Publications by authors named "Adam Godzik"

100Publications

Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage.

EMBO J 2020 Dec 19;39(23):e104523. Epub 2020 Oct 19.

Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK.

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December 2020

Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence.

Bioinformatics 2020 08;36(15):4360-4362

Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA 92521, USA.

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August 2020

FATCAT 2.0: towards a better understanding of the structural diversity of proteins.

Nucleic Acids Res 2020 07;48(W1):W60-W64

Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA 92521, USA.

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July 2020

Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2.

Protein Sci 2020 07 2;29(7):1596-1605. Epub 2020 May 2.

Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.

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July 2020

Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era.

FEBS Lett 2020 Dec 28;594(24):4233-4246. Epub 2020 Apr 28.

Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA.

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December 2020

Difference contact maps: From what to why in the analysis of the conformational flexibility of proteins.

PLoS One 2020 12;15(3):e0226702. Epub 2020 Mar 12.

Biosciences Division, University of California Riverside School of Medicine, Riverside, CA, United States of America.

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May 2020

Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets.

Nucleic Acids Res 2019 01;47(D1):D895-D899

Bioinformatics and Systems Biology Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

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January 2019

Draft Genome Sequences of Two Strains Associated with Gastroenteritis after Raw Seafood Ingestion in Colorado.

Genome Announc 2018 Jan 18;6(3). Epub 2018 Jan 18.

Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA

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January 2018

The Functional Impact of Alternative Splicing in Cancer.

Cell Rep 2017 Aug;20(9):2215-2226

Computational RNA Biology Group, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain. Electronic address:

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August 2017

Comparison of algorithms for the detection of cancer drivers at subgene resolution.

Nat Methods 2017 Aug 17;14(8):782-788. Epub 2017 Jul 17.

Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.

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August 2017

The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability.

Methods Mol Biol 2017 ;1607:77-115

Bioinformatics and Systems Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.

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March 2018

Mutation Drivers of Immunological Responses to Cancer.

Cancer Immunol Res 2016 09 11;4(9):789-98. Epub 2016 Jul 11.

Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.

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September 2016

Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination.

Proc Natl Acad Sci U S A 2016 08 6;113(32):E4639-47. Epub 2016 Jul 6.

Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109602, Israel; Protein Metabolism Medical Research Center, College of Medicine, Seoul National University, Seoul 110-799, South Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 110-799, South Korea;

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August 2016

Revealing aperiodic aspects of solenoid proteins from sequence information.

Bioinformatics 2016 09 9;32(18):2776-82. Epub 2016 Jun 9.

Department of Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.

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September 2016

Neutralizing antibody affords comparable protection against vaginal and rectal simian/human immunodeficiency virus challenge in macaques.

AIDS 2016 06;30(10):1543-51

aDepartment of Immunology and Microbial Science, IAVI Neutralizing Antibody Center and Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California bEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia cCenter for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts dBioqual, Inc., Rockville, Maryland eBioinformatics and Systems Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA fGenmab, Utrecht, The Netherlands gRagon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA. *Present address: MedImmune, LLC, Gaithersburg, Maryland, USA.

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June 2016

A Distinct Type of Pilus from the Human Microbiome.

Cell 2016 Apr 7;165(3):690-703. Epub 2016 Apr 7.

Joint Center for Structural Genomics, http://www.jcsg.org; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

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April 2016

UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex.

Acta Crystallogr D Struct Biol 2016 Apr 24;72(Pt 4):497-511. Epub 2016 Mar 24.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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April 2016

Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome.

J Biol Chem 2016 Apr 3;291(18):9482-91. Epub 2016 Mar 3.

From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom, the Department of Biology, Centre for Immunology and Infection, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom,

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April 2016

PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB.

Source Code Biol Med 2015 3;10:15. Epub 2015 Dec 3.

Bioinformatics and Systems Biology Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92307 USA.

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December 2015

PDBFlex: exploring flexibility in protein structures.

Nucleic Acids Res 2016 Jan 28;44(D1):D423-8. Epub 2015 Nov 28.

Bioinformatics and Systems Biology Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA

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January 2016

Protael: protein data visualization library for the web.

