Jane S. Richardson

Jane S. Richardson's AcademicInfluence.com Rankings

Jane S. Richardson

Physics

#1913

World Rank

#2900

Historical Rank

#784

USA Rank

Biophysics

#59

World Rank

#63

Historical Rank

#21

USA Rank

physics Degrees

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Physics

Jane S. Richardson's Degrees

PhD Biophysics California Institute of Technology
Masters Physics Stanford University
Bachelors Physics Stanford University

Why Is Jane S. Richardson Influential?

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According to Wikipedia, Jane Shelby Richardson is an American biophysicist best known for developing the Richardson diagram, or ribbon diagram, a method of representing the 3D structure of proteins. Ribbon diagrams have become a standard representation of protein structures that has facilitated further investigation of protein structure and function globally. With interests in astronomy, math, physics, botany, and philosophy, Richardson took an unconventional route to establishing a science career. Today Richardson is a professor in biochemistry at Duke University.

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Jane S. Richardson's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

PHENIX: a comprehensive Python-based system for macromolecular structure solution (2010) (19653)
MolProbity: all-atom structure validation for macromolecular crystallography (2009) (11674)
Structure validation by Cα geometry: ϕ,ψ and Cβ deviation (2003) (3749)
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids (2007) (3595)
The anatomy and taxonomy of protein structure. (1981) (3070)
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019) (2353)
MolProbity: More and better reference data for improved all‐atom structure validation (2018) (1914)
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. (1999) (1251)
Amino acid preferences for specific locations at the ends of alpha helices. (1988) (1245)
The penultimate rotamer library (2000) (989)
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes (2004) (965)
Structure and mechanism of copper, zinc superoxide dismutase (1983) (815)
Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. (1980) (804)
The Phenix software for automated determination of macromolecular structures. (2011) (738)
Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation (2002) (731)
Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. (1999) (534)
β-Sheet topology and the relatedness of proteins (1977) (485)
Electrostatic recognition between superoxide and copper, zinc superoxide dismutase (1983) (472)
Principles and Patterns of Protein Conformation (1989) (403)
A New Generation of Crystallographic Validation Tools for the Protein Data Bank (2011) (390)
Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding (2011) (357)
De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. (1990) (343)
Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands. (1975) (307)
Alternate states of proteins revealed by detailed energy landscape mapping. (2011) (265)
The backrub motion: how protein backbone shrugs when a sidechain dances. (2006) (250)
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). (2008) (235)
Three dimensional structure of erabutoxin b neurotoxic protein: inhibitor of acetylcholine receptor. (1976) (210)
RNA backbone is rotameric (2003) (202)
The beta bulge: a common small unit of nonrepetitive protein structure. (1978) (196)
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution (2012) (192)
The kinemage: A tool for scientific communication (1992) (192)
A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing. (1971) (191)
Scientific benchmarks for guiding macromolecular energy function improvement. (2013) (191)
Structure Validation by C a Geometry : f , y and C b Deviation (2002) (179)
The de novo design of protein structures. (1989) (170)
Simultaneous comparison of three protein sequences. (1985) (151)
Similarity of three-dimensional structure between the immunoglobulin domain and the copper, zinc superoxide dismutase subunit. (1976) (150)
Recommendations of the wwPDB NMR Validation Task Force. (2013) (141)
Handedness of crossover connections in beta sheets. (1976) (141)
The toxin-agglutinin fold. A new group of small protein structures organized around a four-disulfide core. (1980) (140)
Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein. (1994) (136)
Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992. (1992) (128)
Graphical tools for macromolecular crystallography in PHENIX (2012) (128)
OSPREY: protein design with ensembles, flexibility, and provable algorithms. (2013) (112)
The tyrosine corner: A feature of most greek key β‐barrel proteins (1994) (109)
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics (2010) (108)
The Alacoil: A very tight, antiparallel coiled‐coil of helices (1995) (102)
Schematic drawings of protein structures. (1985) (90)
Sculpting proteins interactively: Continual energy minimization embedded in a graphical modeling system (1994) (89)
beta-Sheet topology and the relatedness of proteins. (1977) (88)
Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. (2013) (88)
Algorithm for backrub motions in protein design (2008) (86)
The other 90% of the protein: Assessment beyond the Cαs for CASP8 template‐based and high‐accuracy models (2009) (83)
Molecular conformation of erabutoxin b; atomic coordinates at 2.5 A resolution. (1979) (78)
The RNA Ontology Consortium: an open invitation to the RNA community. (2006) (78)
Molprobity's ultimate rotamer‐library distributions for model validation (2016) (78)
New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics (2019) (72)
Corrections: Amino Acid Preferences for Specific Locations at the Ends of α Helices (1988) (72)
The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase. (1986) (72)
Teaching molecular 3‐D literacy (2002) (69)
Alpha-carbon coordinates for bovine Cu,Zn superoxide dismutase. (1975) (54)
Kinemages--simple macromolecular graphics for interactive teaching and publication. (1994) (54)
New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey (2015) (54)
A test of enhancing model accuracy in high-throughput crystallography (2005) (51)
Describing patterns of protein tertiary structure. (1985) (49)
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data (2009) (47)
The extracellular nuclease of Staphylococcus aureus: structures of the native enzyme and an enzyme-inhibitor complex at 4 A resolution. (1969) (45)
Folding kinetics of a fluorescent variant of monomeric lambda repressor. (1998) (45)
The tyrosine corner: a feature of most Greek key beta-barrel proteins. (1994) (45)
Early ribbon drawings of proteins (2000) (43)
Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. (1999) (42)
Target domain definition and classification in CASP8 (2009) (42)
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge (2021) (40)
VIEW: an exploratory molecular visualization system with user-definable interaction sequences (1993) (39)
Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity. (2014) (39)
Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place (2008) (38)
Automated identification of elemental ions in macromolecular crystal structures (2014) (36)
Comparative architecture of transposase and integrase complexes (2001) (35)
The Role of Local Backrub Motions in Evolved and Designed Mutations (2012) (33)
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone (2007) (31)
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage (2014) (30)
Recent developments in phasing and structure refinement for macromolecular crystallography. (2009) (29)
Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding. (2017) (28)
Helix lap‐joints as ion‐binding sites: DNA‐binding motifs and Ca‐binding “EF hands” are related by charge and sequence reversal (1988) (28)
"Active" conformation of an inactive semi-synthetic ribonuclease-S. (1981) (28)
Computational Methods for RNA Structure Validation and Improvement. (2015) (27)
The cis‐pro touch‐turn: A rare motif preferred at functional sites (2004) (27)
Improved AlphaFold modeling with implicit experimental information (2022) (27)
New tools and data for improving structures, using all-atom contacts. (2003) (26)
“THE PLOT” THICKENS: MORE DATA, MORE DIMENSIONS, MORE USES (2013) (25)
Interpretation of electron density maps. (1985) (24)
The high-throughput protein-to-structure pipeline at SECSG. (2005) (24)
KinImmerse: Macromolecular VR for NMR ensembles (2009) (24)
Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry (2002) (24)
Model validation: local diagnosis, correction and when to quit (2018) (23)
Structural genomics of Pyrococcus furiosus: X‐ray crystallography reveals 3D domain swapping in rubrerythrin (2004) (23)
