Publications by authors named "Ram Samudrala"

100Publications

Linking Genome and Exposome: Computational Analysis of Human Variation in Chemical-Target Interactions.

Stud Health Technol Inform 2020 Jun;270:1331-1332

Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK.

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http://dx.doi.org/10.3233/SHTI200427DOI Listing
June 2020

Association of C>U RNA Editing with Human Disease Variants.

Stud Health Technol Inform 2020 Jun;270:1205-1206

Department of Biomedical Informatics, University at Buffalo, Buffalo, NY, USA.

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http://dx.doi.org/10.3233/SHTI200364DOI Listing
June 2020

cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data.

J Chem Inf Model 2020 Sep 26;60(9):4131-4136. Epub 2020 Jun 26.

Department of Biomedical Informatics, University at Buffalo, Buffalo, New York 14120, United States.

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http://dx.doi.org/10.1021/acs.jcim.0c00110DOI Listing
September 2020

Shotgun drug repurposing biotechnology to tackle epidemics and pandemics.

ChemRxiv 2020 May 4. Epub 2020 May 4.

Department of Biomedical Informatics, University at Buffalo, Buffalo, NY, 14120, United States.

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http://dx.doi.org/10.26434/chemrxiv.12045318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7252447PMC
May 2020

Shotgun drug repurposing biotechnology to tackle epidemics and pandemics.

Drug Discov Today 2020 Jul 13;25(7):1126-1128. Epub 2020 May 13.

Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, United States. Electronic address:

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http://dx.doi.org/10.1016/j.drudis.2020.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217781PMC
July 2020

Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. Corrigendum.

Acta Crystallogr F Struct Biol Commun 2020 04 2;76(Pt 4):192-193. Epub 2020 Apr 2.

Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA.

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http://dx.doi.org/10.1107/S2053230X2000271XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7137385PMC
April 2020

CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials.

J Chem Inf Model 2020 03 3;60(3):1509-1527. Epub 2020 Mar 3.

Department of Chemistry, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 47906, United States.

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http://dx.doi.org/10.1021/acs.jcim.9b00686DOI Listing
March 2020

Fingerprinting CANDO: Increased Accuracy with Structure- and Ligand-Based Shotgun Drug Repurposing.

ACS Omega 2019 Oct 9;4(17):17393-17403. Epub 2019 Oct 9.

Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences at the University at Buffalo, Buffalo, New York 14203, United States.

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http://dx.doi.org/10.1021/acsomega.9b02160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6812124PMC
October 2019

Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization.

Acta Crystallogr F Struct Biol Commun 2019 Oct 24;75(Pt 10):646-651. Epub 2019 Sep 24.

Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA.

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http://dx.doi.org/10.1107/S2053230X19012652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777135PMC
October 2019

Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications.

Sci Rep 2019 09 11;9(1):13155. Epub 2019 Sep 11.

Department of Chemistry, Purdue University, West Lafayette, IN, USA.

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http://dx.doi.org/10.1038/s41598-019-49515-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739337PMC
September 2019

Exploration of interaction scoring criteria in the CANDO platform.

BMC Res Notes 2019 Jun 7;12(1):318. Epub 2019 Jun 7.

Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 77 Goodell St., Suite 540, Buffalo, NY, 14203, USA.

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http://dx.doi.org/10.1186/s13104-019-4356-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6555930PMC
June 2019

Identifying Protein Features Responsible for Improved Drug Repurposing Accuracies Using the CANDO Platform: Implications for Drug Design.

Molecules 2019 Jan 4;24(1). Epub 2019 Jan 4.

Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA.

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http://dx.doi.org/10.3390/molecules24010167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337359PMC
January 2019

A Systematic Review of Computational Drug Discovery, Development, and Repurposing for Ebola Virus Disease Treatment.

Molecules 2017 Oct 20;22(10). Epub 2017 Oct 20.

Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14203, USA.

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http://dx.doi.org/10.3390/molecules22101777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151658PMC
October 2017

Combating Ebola with Repurposed Therapeutics Using the CANDO Platform.

Molecules 2016 Nov 25;21(12). Epub 2016 Nov 25.

Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA.

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http://dx.doi.org/10.3390/molecules21121537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5958544PMC
November 2016

Mycobacterium Cytidylate Kinase Appears to Be an Undruggable Target.

J Biomol Screen 2016 Aug 4;21(7):695-700. Epub 2016 May 4.

Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Reemerging Infectious Disease (CERID), University of Washington, Seattle, WA, USA Departments of Global Health and Microbiology, University of Washington, Seattle, WA, USA

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http://dx.doi.org/10.1177/1087057116646702DOI Listing
August 2016

Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform.

Curr Pharm Des 2016 ;22(21):3109-23

Department of Biomedical Informatics, SUNY, Buffalo, NY, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376875PMC
http://dx.doi.org/10.2174/1381612822666160325121943DOI Listing
November 2017

Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development.

Viruses 2015 Nov 4;7(11):5718-35. Epub 2015 Nov 4.

Department of Microbiology, University ofWashington, Seattle,WA 98195-8070, USA.

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http://dx.doi.org/10.3390/v7112901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664974PMC
November 2015

Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform.

Mini Rev Med Chem 2015 ;15(8):705-17

Department of Biomedical Informatics, School of Medicine and Biomedical Sciences, State University of New York (SUNY), 923 Main Street, Buffalo, NY 14203, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5903852PMC
http://dx.doi.org/10.2174/1389557515666150219145148DOI Listing
January 2016

Preferential Promotion of Lycopersicon esculentum (Tomato) Growth by Plant Growth Promoting Bacteria Associated with Tomato.

Indian J Microbiol 2014 Dec 15;54(4):403-12. Epub 2014 May 15.

Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046 AP India.

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http://dx.doi.org/10.1007/s12088-014-0470-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4186933PMC
December 2014

CANDO and the infinite drug discovery frontier.

Drug Discov Today 2014 Sep 26;19(9):1353-63. Epub 2014 Jun 26.

University of Washington, Department of Microbiology, Seattle, WA 98109, United States. Electronic address:

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http://dx.doi.org/10.1016/j.drudis.2014.06.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4167471PMC
September 2014

Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin.

PLoS One 2013 2;8(9):e74053. Epub 2013 Sep 2.

Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand ; Genomics Institute, National Center for Genetic Engineering and Biotechnology, Pathumtani, Thailand ; Department of Microbiology, University of Washington, Seattle, Washington, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0074053PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759441PMC
April 2014

Structure prediction of partial-length protein sequences.

Int J Mol Sci 2013 Jul 17;14(7):14892-907. Epub 2013 Jul 17.

Department of Computer Science & Engineering, University of Washington, Seattle, WA 98195-2350, USA.

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http://dx.doi.org/10.3390/ijms140714892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3742278PMC
July 2013

Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens.

BMC Plant Biol 2013 Mar 15;13:43. Epub 2013 Mar 15.

Department of Molecular Biology, Microbiology and Biochemistry and Center for Excellence the Illinois Soybean Center, Southern Illinois University at Carbondale, IL 62901, USA.

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http://dx.doi.org/10.1186/1471-2229-13-43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626623PMC
March 2013

The Promise and Challenge of Digital Biology.

J Bioeng Biomed Sci 2013 4;3(3). Epub 2013 Dec 4.

Microbiology Department, University of Washington, USA.

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http://dx.doi.org/10.4172/2155-9538.1000e118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191183PMC
December 2013

Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils.

Biomacromolecules 2012 Nov 28;13(11):3494-502. Epub 2012 Sep 28.

Department of Preventative and Restorative Dental Sciences, University of California, 707 Parnassus Avenue, San Francisco, CA 94143, USA.

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http://pubs.acs.org/doi/10.1021/bm300942c
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http://dx.doi.org/10.1021/bm300942cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496023PMC
November 2012

The enzymatic and metabolic capabilities of early life.

PLoS One 2012 10;7(9):e39912. Epub 2012 Sep 10.

Department of Ecology and Evolutionary Biology, Princeton, New Jersey, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039912PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438178PMC
May 2013

Accelerated protein structure comparison using TM-score-GPU.

