Richard D. Smith

Publication Activity (10 Years)

Years Active: 1967-2021
Publications (10 Years): 9

Top Topics

Protein Structure

Mass Spectrometry

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Richard D. Smith, Heather A. Carlson
Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. J. Chem. Inf. Model. 61 (3) (2021)
Joon-Yong Lee, Aivett Bilbao, Christopher R. Conant, Kent J. Bloodsworth, Daniel J. Orton, Mowei Zhou, Jesse W. Wilson, Xueyun Zheng, Ian K. Webb, Ailin Li, Kim K. Hixson, John C. Fjeldsted, Yehia M. Ibrahim, Samuel H. Payne, Christer Jansson, Richard D. Smith, Thomas O. Metz
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry-mass spectrometry. Bioinform. 37 (22) (2021)
Jordan J. Clark, Mark L. Benson, Richard D. Smith, Heather A. Carlson
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. PLoS Comput. Biol. 15 (1) (2019)
Sarah E. Graham, Richard D. Smith, Heather A. Carlson
Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics. J. Chem. Inf. Model. 58 (2) (2018)
Jian Ma, Cameron P. Casey, Xueyun Zheng, Yehia M. Ibrahim, Christopher S. Wilkins, Ryan S. Renslow, Dennis G. Thomas, Samuel H. Payne, Matthew E. Monroe, Richard D. Smith, Justin G. Teeguarden, Erin S. Baker, Thomas O. Metz
PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. Bioinform. 33 (17) (2017)
Jennifer E. Kyle, Kevin L. Crowell, Cameron P. Casey, Grant M. Fujimoto, Sangtae Kim, Sydney E. Dautel, Richard D. Smith, Samuel H. Payne, Thomas O. Metz
LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. Bioinform. 33 (11) (2017)
Richard D. Smith, Jing Lu, Heather A. Carlson
Are there physicochemical differences between allosteric and competitive ligands? PLoS Comput. Biol. 13 (11) (2017)
Richard D. Smith, Kelly L. Damm-Ganamet, James B. Dunbar Jr., Aqeel Ahmed, Krishnapriya Chinnaswamy, James Delproposto, Ginger Kubish, Christine E. Tinberg, Sagar D. Khare, Jiayi Dou, Lindsey Doyle, Jeanne A. Stuckey, David Baker, Heather A. Carlson
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. J. Chem. Inf. Model. 56 (6) (2016)
Heather A. Carlson, Richard D. Smith, Kelly L. Damm-Ganamet, Jeanne A. Stuckey, Aqeel Ahmed, Maire A. Convery, Donald O. Somers, Michael Kranz, Patricia A. Elkins, Guanglei Cui, Catherine E. Peishoff, Millard H. Lambert, James B. Dunbar Jr.
CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. J. Chem. Inf. Model. 56 (6) (2016)
Aqeel Ahmed, Richard D. Smith, Jordan J. Clark, James B. Dunbar Jr., Heather A. Carlson
Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. Nucleic Acids Res. 43 (Database-Issue) (2015)
So Young Ryu, Wei-Jun Qian, David G. Camp II, Richard D. Smith, Ronald G. Tompkins, Ronald W. Davis, Wenzhong Xiao
Detecting differential protein expression in large-scale population proteomics. Bioinform. 30 (19) (2014)
Kelly L. Damm-Ganamet, Richard D. Smith, James B. Dunbar Jr., Jeanne A. Stuckey, Heather A. Carlson
CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series. J. Chem. Inf. Model. 53 (8) (2013)
David L. Gibbs, Arie Baratt, Ralph S. Baric, Yoshihiro Kawaoka, Richard D. Smith, Eric S. Orwoll, Michael G. Katze, Shannon K. McWeeney
Protein co-expression network analysis (ProCoNA). J. Clin. Bioinform. 3 (2013)
Kevin L. Crowell, Gordon W. Slysz, Erin S. Baker, Brian L. LaMarche, Matthew E. Monroe, Yehia M. Ibrahim, Samuel H. Payne, Gordon A. Anderson, Richard D. Smith
LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets. Bioinform. 29 (21) (2013)
Nicolas Tchitchek, Amie J. Eisfeld, Jennifer Tisoncik-Go, Laurence Josset, Lisa E. Gralinski, Christophe Bécavin, Susan C. Tilton, Bobbie-Jo M. Webb-Robertson, Martin T. Ferris, Allison L. Totura, Chengjun Li, Gabriele Neumann, Thomas O. Metz, Richard D. Smith, Katrina M. Waters, Ralph S. Baric, Yoshihiro Kawaoka, Michael G. Katze
Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. BMC Syst. Biol. 7 (2013)
James B. Dunbar Jr., Richard D. Smith, Kelly L. Damm-Ganamet, Aqeel Ahmed, Emilio Xavier Esposito, James Delproposto, Krishnapriya Chinnaswamy, You-Na Kang, Ginger Kubish, Jason E. Gestwicki, Jeanne A. Stuckey, Heather A. Carlson
CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys. J. Chem. Inf. Model. 53 (8) (2013)
Brian L. LaMarche, Kevin L. Crowell, Navdeep Jaitly, Vladislav A. Petyuk, Anuj R. Shah, Ashoka D. Polpitiya, John D. Sandoval, Gary R. Kiebel, Matthew E. Monroe, Stephen J. Callister, Thomas O. Metz, Gordon A. Anderson, Richard D. Smith
MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. BMC Bioinform. 14 (2013)
