Nicholas G. M. Wells, Colin A. Smith

Predicting binding affinity changes from long-distance mutations using molecular dynamics simulations and Rosetta Journal Article

In: Proteins, 2023.

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Emma R. Hostetter, Jeffrey R. Keyes, Ivy Poon, Justin P. Nguyen, Jacob M. Nite, Carlos A. Jimenez Hoyos, Colin A. Smith

Prediction of Fluorophore Brightness in Designed Mini Fluorescence Activating Proteins Journal Article

In: Journal of Chemical Theory and Computation, 2022, ISBN: 1549-9618.

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Nicholas G M Wells, Grant A Tillinghast, Alison L O'Neil, Colin A Smith

Free Energy Calculations of ALS-Causing SOD1 Mutants Reveal Common Perturbations to Stability and Dynamics along the Maturation Pathway Journal Article

In: Protein Sci, 2021.

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Joshua A Dudley, Sojeong Park, Meagan E MacDonald, Emanual Fetene, Colin A Smith

Resolving overlapped signals with automated FitNMR analytical peak modeling Journal Article

In: J Magn Reson, vol. 318, pp. 106773, 2020.

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Julia Koehler Leman, Brian D Weitzner, Douglas P Renfrew, Steven M Lewis, Rocco Moretti, Andrew M Watkins, Vikram Khipple Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason W Labonte, Justyna Krys, Christopher Bystroff, William Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland Dunbrack, Tanja Kortemme, Andrew Leaver-Fay, Charlie E M Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J Gray, Richard Bonneau

Better together: Elements of successful scientific software development in a distributed collaborative community Journal Article

In: PLoS Comput Biol, vol. 16, no. 5, pp. e1007507, 2020.

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Colin A Smith, Adam Mazur, Ashok K Rout, Stefan Becker, Donghan Lee, Bert L de Groot, Christian Griesinger

Enhancing NMR derived ensembles with kinetics on multiple timescales Journal Article

In: J Biomol NMR, vol. 74, no. 1, pp. 27–43, 2020.

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Petra Rovó, Colin A Smith, Diego Gauto, Bert L de Groot, Paul Schanda, Rasmus Linser

Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary (15)N and (1)H Relaxation Dispersion Techniques Journal Article

In: J Am Chem Soc, vol. 141, no. 2, pp. 858–869, 2019.

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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

In: Arch Biochem Biophys, vol. 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

In: Proc Natl Acad Sci U S A, vol. 113, no. 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

In: Angew Chem Int Ed Engl, vol. 54, no. 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

In: J Biomol NMR, vol. 58, no. 4, pp. 287-301, 2014.

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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

In: Structure, vol. 21, no. 1, pp. 54-64, 2013.

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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

In: Methods Enzymol, vol. 523, pp. 61-85, 2013.

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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

In: PLoS One, vol. 6, no. 7, 2011.

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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

In: Methods Enzymol, vol. 487, pp. 545-574, 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

In: J Mol Biol, vol. 402, no. 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

In: Nucleic Acids Res, vol. 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

In: J Mol Biol, vol. 380, no. 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

In: J Mol Biol, vol. 380, no. 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

In: J Comput Biol, vol. 15, no. 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

In: Spectr-Int J, vol. 22, no. 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

In: Biochem Biophys Res Commun, vol. 358, no. 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

In: Metabolomics, vol. 2, no. 3, pp. 145-154, 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

In: Anal Chem, vol. 78, no. 3, pp. 743-752, 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

In: Anal Chem, vol. 78, no. 3, pp. 779-787, 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

In: Ther Drug Monit, vol. 27, no. 6, pp. 747-751, 2005.

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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

In: J Biol Chem, vol. 280, no. 40, pp. 34073-34079, 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

In: Genome Biol, vol. 5, no. 10, 2004.

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