Bioinformatics 2012 Aug 19;28(16):2191-2. Epub 2012 Jun 19.

Department of Microbiology, University of Washington, Seattle, WA 98195-7735, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413391PMC
August 2012

LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates.

BMC Bioinformatics 2011 Sep 15;12:368. Epub 2011 Sep 15.

Department of Microbiology, University of Washington, Box 357735, Seattle, Washington 98195-7242, USA.

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http://dx.doi.org/10.1186/1471-2105-12-368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184297PMC
September 2011

GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition.

BMC Res Notes 2011 Apr 1;4:97. Epub 2011 Apr 1.

Department of Microbiology, University of Washington, Seattle WA USA.

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http://dx.doi.org/10.1186/1756-0500-4-97DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087690PMC
April 2011

Evolutionary transients in the rice transcriptome.

Genomics Proteomics Bioinformatics 2010 Dec;8(4):211-28

Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.

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https://linkinghub.elsevier.com/retrieve/pii/S16720229106002
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http://dx.doi.org/10.1016/S1672-0229(10)60023-XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054128PMC
December 2010

Caries induced cytokine network in the odontoblast layer of human teeth.

BMC Immunol 2011 Jan 24;12. Epub 2011 Jan 24.

Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, 513 Parnassus Street, San Francisco, CA 94143, Box 0422, USA.

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http://dx.doi.org/10.1186/1471-2172-12-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3036664PMC
January 2011

IGF1R variants associated with isolated single suture craniosynostosis.

Am J Med Genet A 2011 Jan;155A(1):91-7

Seattle Children's Hospital Craniofacial Center, University of Washington, 98195, USA.

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http://dx.doi.org/10.1002/ajmg.a.33781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059230PMC
January 2011

Viral entry inhibitors block dengue antibody-dependent enhancement in vitro.

Antiviral Res 2011 Jan 18;89(1):71-4. Epub 2010 Nov 18.

Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965, USA.

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http://dx.doi.org/10.1016/j.antiviral.2010.11.008DOI Listing
January 2011

Computational prediction of type III and IV secreted effectors in gram-negative bacteria.

Infect Immun 2011 Jan 25;79(1):23-32. Epub 2010 Oct 25.

Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, MSIN: J4-33, 902 Battelle Boulevard, P.O. Box 999, Richland, WA 99352, USA.

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http://iai.asm.org/lookup/doi/10.1128/IAI.00537-10
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http://dx.doi.org/10.1128/IAI.00537-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019878PMC
January 2011

Solution study of engineered quartz binding peptides using replica exchange molecular dynamics.

Biomacromolecules 2010 Dec 22;11(12):3266-74. Epub 2010 Oct 22.

Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom.

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http://dx.doi.org/10.1021/bm100646zDOI Listing
December 2010

Disease risk of missense mutations using structural inference from predicted function.

Curr Protein Pept Sci 2010 Nov;11(7):573-88

Department of Microbiology School of Medicine, University of Washington, 1959 NE Pacific St 357132, Seattle, WA 98195, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095817PMC
http://dx.doi.org/10.2174/138920310794109139DOI Listing
November 2010

A protein sequence meta-functional signature for calcium binding residue prediction.

Pattern Recognit Lett 2010 Oct;31(14):2103-2112

Department of Oral Biology, School of Dentistry, University of Washington, 1959 NE Pacific St #357132, Seattle, WA 98195.

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http://dx.doi.org/10.1016/j.patrec.2010.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932634PMC
October 2010

Structural optimization and de novo design of dengue virus entry inhibitory peptides.

PLoS Negl Trop Dis 2010 Jun 22;4(6):e721. Epub 2010 Jun 22.

Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, Florida, United States of America.

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http://dx.doi.org/10.1371/journal.pntd.0000721DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889824PMC
June 2010

Probing the molecular mechanisms of quartz-binding peptides.

Langmuir 2010 Jul;26(13):11003-9

Department of Materials Science and Engineering, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1021/la100049sDOI Listing
July 2010

The evolution and functional repertoire of translation proteins following the origin of life.