Yuliya V. Karpievitch, Alan R. Dabney, Richard D. Smith
Normalization and missing value imputation for label-free LC-MS analysis. BMC Bioinform. 13 (S-16) (2012)
Thomas Taverner, Yuliya V. Karpievitch, Ashoka D. Polpitiya, Joseph N. Brown, Alan R. Dabney, Gordon A. Anderson, Richard D. Smith
DanteR: an extensible R-based tool for quantitative analysis of -omics data. Bioinform. 28 (18) (2012)
Richard D. Smith, Alaina L. Engdahl, James B. Dunbar Jr., Heather A. Carlson
Biophysical Limits of Protein-Ligand Binding. J. Chem. Inf. Model. 52 (8) (2012)
Xuan Wang, Gordon A. Anderson, Richard D. Smith, Alan R. Dabney
A hybrid approach to protein differential expression in mass spectrometry-based proteomics. Bioinform. 28 (12) (2012)
Uma K. Aryal, Jana Stöckel, Ravi K. Krovvidi, Marina A. Gritsenko, Matthew E. Monroe, Ronald J. Moore, David W. Koppenaal, Richard D. Smith, Himadri B. Pakrasi, Jon M. Jacobs
Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles. BMC Syst. Biol. 5 (2011)
James B. Dunbar Jr., Richard D. Smith, Chao-Yie Yang, Peter Man-Un Ung, Katrina W. Lexa, Nickolay A. Khazanov, Jeanne A. Stuckey, Shaomeng Wang, Heather A. Carlson
Correction to CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. J. Chem. Inf. Model. 51 (9) (2011)
Richard D. Smith, James B. Dunbar Jr., Peter Man-Un Ung, Emilio Xavier Esposito, Chao-Yie Yang, Shaomeng Wang, Heather A. Carlson
CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions. J. Chem. Inf. Model. 51 (9) (2011)
James B. Dunbar Jr., Richard D. Smith, Chao-Yie Yang, Peter Man-Un Ung, Katrina W. Lexa, Nickolay A. Khazanov, Jeanne A. Stuckey, Shaomeng Wang, Heather A. Carlson
CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. J. Chem. Inf. Model. 51 (9) (2011)
Hyunjin Yoon, Charles Ansong, Jason E. McDermott, Marina A. Gritsenko, Richard D. Smith, Fred Heffron, Joshua N. Adkins
Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella. BMC Syst. Biol. 5 (2011)
Anuj R. Shah, Khushbu Agarwal, Erin S. Baker, Mudita Singhal, Anoop M. Mayampurath, Yehia M. Ibrahim, Lars J. Kangas, Matthew E. Monroe, Rui Zhao, Mikhail E. Belov, Gordon A. Anderson, Richard D. Smith
Machine learning based prediction for peptide drift times in ion mobility spectrometry. Bioinform. 26 (13) (2010)
Navdeep Jaitly, Anoop M. Mayampurath, Kyle Littlefield, Joshua N. Adkins, Gordon A. Anderson, Richard D. Smith
Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinform. 10 (2009)
Yuliya V. Karpievitch, Thomas Taverner, Joshua N. Adkins, Stephen J. Callister, Gordon A. Anderson, Richard D. Smith, Alan R. Dabney
Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition. Bioinform. 25 (19) (2009)
Anuj R. Shah, Navdeep Jaitly, Nino Zuljevic, Matthew E. Monroe, Andrei Liyu, Ashoka D. Polpitiya, Joshua N. Adkins, Mikhail E. Belov, Gordon A. Anderson, Richard D. Smith, Ian Gorton
An Architecture for Real Time Data Acquisition and Online Signal Processing for High Throughput Tandem Mass Spectrometry. eScience (2009)
Yuliya V. Karpievitch, Jeff Stanley, Thomas Taverner, Jianhua Huang, Joshua N. Adkins, Charles Ansong, Fred Heffron, Thomas O. Metz, Wei-Jun Qian, Hyunjin Yoon, Richard D. Smith, Alan R. Dabney
A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinform. 25 (16) (2009)
Matthew E. Monroe, Jason L. Shaw, Don Simone Daly, Joshua N. Adkins, Richard D. Smith
MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features. Comput. Biol. Chem. 32 (3) (2008)
Ashoka D. Polpitiya, Wei-Jun Qian, Navdeep Jaitly, Vladislav A. Petyuk, Joshua N. Adkins, David G. Camp II, Gordon A. Anderson, Richard D. Smith
DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinform. 24 (13) (2008)
Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John E. Beaver, Peter Dresslar, Jason Nerothin, Heather A. Carlson
Binding MOAD, a high-quality protein-ligand database. Nucleic Acids Res. 36 (Database-Issue) (2008)
Anoop M. Mayampurath, Navdeep Jaitly, Samuel O. Purvine, Matthew E. Monroe, Kenneth J. Auberry, Joshua N. Adkins, Richard D. Smith
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinform. 24 (7) (2008)
Matthew E. Monroe, Nikola Tolic, Navdeep Jaitly, Jason L. Shaw, Joshua N. Adkins, Richard D. Smith
VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinform. 23 (15) (2007)
Richard D. Smith, Richard A. Dudek
Errata. Oper. Res. 17 (4) (1969)
Richard D. Smith, Richard A. Dudek
-Machine Sequencing Problem of the Flow Shop. Oper. Res. 15 (1) (1967)