J. Richardson

发表

J. Richardson, D. Richardson, S. Lovell, 2000, Proteins.

A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing.

J. Richardson, D. Richardson, A. Yonath, 1971, The Journal of biological chemistry.

Molecular Traffic Jams on DNA

J. Richardson, D. Barber, M. Jacobson, 2018 .

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Christopher J. Williams, Randy J Read, Gábor Bunkóczi, 2019, Acta crystallographica. Section D, Structural biology.

Osprey: Protein Design with Ensembles, Flexibility, and Provable Algorithms

Pablo Gainza, Ivelin Georgiev, Cheng-Yu Chen, 2022 .

Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry

J. Richardson, D. Richardson, R. Bateman, 2002 .

Structure validation by Cα geometry: ϕ,ψ and Cβ deviation

Ian W. Davis, W. B. Arendall, J. Richardson, 2003, Proteins.

The Anatomy & Taxonomy of Protein Structure

J. Richardson, J. Richardson, 2007 .

Structure Validation by C a Geometry : f , y and C b Deviation

Ian W. Davis, W. B. Arendall, J. Richardson, 2002 .

The anatomy and taxonomy of protein structure.

J. Richardson, Jane S. Richardson, J. Richardson, 1981, Advances in protein chemistry.

Principles and Patterns of Protein Conformation

J. Richardson, D. Richardson, D. Richardson, 1989 .

The kinemage: A tool for scientific communication

D C Richardson, J S Richardson, J. Richardson, 1992, Protein science : a publication of the Protein Society.

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

Jason M. Swails, Pawel A. Janowski, D. Case, 2019, bioRxiv.

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

Christopher J. Williams, J. Richardson, R. Read, 2023, bioRxiv.

Accelerating crystal structure determination with iterative AlphaFold prediction

Christopher J. Williams, J. Richardson, R. Read, 2022, bioRxiv.

Improved AlphaFold modeling with implicit experimental information

J. Richardson, R. Read, P. Adams, 2022, bioRxiv.

MolProbity: More and better reference data for improved all‐atom structure validation

Christopher J. Williams, Jack Snoeyink, Vishal Verma, 2018, Protein science : a publication of the Protein Society.

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

M. Zalis, J. Richardson, D. Richardson, 1999, Journal of molecular biology.

High-Grade Ore for Data Mining in 3D Structures

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

Amino acid preferences for specific locations at the ends of alpha helices.

J. Richardson, D. Richardson, David H. S. Richardson, 1988, Science.

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).

Helen M Berman, David C Richardson, Anna Marie Pyle, 2008, RNA.

Schematic drawings of protein structures.

J S Richardson, J. Richardson, J. Richardson, 1985, Methods in enzymology.

New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics

Christopher J. Williams, Vincent B. Chen, Vincent B Chen, 2019, Protein science : a publication of the Protein Society.

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..

New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey

J. Richardson, H. Al‐Hashimi, Huiqing Zhou, 2015, Nucleic acids research.

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.

J. Richardson, D. Richardson, S. Lovell, 1999, Journal of molecular biology.

Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.

David Baker, Randy J Read, Frank DiMaio, 2013, Annual review of biophysics.

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

Randy J. Read, Paul D. Adams, Gerard J. Kleywegt, 2011, Structure.

Seeing the PDB

D. Goodsell, J. Richardson, D. Richardson, 2021, The Journal of biological chemistry.

Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein.

J. Richardson, D. Richardson, T. Quinn, 1994, Proceedings of the National Academy of Sciences of the United States of America.

De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence.

J. Richardson, D. Richardson, M. Hecht, 1990, Science.

Protein engineering: Design and synthesis of betabellin 7

J. Richardson, D. Richardson, B. W. Erickson, 1988 .

Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase.

J. Richardson, D. Richardson, J. Tainer, 1980, Journal of molecular biology.

Cis-nonPro Peptides: Genuine Occurrences and their Functional Roles

Christopher J. Williams, Lizbeth L. Videau, J. Richardson, 2018, bioRxiv.

RNA backbone is rotameric

W. B. Arendall, J. Richardson, D. Richardson, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding

Vincent B. Chen, Vincent B Chen, Michael B. Feldman, 2011, Science.

β-Sheet topology and the relatedness of proteins

J. Richardson, J. Richardson, 1977, Nature.

Studying and polishing the PDB's macromolecules.

David C Richardson, J. Richardson, D. Richardson, 2013, Biopolymers.

Recommendations of the wwPDB NMR Validation Task Force.

G. Montelione, D. Wishart, A. Bax, 2013, Structure.

The Alacoil: A very tight, antiparallel coiled‐coil of helices

D C Richardson, J S Richardson, Mark C. Surles, 1995, Protein science : a publication of the Protein Society.