Doing molecular biophysics: finding, naming, and picturing signal within complexity. (2013) (22)
The simple construction of protein alpha-carbon models. (1972) (21)
Two crystal forms of bovine superoxide dismutase. (1972) (21)
Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix (2019) (20)
Protein imperfections: separating intrinsic from extrinsic variation of torsion angles. (2005) (19)
Kinetic role of helix caps in protein folding is context-dependent. (2004) (19)
The crystal structure of bovine Cu2+,Zn2+ superoxide dismutase at 5.5-A resolution. (1974) (18)
Manganese superoxide dismutases from Escherichia coli and from yeast mitochondria: preliminary x-ray crystallographic studies. (1976) (16)
Assessment of molecular construction in undergraduate biochemistry (2005) (16)
Crystallographic model validation: from diagnosis to healing. (2013) (16)
The singly-wound parallel beta barrel: a proposed structure for 2-keto-3-deoxy-6-phosphogluconate aldolase. (1979) (14)
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. (2018) (14)
Improving SARS-CoV-2 structures: Peer review by early coordinate release (2021) (13)
Seeing the PDB (2021) (12)
Preliminary X-ray diffraction studies of acyl carrier protein from Escherichia coli. (1985) (12)
RNA backbone rotamers--finding your way in seven dimensions. (2005) (12)
Protein design and folding: template trapping of self‐assembled helical bundles (2001) (11)
Away from the edge II: in-house Se-SAS phasing with chromium radiation. (2005) (10)
Biophysical highlights from 54 years of macromolecular crystallography. (2014) (10)
Cis-nonPro Peptides: Genuine Occurrences and their Functional Roles (2018) (10)
Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons. (2018) (9)
Studying and polishing the PDB's macromolecules. (2013) (9)
All-atom contacts: a new approach to structure validation. (2003) (8)
AlphaFold predictions: great hypotheses but no match for experiment (2022) (8)
Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution (2020) (7)
Protein engineering: Design and synthesis of betabellin 7 (1988) (7)
Programs and program systems in wide use (2006) (5)
Facile chemical synthesis and equilibrium unfolding properties of CopG (2004) (5)
Mismodeled purines: implicit alternates and hidden Hoogsteens. (2017) (5)
Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution. (2007) (5)
Making the invisible enemy visible (2021) (5)
Introduction: Protein Motifs (1994) (5)
Protein structure: A new twist for hairpin turns (1985) (5)
Improving AlphaFold modeling using implicit information from experimental density maps (2022) (4)
The Anatomy & Taxonomy of Protein Structure (2007) (4)
Making the invisible enemy visible (2020) (4)
SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics. (2000) (3)
The Zen of Model Anomalies – Correct Most of Them. Treasure the Meaningful Valid Few. Live Serenely with the Rest! (2013) (3)
Puzzle pieces defined: locating common packing units in tertiary protein contacts. (1996) (2)
An algorithm for smoothly tessellating β-sheet structures in proteins (1995) (2)
Alanine aminotransferase from Pyrococcus furiosus Pfu-1397077-001 (2004) (2)
Accelerating crystal structure determination with iterative AlphaFold prediction (2022) (2)
Divalent cation tolerant protein CUTA from Homo sapiens O60888 (2004) (1)
THE IMPACT OF LOCAL ACCURACY IN PROTEIN AND RNA STRUCTURES : VALIDATION AS AN ACTIVE TOOL (2008) (1)
The importance of residue-level filtering, and the Top2018 best-parts dataset of high-quality protein residues (2021) (1)
The protein surface is a moving target. (2004) (1)
A Second Look at the HDV Ribozyme Structure and Dynamics. (2014) (1)
The importance of residue‐level filtering and the Top2018 best‐parts dataset of high‐quality protein residues (2021) (1)
Endoplasmic reticulum protein Rp19 O95881 (2004) (1)
Conserved hypothetical protein from Pyrococcus furiosus Pfu-1581948-001 (2004) (1)
Art and Analogy Help Scientists "See" Big Biological Molecules in 3D (2020) (1)
Structural Characteristics of Felix, a Designed Protein (1993) (1)
High-Grade Ore for Data Mining in 3D Structures (2003) (1)
SCULPTING PROTEINS INTERACTIVELY: REAL-TIME ENERGY MINIMIZATION EMBEDDED IN A GEOMETRICAL MODELING SYSTEM (1995) (1)
Conserved hypothetical protein Pfu-838710-001 from Pyrococcus furiosus (2005) (1)
