David C. Richardson

发表

Graphical tools for macromolecular crystallography in PHENIX

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2012, Journal of applied crystallography.

The use of high-frequency data to engage students in quantitative reasoning and scientific discourse

Thomas Meixner, David C. Richardson, Catherine M. O'Reilly, 2014 .

CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation

Christopher J. Williams, Vincent B. Chen, David C. Richardson, 2019, bioRxiv.

Protein molecules in 3D: complex behavior from simple local geometry plus weak interactions

David C. Richardson, Jane S. Richardson, 2012, SoCG '12.

KiNG and kinemages

Vincent B. Chen, David C. Richardson, Jane S. Richardson, 2012 .

Defining, computing, and visualizing molecular interfaces

Dinesh Manocha, Frederick P. Brooks, Amitabh Varshney, 1995, Proceedings Visualization '95.

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

Paul D. Adams, Nathaniel Echols, Ralf W. Grosse-Kunstleve, 2012, Acta crystallographica. Section D, Biological crystallography.

A test of enhancing model accuracy in high-throughput crystallography

Shuren Wang, Weihong Zhou, David C. Richardson, 2005, Journal of Structural and Functional Genomics.

Model validation: local diagnosis, correction and when to quit

Christopher J. Williams, Vincent B. Chen, David C. Richardson, 2018, Acta crystallographica. Section D, Structural biology.

KinImmerse: Macromolecular VR for NMR ensembles

David J. Zielinski, Rachael Brady, Vincent B. Chen, 2008, Source Code for Biology and Medicine.

Programs and program systems in wide use

Randy J. Read, Paul D. Adams, Anastassis Perrakis, 2006 .

High-Grade Ore for Data Mining in 3D Structures

David C. Richardson, Jane S. Richardson, J. Richardson, 2003, Computational Biology and Genome Informatics.

Acta Crystallographica Section D Biological

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2003 .

A Model for using Environmental Data-Driven Inquiry and Exploration to Teach Limnology to Undergraduates

David C. Richardson, Catherine M. O'Reilly, Cayelan C. Carey, 2015 .

Analysis of high‐frequency and long‐term data in undergraduate ecology classes improves quantitative literacy

David C. Richardson, Cayelan C. Carey, Jennifer L. Klug, 2017 .

Phenix - a comprehensive python-based system for macromolecular structure solution

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2012 .

The Role of Local Backrub Motions in Evolved and Designed Mutations

Bruce Randall Donald, Ivelin Georgiev, David C. Richardson, 2012, PLoS Comput. Biol..

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Jack Snoeyink, Andrew Leaver-Fay, Xueyi Wang, 2007, Nucleic Acids Res..

MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes

David C. Richardson, Jane S. Richardson, Ian W. Davis, 2004, Nucleic Acids Res..

VIEW: an exploratory molecular visualization system with user-definable interaction sequences

Frederick P. Brooks, Lawrence D. Bergman, David C. Richardson, 1993, SIGGRAPH.

Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems Annual Review of Biophysics

Randy J. Read, Paul D. Adams, David Baker, 2012 .

An algorithm for smoothly tessellating β-sheet structures in proteins

Lawrence D. Bergman, David C. Richardson, Jane S. Richardson, 1995 .

SCULPTING PROTEINS INTERACTIVELY: REAL-TIME ENERGY MINIMIZATION EMBEDDED IN A GEOMETRICAL MODELING SYSTEM

David C. Richardson, Jane S. Richardson, Mark C. Surles, 1995 .

Project EDDIE: Improving Big Data skills in the classroom

Thomas Meixner, Dax C. Soule, David C. Richardson, 2015 .

Algorithm for backrub motions in protein design

Bruce Randall Donald, Ivelin Georgiev, David C. Richardson, 2008, ISMB.

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen, Jeffrey J. Headd, David C. Richardson, 2009, Acta crystallographica. Section D, Biological crystallography.

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage

Jennifer A. Doudna, David C. Richardson, Swati Jain, 2014, Nucleic acids research.

Divalent cation tolerant protein CUTA from Homo sapiens O60888

David C. Richardson, Wolfram Tempel, Zhi-Jie Liu, 2004 .

Electrostatic recognition between superoxide and copper, zinc superoxide dismutase

Peter A. Kollman, Paul K. Weiner, John A. Tainer, 1983, Nature.

Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place

Jeffrey J. Headd, David C. Richardson, Paul Emsley, 2008, Journal of Structural and Functional Genomics.

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

Paul D. Adams, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, 2010, Journal of applied crystallography.

Structure and mechanism of copper, zinc superoxide dismutase

John A. Tainer, David C. Richardson, Elizabeth D. Getzoff, 1983, Nature.