Biol Direct 2010 Apr 8;5:15. Epub 2010 Apr 8.

Department of Microbiology, University of Washington, Box 357242, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/1745-6150-5-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873265PMC
April 2010

Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix.

Mol Microbiol 2010 Feb 17;75(4):827-42. Epub 2010 Jan 17.

Department of Microbiology, University of Washington, Box 357242, Seattle, WA 98195-7242, USA.

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http://dx.doi.org/10.1111/j.1365-2958.2009.06991.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847200PMC
February 2010

Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea.

BMC Evol Biol 2009 Aug 11;9:199. Epub 2009 Aug 11.

Department of Microbiology, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1186/1471-2148-9-199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739858PMC
August 2009

A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction.

Proteins 2009 Oct;77(1):220-34

Department of Genetics, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1002/prot.22434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874729PMC
October 2009

Protinfo PPC: a web server for atomic level prediction of protein complexes.

Nucleic Acids Res 2009 Jul 6;37(Web Server issue):W519-25. Epub 2009 May 6.

Department of Microbiology, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1093/nar/gkp306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703994PMC
July 2009

Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems.

PLoS Pathog 2009 Apr 24;5(4):e1000375. Epub 2009 Apr 24.

Department of Microbiology, University of Washington, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1000375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668754PMC
April 2009

Inferring molecular interactions pathways from eQTL data.

Methods Mol Biol 2009 ;541:211-23

Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1007/978-1-59745-243-4_10DOI Listing
June 2009

The Bioverse API and web application.

Methods Mol Biol 2009 ;541:511-34

Department of Microbiology, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1007/978-1-59745-243-4_22DOI Listing
June 2009

Computational representation of biological systems.

Methods Mol Biol 2009 ;541:535-49

Department of Microbiology, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1007/978-1-59745-243-4_23DOI Listing
June 2009

Prediction and integration of regulatory and protein-protein interactions.

Methods Mol Biol 2009 ;541:101-43

BIOTEC, Pathumthani, Thailand.

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http://dx.doi.org/10.1007/978-1-59745-243-4_6DOI Listing
June 2009

A generalized knowledge-based discriminatory function for biomolecular interactions.

Proteins 2009 Jul;76(1):115-28

Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1002/prot.22323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2891153PMC
July 2009

Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information.

PLoS Comput Biol 2008 Sep 26;4(9):e1000181. Epub 2008 Sep 26.

Department of Microbiology, Computational Genomics Group, University of Washington, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2526173PMC
September 2008

Improving the accuracy of template-based predictions by mixing and matching between initial models.

BMC Struct Biol 2008 May 5;8:24. Epub 2008 May 5.

Department of Microbiology, University of Washington, School of Medicine, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/1472-6807-8-24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2424052PMC
May 2008

Structural and functional characterization of an organic hydroperoxide resistance protein from Mycoplasma gallisepticum.

J Bacteriol 2008 Mar 11;190(6):2206-16. Epub 2008 Jan 11.

Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Camden, NSW 2570, Australia.

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http://dx.doi.org/10.1128/JB.01685-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258871PMC
March 2008

Novel paradigms for drug discovery: computational multitarget screening.

Trends Pharmacol Sci 2008 Feb 10;29(2):62-71. Epub 2008 Jan 10.

Department of Microbiology, School of Medicine, University of Washington, Box 357242, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1016/j.tips.2007.11.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551513PMC
February 2008

Scoring functions for de novo protein structure prediction revisited.

Methods Mol Biol 2008 ;413:243-81

Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA.

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http://dx.doi.org/10.1007/978-1-59745-574-9_10DOI Listing
June 2008

A novel knowledge-based approach to design inorganic-binding peptides.

Bioinformatics 2007 Nov 17;23(21):2816-22. Epub 2007 Sep 17.

Materials Science and Engineering Department, University of Washington, Seattle, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm436DOI Listing
November 2007

Identification of potential HIV-1 targets of minocycline.

Bioinformatics 2007 Oct 5;23(20):2797-9. Epub 2007 Sep 5.

National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Pahonyothin Road, Klong 1, Klongluang, Pathumtani 12120, Thailand.

