Publications

D Ban, C A Smith, B L de Groot, C Griesinger, D Lee

Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy Journal Article

Arch Biochem Biophys, 628 , pp. 81-91, 2017.

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C A Smith, D Ban, S Pratihar, K Giller, M Paulat, S Becker, C Griesinger, D Lee, B L de Groot

Allosteric switch regulates protein-protein binding through collective motion Journal Article

Proc Natl Acad Sci U S A, 113 (12), pp. 3269-3274, 2016.

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C A Smith, D Ban, S Pratihar, K Giller, C Schwiegk, B L de Groot, S Becker, C Griesinger, D Lee

Population Shuffling of Protein Conformations Journal Article

Angew Chem Int Ed Engl, 54 (1), pp. 207-10, 2015.

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T M Sabo, C A Smith, D Ban, A Mazur, D Lee, C Griesinger

ORIUM: optimized RDC-based Iterative and Unified Model-free analysis Journal Article

J Biomol NMR, 58 (4), pp. 287-301, 2014.

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N Ollikainen, C A Smith, J S Fraser, T Kortemme

Flexible backbone sampling methods to model and design protein alternative conformations Journal Article

Methods Enzymol, 523 , pp. 61-85, 2013.

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C A Smith, C A Shi, M K Chroust, T E Bliska, M J Kelly, M P Jacobson, T Kortemme

Design of a phosphorylatable PDZ domain with peptide-specific affinity changes Journal Article

Structure, 21 (1), pp. 54-64, 2013.

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Andrew Leaver-Fay, Michael Tyka, Steven M Lewis, Oliver F Lange, James Thompson, Ron Jacak, Kristian W Kaufmann, Douglas P Renfrew, Colin A Smith, Will Sheffler, Ian W Davis, Seth Cooper, Adrien Treuille, Daniel J Mandell, Florian Richter, Yih-En Andrew Ban, Sarel J Fleishman, Jacob E Corn, David E Kim, Sergey Lyskov, Monica Berrondo, Stuart Mentzer, Zoran Popovic, James J Havranek, John Karanicolas, Rhiju Das, Jens Meiler, Tanja Kortemme, Jeffrey J Gray, Brian Kuhlman, David Baker, Philip Bradley

ROSETTA3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules Journal Article

Methods Enzymol, 487 , pp. 545-574, 2011.

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C A Smith, T Kortemme

Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design Journal Article

PLoS One, 6 (7), 2011.

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C A Smith, T Kortemme

Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains Journal Article

J Mol Biol, 402 (2), pp. 460-474, 2010.

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F Lauck, C A Smith, G F Friedland, E L Humphris, T Kortemme

RosettaBackrub--a web server for flexible backbone protein structure modeling and design Journal Article

Nucleic Acids Res, 38 Suppl , pp. 569-575, 2010.

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G D Friedland, A J Linares, C A Smith, T Kortemme

A simple model of backbone flexibility improves modeling of side-chain conformational variability Journal Article

J Mol Biol, 380 (4), pp. 757-774, 2008.

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C A Smith, T Kortemme

Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction Journal Article

J Mol Biol, 380 (4), pp. 742-756, 2008.

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George Nicola, Colin A Smith, Ruben Abagyan

New method for the assessment of all drug-like pockets across a structural genome Journal Article

J Comput Biol, 15 (3), pp. 231-240, 2008.

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Grace O'Maille, Eden P Go, Linh Hoang, Elizabeth J Want, Colin Smith, Paul O'Maille, Anders Nordstrom, Hirotoshi Morita, Chuan Qin, Wilasinee Uritboonthai, Junefredo Apon, Richard Moore, James Garrett, Gary Siuzdak

Metabolomics relative quantitation with mass spectrometry using chemical derivatization and isotope labeling Journal Article

Spectr-Int J, 22 (5), pp. 327-343, 2008.

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George Nicola, Colin A Smith, Edinson Lucumi, Mack R Kuo, Luchezar Karagyozov, David A Fidock, James C Sacchettin, Ruben Abagyan

Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening Journal Article

Biochem Biophys Res Commun, 358 (3), pp. 686-691, 2007.

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Elizabeth J Want, Colin A Smith, Chuan Qin, K C VanHorne, Gary Siuzdak

Phospholipid capture combined with non-linear chromatographic correction for improved serum metabolite profiling Journal Article

Metabolomics, 2 (3), pp. 145-154, 2006.

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C A Smith, E J Want, G O'Maille, R Abagyan, G Siuzdak

XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Journal Article

Anal Chem, 78 (3), pp. 779-787, 2006.

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EJ Want, G O'Maille, CA Smith, TR Brandon, W Uritboonthai, C Qin, SA Trauger, G Siuzdak

Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry Journal Article

Anal Chem, 78 (3), pp. 743-752, 2006.

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CA Smith, G O'Maille, EJ Want, C Qin, SA Trauger, TR Brandon, DE Custodio, R Abagyan, G Siuzdak

METLIN - A metabolite mass spectral database Journal Article

Ther Drug Monit, 27 (6), pp. 747-751, 2005.

Abstract

YX Huang, CA Smith, HB Song, BP Morgan, R Abagyan, S Tomlinson

Insights into the human CD59 complement binding interface toward engineering new therapeutics Journal Article

J Biol Chem, 280 (40), pp. 34073-34079, 2005.

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CA Smith, W Huber, RC Gentleman

Interactive Outputs Incollection

Gentleman, Robert; Carey, Vincent J; Huber, Wolfgang; Irizarry, Rafael A; Dudoit, Sandrine (Ed.): Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pp. 147-160, Springer, New York, 2005.

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CA Smith

Browser-based Affymetrix Analysis and Annotation Incollection

Gentleman, Robert; Carey, Vincent J; Huber, Wolfgang; Irizarry, Rafael A; Dudoit, Sandrine (Ed.): Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pp. 313-326, Springer, New York, 2005.

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RC Gentleman, VJ Carey, DM Bates, B Bolstad, M Dettling, S Dudoit, B Ellis, L Gautier, YC Ge, J Gentry, K Hornik, T Hothorn, W Huber, S Iacus, R Irizarry, F Leisch, C Li, M Maechler, AJ Rossini, G Sawitzki, C Smith, G Smyth, L Tierney, JYH Yang, JH Zhang

Bioconductor: open software development for computational biology and bioinformatics Journal Article

Genome Biol, 5 (10), 2004.

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