Bioinformatics 2016 Feb 29;32(4):602-4. Epub 2015 Oct 29.

Bioinformatics and Systems Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92307, USA and Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA.

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February 2016

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces.

PLoS Comput Biol 2015 Oct 20;11(10):e1004518. Epub 2015 Oct 20.

Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America.

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October 2015

Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains.

mBio 2015 Sep 15;6(5):e02327-14. Epub 2015 Sep 15.

Joint Center for Structural Genomics‡ Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA

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September 2015

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction.

Bioinformatics 2015 Jul 19;31(13):2098-105. Epub 2015 Feb 19.

Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.

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July 2015

Analysis of individual protein regions provides novel insights on cancer pharmacogenomics.

PLoS Comput Biol 2015 Jan 8;11(1):e1004024. Epub 2015 Jan 8.

Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America.

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January 2015

Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.

Structure 2014 Dec 20;22(12):1799-1809. Epub 2014 Nov 20.

Joint Center for Structural Genomics (JCSG); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

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December 2014

Cancer3D: understanding cancer mutations through protein structures.

Nucleic Acids Res 2015 Jan 11;43(Database issue):D968-73. Epub 2014 Nov 11.

Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA

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January 2015

Phylogenomic analysis of glycogen branching and debranching enzymatic duo.

BMC Evol Biol 2014 Aug 23;14:183. Epub 2014 Aug 23.

Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 N, Torrey Pines Road, La Jolla 92037, CA, USA.

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August 2014

e-Driver: a novel method to identify protein regions driving cancer.

Bioinformatics 2014 Nov 26;30(21):3109-14. Epub 2014 Jul 26.

Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

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November 2014

Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake.

Protein Sci 2014 Oct 12;23(10):1380-91. Epub 2014 Aug 12.

Joint Center for Structural Genomics, http://www.jcsg.org; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, 94025.

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October 2014

PubServer: literature searches by homology.

Nucleic Acids Res 2014 Jul 23;42(Web Server issue):W430-5. Epub 2014 Jun 23.

Joint Center for Structural Genomics (http://www.jcsg.org) Bioinformatics and Systems Biology Program, Sanford Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0446, USA

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July 2014

Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase.

BMC Bioinformatics 2014 Jun 17;15:196. Epub 2014 Jun 17.

Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

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June 2014

POSA: a user-driven, interactive multiple protein structure alignment server.

Nucleic Acids Res 2014 Jul 16;42(Web Server issue):W240-5. Epub 2014 May 16.

Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA

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July 2014

AIDA: ab initio domain assembly server.

Nucleic Acids Res 2014 Jul 15;42(Web Server issue):W308-13. Epub 2014 May 15.

Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0446, USA Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia

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July 2014

ConSole: using modularity of contact maps to locate solenoid domains in protein structures.

BMC Bioinformatics 2014 Apr 27;15:119. Epub 2014 Apr 27.

Program in Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 92037 La Jolla, CA, USA.

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April 2014

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase.

BMC Bioinformatics 2014 Apr 17;15:112. Epub 2014 Apr 17.

Joint Center for Structural Genomics, 10550 North Torrey Pines Road, BCC-206, La Jolla, California 92037, USA.

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April 2014

Improving the chances of successful protein structure determination with a random forest classifier.

Acta Crystallogr D Biol Crystallogr 2014 Mar 15;70(Pt 3):627-35. Epub 2014 Feb 15.

Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92307, USA.

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March 2014

bNAber: database of broadly neutralizing HIV antibodies.

Nucleic Acids Res 2014 Jan 7;42(Database issue):D1133-9. Epub 2013 Nov 7.

Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, 10550 North Torrey Pines Road La Jolla, CA 92037, USA, Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA, Department of Immunology & Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, Ragon Institute of MGH, MIT and Harvard, 400 Technology Square, Cambridge, MA 02139, USA and Center for Research in Biological Systems, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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January 2014

Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family.

Proteins 2014 Jun 22;82(6):1086-92. Epub 2013 Nov 22.

Joint Center for Structural Genomics; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California.

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June 2014

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking.

Bioinformatics 2014 Mar 15;30(5):660-7. Epub 2013 Oct 15.

Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia.

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March 2014

Divergent evolution of protein conformational dynamics in dihydrofolate reductase.

Nat Struct Mol Biol 2013 Nov 29;20(11):1243-9. Epub 2013 Sep 29.

1] Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA. [2] Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California, USA. [3].

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November 2013

Structures of a bifunctional cell wall hydrolase CwlT containing a novel bacterial lysozyme and an NlpC/P60 DL-endopeptidase.

J Mol Biol 2014 Jan 16;426(1):169-84. Epub 2013 Sep 16.

Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address:

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January 2014

Crystal structure of a member of a novel family of dioxygenases (PF10014) reveals a conserved cupin fold and active site.

Proteins 2014 Jan 10;82(1):164-70. Epub 2013 Sep 10.

Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, 94025.

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January 2014

MORPH-PRO: a novel algorithm and web server for protein morphing.

Algorithms Mol Biol 2013 Jul 11;8(1):19. Epub 2013 Jul 11.

Algorithmic Biology Laboratory, Saint Petersburg Academic University, Saint Petersburg, Russia.

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July 2013

Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli.

Science 2013 Jun;340(6137):1220-3

Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093-0412, USA.

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June 2013

Evolution of the animal apoptosis network.

Cold Spring Harb Perspect Biol 2013 Mar 1;5(3):a008649. Epub 2013 Mar 1.

Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA.

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March 2013

This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes.

PLoS Comput Biol 2012 15;8(11):e1002701. Epub 2012 Nov 15.

Program in Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA.

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April 2013

The FGGY carbohydrate kinase family: insights into the evolution of functional specificities.

PLoS Comput Biol 2011 Dec 22;7(12):e1002318. Epub 2011 Dec 22.

Graduate School of Biomedical Sciences, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America.

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December 2011

CARD8 and NLRP1 undergo autoproteolytic processing through a ZU5-like domain.

PLoS One 2011 8;6(11):e27396. Epub 2011 Nov 8.

Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America.

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May 2012

FFAS server: novel features and applications.

Nucleic Acids Res 2011 Jul;39(Web Server issue):W38-44

Bioinformatics and Systems Biology Program, Sanford Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA.

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July 2011

Structural determinants of limited proteolysis.

J Proteome Res 2011 Aug 8;10(8):3642-51. Epub 2011 Jul 8.

Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA.

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August 2011

Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering.

Proteins 2011 Aug 31;79(8):2389-402. Epub 2011 May 31.

Joint Center for Structural Genomics, Center for Research in Biological Systems, University of California, San Diego, California 92093-0446, USA.

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August 2011

Dynamics of coregulator-induced conformational perturbations in androgen receptor ligand binding domain.

Mol Cell Endocrinol 2011 Jul 14;341(1-2):1-8. Epub 2011 May 14.

Section of Endocrinology, Boston University School of Medicine, 670 Albany St., Boston, MA 02118, USA.

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July 2011

Metagenomics and the protein universe.

Authors:
Adam Godzik

Curr Opin Struct Biol 2011 Jun 14;21(3):398-403. Epub 2011 Apr 14.

Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

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June 2011

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires.

Genome Biol 2011 17;12(1):R4. Epub 2011 Jan 17.

Program in Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.

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February 2012

Structural insights into inhibition of Bacillus anthracis sporulation by a novel class of non-heme globin sensor domains.

J Biol Chem 2011 Mar 7;286(10):8448-58. Epub 2011 Jan 7.

Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA.

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March 2011

TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog.

Dev Comp Immunol 2011 Apr 24;35(4):461-8. Epub 2010 Nov 24.

Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

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April 2011

A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins.

BMC Genomics 2010 Oct 21;11:590. Epub 2010 Oct 21.

Institute of Biochemistry and Biophysics, PAS, Pawińskiego 5A, 02-106 Warsaw, Poland.

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October 2010

TOPSAN: a dynamic web database for structural genomics.

Nucleic Acids Res 2011 Jan 20;39(Database issue):D494-6. Epub 2010 Oct 20.

Joint Center for Structural Genomics, Bioinformatics Core, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

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January 2011