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http://dx.doi.org/10.1093/bioinformatics/btm424DOI Listing
October 2007

Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation.

J Bacteriol 2007 Jun 23;189(11):3935-44. Epub 2007 Mar 23.

Department of Microbiology, University of Washington, Seattle, WA 98195-2700, USA.

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http://dx.doi.org/10.1128/JB.01861-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913382PMC
June 2007

An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data.

J Biomol NMR 2006 Nov 3;36(3):189-98. Epub 2006 Oct 3.

Department of Microbiology, University of Washington, Rosen Building, 960 Republican, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1007/s10858-006-9082-1DOI Listing
November 2006

Incorporating background frequency improves entropy-based residue conservation measures.

BMC Bioinformatics 2006 Aug 17;7:385. Epub 2006 Aug 17.

Computational Genomics Group, Department of Microbiology, University of Washington, USA.

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http://dx.doi.org/10.1186/1471-2105-7-385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1562451PMC
August 2006

The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection.

Protein Eng Des Sel 2006 Sep 14;19(9):431-7. Epub 2006 Jul 14.

Department of Microbiology, University of Washington, School of Medicine, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/protein/gzl027DOI Listing
September 2006

Crystal structure and mutational analysis of the DaaE adhesin of Escherichia coli.

J Biol Chem 2006 Aug 2;281(31):22367-77. Epub 2006 Jun 2.

Department of Microbiology, University of Washington, Seattle 98195, USA.

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http://dx.doi.org/10.1074/jbc.M604646200DOI Listing
August 2006

Automated functional classification of experimental and predicted protein structures.

BMC Bioinformatics 2006 Jun 2;7:278. Epub 2006 Jun 2.

Computational Genomics Group, Department of Microbiology, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/1471-2105-7-278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513613PMC
June 2006

Comment on "Evidence for positive epistasis in HIV-1".

Science 2006 May;312(5775):848; author reply 848

Department of Microbiology, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1126/science.1109904DOI Listing
May 2006

Disguising itself--insights into Plasmodium falciparum binding and immune evasion from the DBL crystal structure.

Mol Biochem Parasitol 2006 Jul 4;148(1):1-9. Epub 2006 Apr 4.

Seattle Biomedical Research Institute, WA 98109-5219, USA.

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http://dx.doi.org/10.1016/j.molbiopara.2006.03.004DOI Listing
July 2006

INTEGRATOR: interactive graphical search of large protein interactomes over the Web.

BMC Bioinformatics 2006 Mar 16;7:146. Epub 2006 Mar 16.

Dept. of Biomedical and Health Informatics, University of Washington, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1186/1471-2105-7-146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459205PMC
March 2006

A knowledge-based scoring function based on residue triplets for protein structure prediction.

Protein Eng Des Sel 2006 May 13;19(5):187-93. Epub 2006 Mar 13.

Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/protein/gzj018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441915PMC
May 2006

Heptad-repeat-2 mutations enhance the stability of the enfuvirtide-resistant HIV-1 gp41 hairpin structure.

Antivir Ther 2005 ;10(8):893-900

Department of Microbiology, University of Washington, School of Medicine, Seattle, WA 98195, USA.

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February 2006

Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.

Nucleic Acids Res 2005 13;33(18):5861-7. Epub 2005 Oct 13.

Department of Biochemistry, University of Washington Seattle, Washington, USA.

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http://dx.doi.org/10.1093/nar/gki894DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1258172PMC
October 2005

Identification of potential multitarget antimalarial drugs.

JAMA 2005 Sep;294(12):1490-1

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http://dx.doi.org/10.1001/jama.294.12.1490DOI Listing
September 2005

Structural insights into the cellular retinaldehyde-binding protein (CRALBP).

Proteins 2005 Nov;61(2):412-22

Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1002/prot.20621DOI Listing
November 2005

Origin and evolution of new exons in rodents.

Genome Res 2005 Sep 18;15(9):1258-64. Epub 2005 Aug 18.

CAS-Max Planck Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.

