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List of works by Jane Shelby Richardson

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

scientific article

A new generation of crystallographic validation tools for the protein data bank

scientific article

A new way to see RNAs

scientific article published on 01 July 2020

A test of enhancing model accuracy in high-throughput crystallography

scientific article

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

scientific article published on 28 February 2013

Algorithm for backrub motions in protein design

scientific article published on July 2008

All-atom contacts: a new approach to structure validation

scientific article

Alpha-carbon coordinates for bovine Cu,Zn superoxide dismutase

scientific article published on April 21, 1975

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

scientific article (publication date: 17 June 1988)

An algorithm for smoothly tessellating beta-sheet structures in proteins

scientific article

An illustrated museum of protein structures

scientific article

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

scientific article (publication date: 29 January 1999)

Assessment of Molecular Construction in Undergraduate Biochemistry

article

Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale

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

scientific article

Automated identification of elemental ions in macromolecular crystal structures

scientific article published on 20 March 2014

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

scientific article published on 24 June 2005

Biophysical highlights from 54 years of macromolecular crystallography

scientific article (publication date: 4 February 2014)

Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding

scientific article published on 20 March 2017

Computational Methods for RNA Structure Validation and Improvement

scientific article

Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons

scientific article published on 07 August 2018

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

scientific article published on 04 February 2021

Crystallographic model validation: from diagnosis to healing

scientific article

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

scientific article published in August 1990

Describing patterns of protein tertiary structure

scientific article published in January 1985

Doing Molecular Biophysics: Finding, Naming, and Picturing Signal Within Complexity ⬇️

scientific article published on February 28, 2013

Electrostatic recognition between superoxide and copper, zinc superoxide dismutase

scientific article published in November 1983

Facile chemical synthesis and equilibrium unfolding properties of CopG.

scientific article published on 28 May 2004

Graphical tools for macromolecular crystallography in PHENIX

scientific article

Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding "EF hands" are related by charge and sequence reversal

scientific article published in January 1988

Improved AlphaFold modeling with implicit experimental information

scientific article published in 2022

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

scientific article published on 01 January 2020

Interpretation of electron density maps

scientific article published in January 1985

KinImmerse: Macromolecular VR for NMR ensembles

scientific article

Kinemages--simple macromolecular graphics for interactive teaching and publication

scientific article published in March 1994

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

scientific article published in April 2004

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

scientific article (publication date: July 2004)

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

scientific article published on 02 October 2019

Making the invisible enemy visible

scientific article published on 07 October 2020

Making the invisible enemy visible

scientific article published on 01 May 2021

Manganese superoxide dismutases from Escherichia coli and from yeast mitochondria: preliminary x-ray crystallographic studies

scientific article published on August 5, 1976

Mismodeled purines: implicit alternates and hidden Hoogsteens

scientific article published on 2 October 2017

Model validation: local diagnosis, correction and when to quit.

scientific article published in February 2018

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

scientific article published on 25 October 2017

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

scientific article

MolProbity: all-atom structure validation for macromolecular crystallography

scientific article

Molecular conformation of erabutoxin b; Atomic coordinates at 2.5 Å resolution ⬇️

scientific article published on June 13, 1979

Molprobity's ultimate rotamer-library distributions for model validation

scientific article

Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity

scientific article

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

scientific article

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

scientific article

New tools and data for improving structures, using all-atom contacts

scientific article published in January 2003

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

scientific article published on 10 December 2019

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

scientific article

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

scientific article

PHENIX: a comprehensive Python-based system for macromolecular structure solution

scientific article

Preliminary X-ray diffraction studies of acyl carrier protein from Escherichia coli

scientific article published in April 1985

Protein imperfections: separating intrinsic from extrinsic variation of torsion angles.

scientific article

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

scientific article published on January 1, 1996

RNA backbone is rotameric ⬇️

scientific article published on November 11, 2003

RNA backbone rotamers--finding your way in seven dimensions

scientific article published in June 2005

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

scientific article

Recent developments in phasing and structure refinement for macromolecular crystallography

scientific article published on 21 August 2009

Recommendations of the wwPDB NMR Validation Task Force

scientific article

Schematic drawings of protein structures

scientific article

Scientific benchmarks for guiding macromolecular energy function improvement

scientific article (publication date: 2013)

Simultaneous comparison of three protein sequences

scientific article published on May 1985

Structural and transcriptional analyses of a purine nucleotide-binding protein from Pyrococcus furiosus: a component of a novel, membrane-bound multiprotein complex unique to this hyperthermophilic archaeon

scientific article published on March 2007

Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin

scientific article

Structure and mechanism of copper, zinc superoxide dismutase ⬇️

scientific article published on November 17, 1983

Structure of the hypothetical protein PF0899 fromPyrococcus furiosusat 1.85 Å resolution

scientific article

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

scientific article (publication date: 15 February 2003)

Structures of the bacterial ribosome in classical and hybrid states of tRNA binding

scientific article

Studying and polishing the PDB's macromolecules

scientific article

SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics.

scientific article

THE DE NOVO DESIGN OF PROTEIN STRUCTURES

scientific article published in 1990

Target domain definition and classification in CASP8

scientific article

Teaching and Assessing Three-Dimensional Molecular Literacy in Undergraduate Biochemistry

scientific article published in May 2002

Teaching molecular 3-D literacy

scientific article published in January 2002

The Phenix software for automated determination of macromolecular structures

scientific article (publication date: September 2011)

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

scientific article published on 16 February 2006

The anatomy and taxonomy of protein structure

scientific article (publication date: 1981)

The backrub motion: how protein backbone shrugs when a sidechain dances

scientific article

The cis-Pro touch-turn: a rare motif preferred at functional sites.

scientific article

The extracellular nuclease of Staphylococcus aureus: structures of the native enzyme and an enzyme-inhibitor complex at 4 A resolution

scientific article

The high-throughput protein-to-structure pipeline at SECSG.

scientific article

The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models

scientific article

The penultimate rotamer library

scientific article (publication date: 15 August 2000)

The penultimate rotamer library

scholarly article by Simon C. Lovell published in January 2000

The protein surface is a moving target

scientific article

The role of local backrub motions in evolved and designed mutations

scientific article

The simple construction of protein alpha-carbon models

scientific article

The singly-wound parallel β barrel: A proposed structure for 2-keto-3-deoxy-6-phosphogluconate aldolase ⬇️

scientific article published on September 12, 1979

The toxin-agglutinin fold. A new group of small protein structures organized around a four-disulfide core

scientific article published in April 1980

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

scientific article published on September 1, 1976

Two Crystal Forms of Bovine Superoxide Dismutase ⬇️

scientific article published on October 10, 1972

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

scientific article published on 16 March 2012

VIEW

scientific article published in 1993

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

scientific article

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

scientific article

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