Richard D. Smith

According to our database, Richard D. Smith authored at least 38 papers between 1967 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2021

AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry-mass spectrometry.

Joon-Yong Lee, Aivett Bilbao, Christopher R. Conant, Kent J. Bloodsworth, Daniel J. Orton, Mowei Zhou, Jesse William 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

Bioinform., November, 2021

Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics.

Richard D. Smith, Heather A. Carlson

J. Chem. Inf. Model., 2021

2019

Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures.

Jordan J. Clark, Mark L. Benson, Richard D. Smith, Heather A. Carlson

PLoS Comput. Biol., 2019

2018

Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics.

Sarah E. Graham, Richard D. Smith, Heather A. Carlson

J. Chem. Inf. Model., 2018

2017

Are there physicochemical differences between allosteric and competitive ligands?

Richard D. Smith, Jing Lu, Heather A. Carlson

PLoS Comput. Biol., 2017

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association.

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

Bioinform., 2017

LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data.

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

Bioinform., 2017

2016

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.

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

J. Chem. Inf. Model., 2016

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma.

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.

J. Chem. Inf. Model., 2016

2015

Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures.

Aqeel Ahmed, Richard D. Smith, Jordan J. Clark, James B. Dunbar Jr., Heather A. Carlson

Nucleic Acids Res., 2015

2014

Detecting differential protein expression in large-scale population proteomics.

So Young Ryu, Wei-Jun Qian, David G. Camp II, Richard D. Smith, Ronald G. Tompkins, Ronald W. Davis, Wenzhong Xiao

Bioinform., 2014

2013

Protein co-expression network analysis (ProCoNA).

David L. Gibbs, Arie Baratt, Ralph S. Baric, Yoshihiro Kawaoka, Richard D. Smith, Eric S. Orwoll, Michael G. Katze, Shannon K. McWeeney

J. Clin. Bioinform., 2013

CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys.

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

J. Chem. Inf. Model., 2013

CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series.

Kelly L. Damm-Ganamet, Richard D. Smith, James B. Dunbar Jr., Jeanne A. Stuckey, Heather A. Carlson

J. Chem. Inf. Model., 2013

Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice.

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

BMC Syst. Biol., 2013

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.

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

BMC Bioinform., 2013

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.

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

Bioinform., 2013

2012

Biophysical Limits of Protein-Ligand Binding.

Richard D. Smith, Alaina L. Engdahl, James B. Dunbar Jr., Heather A. Carlson

J. Chem. Inf. Model., 2012

Normalization and missing value imputation for label-free LC-MS analysis.

Yuliya V. Karpievitch, Alan R. Dabney, Richard D. Smith

BMC Bioinform., 2012

A hybrid approach to protein differential expression in mass spectrometry-based proteomics.

Xuan Wang, Gordon A. Anderson, Richard D. Smith, Alan R. Dabney

Bioinform., 2012

DanteR: an extensible R-based tool for quantitative analysis of -omics data.

Thomas Taverner, Yuliya V. Karpievitch, Ashoka D. Polpitiya, Joseph N. Brown, Alan R. Dabney, Gordon A. Anderson, Richard D. Smith

Bioinform., 2012

2011

CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions.

Richard D. Smith, James B. Dunbar Jr., Peter Man-Un Ung, Emilio Xavier Esposito, Chao-Yie Yang, Shaomeng Wang, Heather A. Carlson

J. Chem. Inf. Model., 2011

Correction to CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes.

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

J. Chem. Inf. Model., 2011

CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes.

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

J. Chem. Inf. Model., 2011

Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella.

Hyunjin Yoon, Charles Ansong, Jason E. McDermott, Marina A. Gritsenko, Richard D. Smith, Fred Heffron, Joshua N. Adkins

BMC Syst. Biol., 2011

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles.

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

BMC Syst. Biol., 2011

2010

Machine learning based prediction for peptide drift times in ion mobility spectrometry.

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

Bioinform., 2010

2009

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.

Navdeep Jaitly, Anoop M. Mayampurath, Kyle Littlefield, Joshua N. Adkins, Gordon A. Anderson, Richard D. Smith

BMC Bioinform., 2009

Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition.

Yuliya V. Karpievitch, Thomas Taverner, Joshua N. Adkins, Stephen J. Callister, Gordon A. Anderson, Richard D. Smith, Alan R. Dabney

Bioinform., 2009

A statistical framework for protein quantitation in bottom-up MS-based proteomics.

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

Bioinform., 2009

An Architecture for Real Time Data Acquisition and Online Signal Processing for High Throughput Tandem Mass Spectrometry.

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

Proceedings of the Fifth International Conference on e-Science, 2009

2008

Binding MOAD, a high-quality protein-ligand database.

Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John E. Beaver, Peter Dresslar, Jason Nerothin, Heather A. Carlson

Nucleic Acids Res., 2008

MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features.

Matthew E. Monroe, Jason L. Shaw, Don Simone Daly, Joshua N. Adkins, Richard D. Smith

Comput. Biol. Chem., 2008

DAnTE: a statistical tool for quantitative analysis of -omics data.

Ashoka D. Polpitiya, Wei-Jun Qian, Navdeep Jaitly, Vladislav A. Petyuk, Joshua N. Adkins, David G. Camp II, Gordon A. Anderson, Richard D. Smith

Bioinform., 2008

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra.

Anoop M. Mayampurath, Navdeep Jaitly, Samuel O. Purvine, Matthew E. Monroe, Kenneth J. Auberry, Joshua N. Adkins, Richard D. Smith

Bioinform., 2008

2007

VIPER: an advanced software package to support high-throughput LC-MS peptide identification.

Matthew E. Monroe, Nikola Tolic, Navdeep Jaitly, Jason L. Shaw, Joshua N. Adkins, Richard D. Smith

Bioinform., 2007

1969

Errata.

Richard D. Smith, Richard A. Dudek

Oper. Res., 1969

1967

A General Algorithm for Solution of the <i>n</i>-Job, <i>M</i>-Machine Sequencing Problem of the Flow Shop.

Richard D. Smith, Richard A. Dudek

Oper. Res., 1967