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http://www.genome.org/cgi/doi/10.1101/gr.3929705
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http://dx.doi.org/10.1101/gr.3929705DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1199540PMC
September 2005

PROTINFO: new algorithms for enhanced protein structure predictions.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W77-80

Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/nar/gki403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160164PMC
July 2005

BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W324-5

Department of Microbiology, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1093/nar/gki401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160162PMC
July 2005

Functional annotation from predicted protein interaction networks.

Bioinformatics 2005 Aug 26;21(15):3217-26. Epub 2005 May 26.

Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bti514DOI Listing
August 2005

FSSA: a novel method for identifying functional signatures from structural alignments.

Bioinformatics 2005 Jul 28;21(13):2969-77. Epub 2005 Apr 28.

Computational Genomics Group, Department of Microbiology, University of Washington Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti471DOI Listing
July 2005

PIRSpred: a web server for reliable HIV-1 protein-inhibitor resistance/susceptibility prediction.

Trends Microbiol 2005 Apr;13(4):150-1

Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, WA 98195, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S0966842X0500046
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http://dx.doi.org/10.1016/j.tim.2005.02.003DOI Listing
April 2005

Virtual screening of HIV-1 protease inhibitors against human cytomegalovirus protease using docking and molecular dynamics.

AIDS 2005 Mar;19(5):529-31

Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1097/01.aids.0000162343.96674.4cDOI Listing
March 2005

Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach.

Antivir Ther 2005 ;10(1):157-66

Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA.

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May 2005

The Genomes of Oryza sativa: a history of duplications.

PLoS Biol 2005 Feb 1;3(2):e38. Epub 2005 Feb 1.

Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, China.

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http://dx.doi.org/10.1371/journal.pbio.0030038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC546038PMC
February 2005

An enhanced Java graph applet interface for visualizing interactomes.

Bioinformatics 2005 Apr 21;21(8):1741-2. Epub 2004 Dec 21.

Biomedical and Health Informatics, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti237DOI Listing
April 2005

Genomic organization and sequence variation of the human integrin subunit alpha8 gene (ITGA8).

Matrix Biol 2004 Nov;23(7):487-96

Department of Pediatrics, Mount Sinai School of Medicine, New York, NY, USA.

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http://dx.doi.org/10.1016/j.matbio.2004.08.005DOI Listing
November 2004

Antivirogram or phenosense: a comparison of their reproducibility and an analysis of their correlation.

Antivir Ther 2004 Oct;9(5):703-12

Department of Microbiology, University of Washington, Wash., USA.

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October 2004

Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs.

Nature 2004 Oct;431(7010):1 p following 757; discussion following 757

James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310007, China.

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October 2004

Simple linear model provides highly accurate genotypic predictions of HIV-1 drug resistance.

Antivir Ther 2004 Jun;9(3):343-52

Department of Microbiology, University of Washington, Seattle, Wash., USA.

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June 2004

Improved protein structure selection using decoy-dependent discriminatory functions.

BMC Struct Biol 2004 Jun 18;4. Epub 2004 Jun 18.

Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/1472-6807-4-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC449718PMC
June 2004

Enhanced functional information from predicted protein networks.

Trends Biotechnol 2004 Feb;22(2):60-2; discussion 62-3

Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1016/j.tibtech.2003.11.010DOI Listing
February 2004

Identifying inhibitors of the SARS coronavirus proteinase.

Bioorg Med Chem Lett 2003 Nov;13(22):3989-92

Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1016/j.bmcl.2003.08.066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119134PMC
November 2003

Bioverse: Functional, structural and contextual annotation of proteins and proteomes.

Nucleic Acids Res 2003 Jul;31(13):3736-7

Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168957PMC
http://dx.doi.org/10.1093/nar/gkg550DOI Listing
July 2003

PROTINFO: Secondary and tertiary protein structure prediction.

Nucleic Acids Res 2003 Jul;31(13):3296-9

Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168948PMC
http://dx.doi.org/10.1093/nar/gkg541DOI Listing
July 2003

Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations.

BMC Struct Biol 2003 Apr 1;3. Epub 2003 Apr 1.

Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC154089PMC
http://dx.doi.org/10.1186/1472-6807-3-2DOI Listing
April 2003