An illustrated museum of protein structures. (1980) (1)
A new way to see RNAs (2020) (1)
Molecular Mechanisms of RNA Interference (2016) (1)
Hypothetical protein from Pyrococcus furiosus Pfu-1801964 (2004) (0)
Teaching Molecular Three-dimensional Literacy * (2005) (0)
Putative acetyl transferase from Pyrococcus furiosus (2004) (0)
Structure of a transcriptional regulator from Clostridium thermocellum Cth-833 (2004) (0)
Putative molybdopterin converting factor, subunit 1 from Pyrococcus furiosus, Pfu-562899-001 (2004) (0)
assessment Authors: (2009) (0)
Putative ABC transporter (ATP-binding protein) from Pyrococcus furiosus Pfu-867808-001 (2004) (0)
Introduction to 'What can and can't we see?' (2021) (0)
Molecular Traffic Jams on DNA (2018) (0)
Protein engineering through chemical synthesis: design and synthesis of betabellins 4 and 5 (1986) (0)
Crystal structure of an uncharacterized protein PF0899 from Pyrococcus furiosus (2007) (0)
HIT family hydrolase from Clostridium thermocellum Cth-393 (2004) (0)
Kinemage authorship in undergraduate biochemistry. (2002) (0)
CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation (2019) (0)
Teaching and Assessing Three-Dimensional M (2002) (0)
High-resolution structure of C domain of staphylococcal protein A at cryogenic temperature (2014) (0)
An algorithm for smoothly tessellating beta-sheet structures in proteins. (1995) (0)
What Do the Folds in Proteins Look Like? (2019) (0)
Thiamine phosphate pyrophosphorylase from Pyrococcus furiosus Pfu-1255191-001 (2004) (0)
Methionyl-tRNA formyltransferase from Clostridium thermocellum (2004) (0)
Real Rotamers using Real-Space Correlation Coefficients (2013) (0)
Chemistry of Blood Type 1853 William F. Coleman Assessment of Molecular Construction in Undergraduate Biochemistry (2005) (0)
Putative DNA-directed RNA polymerase, subunit e'' from Pyrococcus Furiosus Pfu-263306-001 (2004) (0)
Introduction to protein architecture Arthur M. Lesk; Oxford University Press, 2001, 347 pp., Â£24.99, large-format paperback, ISBN 0-19-850474-8 (2001) (0)
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 (2007) (0)
Protein molecules in 3D: complex behavior from simple local geometry plus weak interactions (2012) (0)
Kinemage supplement to introduction to protein structure (1999) (0)
Crystallography - Energetically Innovative at 100 (2014) (0)
Structure Ways & Means A New Generation of Crystallographic Validation Tools for the Protein Data Bank (0)
KiNG and kinemages (2012) (0)
Hypothetical Protein From Pyrococcus Furiosus Pfu-880080-001 (2004) (0)
A. Implications for Noncrystallographic Determination of Protein Structure The Anatomy & Taxonomy of Protein Structure (2007) (0)
High-resolution structure of two tandem B domains of staphylococcal protein A connected by the conserved linker (2014) (0)
Design of small symmetrical four-helix bundle proteins (2002) (0)
NADH oxidase /nitrite reductase from Pyrococcus furiosus Pfu-1140779-001 (2004) (0)
Inorganic pyrophosphatase from Pyrococcus furiosus Pfu-264096-001 (2004) (0)
Graphical tools for structure determination and refinement in PHENIX (2011) (0)
Fitting tips # 19 – Remember to use the information from NCS copies 2 (2020) (0)
Conserved hypothetical protein from Clostridium thermocellum Cth-2968 (2004) (0)
A database of high-quality protein residues for reference data, library construction and motif analysis (2019) (0)
A new way to see RNAs (2020) (0)
THE BETA BULGE: ITS DESCRIPTION, OCCURRENCE, AND IMPORTANCE IN PROTEIN STRUCTURE (1981) (0)
Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems Annual Review of Biophysics (2012) (0)
Hidden Hoogsteens in the Data (2014) (0)
Molecular therapy for 2.5–4 Å models: anecdotes and progress from the Cryo-EM Model Challenge (2018) (0)
2019 EMDataResource Model Metrics Challenge Dataset (2020) (0)
A Common Arch Structure in Beta Sandwich Proteins: the Tyrosine Turn (1993) (0)
Correction: Early ribbon drawings of proteins (2001) (0)
Chorismate mutase from Clostridium thermocellum Cth-682 (2004) (0)
MDFF Error Analysis: A Tool for Determining Stereochemical and Thermodynamic Correct Structures (2019) (0)
Through the Ramachandran Haze: Ca-Parameters Reveal Secondary Structure at Low Resolution (2013) (0)

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Jane S. Richardson's Academic­Influence.com Rankings