D C Richardson, J S Richardson, J. Richardson, 1976, Journal of molecular biology.

The simple construction of protein alpha-carbon models.

B Rubin, J S Richardson, B. Rubin, 1972, Biopolymers.

Away from the edge II: in-house Se-SAS phasing with chromium radiation.

Bi Cheng Wang, W. B. Arendall, J. Richardson, 2005, Acta crystallographica. Section D, Biological crystallography.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

Christopher J. Williams, Soon Wen Hoh, Colin M. Palmer, 2021, Nature Methods.

The Role of Local Backrub Motions in Evolved and Designed Mutations

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

OSPREY: protein design with ensembles, flexibility, and provable algorithms.

Kyle E. Roberts, J. Richardson, R. Lilien, 2013, Methods in enzymology.

Algorithm for backrub motions in protein design

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

The beta bulge: a common small unit of nonrepetitive protein structure.

J. Richardson, D. Richardson, E. Getzoff, 1978, Proceedings of the National Academy of Sciences of the United States of America.

Kinetic role of helix caps in protein folding is context-dependent.

Terrence G Oas, J. Richardson, T. Oas, 2004, Biochemistry.

Structure and mechanism of copper, zinc superoxide dismutase

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

Alternate states of proteins revealed by detailed energy landscape mapping.

D. Baker, F. Dimaio, M. Tyka, 2011, Journal of molecular biology.

Making the invisible enemy visible

Christopher J. Williams, Christopher Williams, Agnel Praveen Joseph, 2020, bioRxiv.

The RNA Ontology Consortium: an open invitation to the RNA community.

James W. Brown, Helen M Berman, Steven E Brenner, 2006, RNA.

The Phenix software for automated determination of macromolecular structures.

Nathaniel Echols, Randy J Read, Gábor Bunkóczi, 2011, Methods.

Role of arginine 180 and glutamic acid 177 of ricin toxin A chain in enzymatic inactivation of ribosomes

J. Richardson, A. Frankel, P. Welsh, 1990, Molecular and cellular biology.

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.

assessment Authors:

Christopher J. Williams, Vincent B. Chen, Jeremy N. Block, 2009 .

Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation

J. Richardson, D. Richardson, D. Richardson, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Electrostatic recognition between superoxide and copper, zinc superoxide dismutase

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

Computational Methods for RNA Structure Validation and Improvement.

Swati Jain, D. Richardson, J. Richardson, 2015, Methods in enzymology.

Molecular Mechanisms of RNA Interference

J. Richardson, D. Barber, M. Jacobson, 2016 .

Automated identification of elemental ions in macromolecular crystal structures

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2014, Acta crystallographica. Section D, Biological crystallography.

Protein design and folding: template trapping of self‐assembled helical bundles

M. Mutter, D. Grell, J. Richardson, 2001, Journal of peptide science : an official publication of the European Peptide Society.

The importance of residue-level filtering, and the Top2018 best-parts dataset of high-quality protein residues

Christopher J. Williams, D. Richardson, J. Richardson, 2021, bioRxiv.

Molecular conformation of erabutoxin b; atomic coordinates at 2.5 A resolution.

J. Richardson, B. W. Low, L. S. Rosen, 1979, Biochemical and biophysical research communications.

THE IMPACT OF LOCAL ACCURACY IN PROTEIN AND RNA STRUCTURES : VALIDATION AS AN ACTIVE TOOL

J. Richardson, D. Richardson, D. Richardson, 2008 .

All-atom contacts: a new approach to structure validation.

J. Richardson, Jane S Richardson, J. Richardson, 2003, Methods of biochemical analysis.

Puzzle pieces defined: locating common packing units in tertiary protein contacts.

K. Gernert, L. D. Bergman, D. Richardson, 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

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.

Scientific benchmarks for guiding macromolecular energy function improvement.

Jack Snoeyink, Yifan Song, James Thompson, 2013, Methods in enzymology.

An illustrated museum of protein structures.

J. Tainer, D. Richardson, J. Richardson, 1980, Biophysical journal.

Three dimensional structure of erabutoxin b neurotoxic protein: inhibitor of acetylcholine receptor.

J. Richardson, B. W. Low, A. Rudko, 1976, Proceedings of the National Academy of Sciences of the United States of America.

Handedness of crossover connections in beta sheets.

J. Richardson, J. Richardson, 1976, Proceedings of the National Academy of Sciences of the United States of America.

Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands.

J. Richardson, D. Richardson, K. A. Thomas, 1975, Proceedings of the National Academy of Sciences of the United States of America.