264PMC
July 2015

FlexAID: Revisiting Docking on Non-Native-Complex Structures.

J Chem Inf Model 2015 Jul 24;55(7):1323-36. Epub 2015 Jun 24.

Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Quebec J1H5N4, Canada.

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http://pubs.acs.org/doi/10.1021/acs.jcim.5b00078
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http://dx.doi.org/10.1021/acs.jcim.5b00078DOI Listing
July 2015

Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering.

Protein Sci 2015 Apr 5;24(4):474-83. Epub 2014 Nov 5.

Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, J1H 5N4, Quebec, Canada.

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http://dx.doi.org/10.1002/pro.2592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380979PMC
April 2015

Achievements and challenges in structural bioinformatics and computational biophysics.

Bioinformatics 2015 Jan 8;31(1):146-50. Epub 2014 Dec 8.

Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btu769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271151PMC
January 2015

Analysis of subpocket selectivity and identification of potent selective inhibitors for matriptase and matriptase-2.

J Med Chem 2014 Dec 21;57(23):10198-204. Epub 2014 Nov 21.

Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health Sciences, Université de Sherbrooke , 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada.

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http://pubs.acs.org/doi/10.1021/jm5015633
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http://dx.doi.org/10.1021/jm5015633DOI Listing
December 2014

A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors.

BMC Syst Biol 2014 Oct 15;8:117. Epub 2014 Oct 15.

Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.

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http://dx.doi.org/10.1186/s12918-014-0117-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207893PMC
October 2014

Deep-sequencing of the peach latent mosaic viroid reveals new aspects of population heterogeneity.

PLoS One 2014 30;9(1):e87297. Epub 2014 Jan 30.

Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087297PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907566PMC
September 2014

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 Comput Biol 2014 Apr 24;10(4):e1003569. Epub 2014 Apr 24.

Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada.

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http://dx.plos.org/10.1371/journal.pcbi.1003569
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http://dx.doi.org/10.1371/journal.pcbi.1003569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998880PMC
April 2014

The mode of action of recombinant Mycobacterium tuberculosis shikimate kinase: kinetics and thermodynamics analyses.

PLoS One 2013 6;8(5):e61918. Epub 2013 May 6.

Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061918PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646032PMC
December 2013

Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree.

PeerJ 2013 8;1:e126. Epub 2013 Aug 8.

Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Québec, Canada.

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http://dx.doi.org/10.7717/peerj.126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740139PMC
August 2013

StAR-related lipid transfer domain protein 5 binds primary bile acids.

J Lipid Res 2012 Dec 26;53(12):2677-89. Epub 2012 Sep 26.

Département de Biochimie, Faculté de médecine et des sciences de lsanté, Université de Sherbrooke, Sherbrooke, Québec, Canada, J1H 5N4.

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http://dx.doi.org/10.1194/jlr.M031245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494239PMC
December 2012

Design and synthesis of potent, selective inhibitors of matriptase.

ACS Med Chem Lett 2012 Jul 11;3(7):530-4. Epub 2012 Apr 11.

Department of Pharmacology and Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke , 3001 12e Avenue Nord, Sherbrooke PQ, J1H5N4, Canada.

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http://dx.doi.org/10.1021/ml3000534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4025795PMC
July 2012

Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events.

Bioinformatics 2012 Jun 30;28(11):1438-45. Epub 2012 Mar 30.

Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 12e Avenue Nord, Sherbrooke, Québec, Canada.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465090PMC
June 2012

Structural chemistry of the histone methyltransferases cofactor binding site.

J Chem Inf Model 2011 Mar 3;51(3):612-23. Epub 2011 Mar 3.

Structural Genomics Consortium, University of Toronto, MaRS Centre, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1021/ci100479zDOI Listing
March 2011

Toll-like receptor stimulation differentially regulates vasoactive intestinal peptide type 2 receptor in macrophages.

J Cell Mol Med 2009 Sep;13(9B):3209-17

CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine, CSIC-University of Seville-UPO-Junta de Andalucia, Seville, Spain.

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http://dx.doi.org/10.1111/j.1582-4934.2009.00662.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516478PMC
September 2009

Structural analysis of metal sites in proteins: non-heme iron sites as a case study.

J Mol Biol 2009 May 2;388(2):356-80. Epub 2009 Mar 2.

Magnetic Resonance Center (CERM)-University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.

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http://dx.doi.org/10.1016/j.jmb.2009.02.052DOI Listing
May 2009

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.

Bioinformatics 2008 Aug;24(16):i105-11

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btn263DOI Listing
August 2008

A method for localizing ligand binding pockets in protein structures.

Proteins 2006 Feb;62(2):479-88

European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1002/prot.20769DOI Listing
February 2006

Prediction of protein function from structure: insights from methods for the detection of local structural similarities.

Biotechniques 2005 Jun;38(6):847, 849, 851

European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.

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https://www.future-science.com/doi/10.2144/05386TE01
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http://dx.doi.org/10.2144/05386TE01DOI Listing
June 2005

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.

Bioinformatics 2005 May 22;21(10):2347-55. Epub 2005 Feb 22.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/bti337DOI Listing
May 2005

Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins.

J Comput Chem 2004 Apr;25(5):712-24

Department of Plant Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel.

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http://doi.wiley.com/10.1002/jcc.10420
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http://dx.doi.org/10.1002/jcc.10420DOI Listing
April 2004

Protein side-chain rearrangement in regions of point mutations.

Proteins 2003 Feb;50(2):272-82

Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1002/prot.10276DOI Listing
February 2003