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Selected Recent Papers



" New Tools in MolProbity Validation: CaBLAM for cryoEM backbone, UnDowser to rethink "waters", and NGL Viewer to recapture online 3D graphics "
Prisant MG, Williams CJ, Chen VB, Richardson JS, Richardson DC (2020) Protein Sci 29 315-329 doi: ??



" Improved chemistry restraints for crystallographic refinement by integrating Amber molecular mechanics into Phenix "
Moriarty NW, Janowski PA, Swails JM, Nguyen H, Richardson JS, Case DA, Adams PD (2020) Acta Cryst D76 51-62 doi: 10.1107/S2059798319015134



" Macromolecular structure determination using X-rays, neutrons, and electrons: Recent developments in Phenix "
Liebschner D. Afonine PV, Baker ML, Bunkoczi G, Chen VB, Croll TI. Hintze BJ, Hung L-W, Jain S, Liebschner D. Afonine PV, Baker ML, Bunkoczi G, Chen VB, Croll TI. Hintze BJ, Hung L-W, Jain S, DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD (2019) Acta Cryst D75 861-877 doi: ??



" Art and Analogy Help Scientists "See" Big Biological Molecules in 3D "
Richardson JS (2018) SciArt Mag 33 1-6 doi: ??



" Cis-nonPro peptides: Genuine occurrences and their functional roles "
Williams CJ, Videau LL, Hintze BJ, Richardson JS, Richardson DC (2018) bioRxiv ?? ??-?? doi: 10.1101/324517


SuppInfo (1.8M)

" MolProbity: More and better reference data for improved all-atom structure validation "
Williams CJ, Hintze BJ, Headd JJ, Moriarty NW, Chen VB, Jain S, Prisant MG Lewis SM, Videau LL, Keedy DA, Deis LN, Arendall WB III, Verma V, Snoeyink JS, Adams PD, Lovell SC, Richardson JS, Richardson DC (2018) ProtSci 27 293-315 doi: 10.1002/pro.3330, PMC5734394



" Assessment of detailed conformations suggests strategies for improving cryoEM models: helix at lower resolution, ensembles, pre-refinement fixups, and validation at a multi-residue length scale "
Richardson JS, Williams CJ, Videau LL, Chen VB, Richardson DC (2018) J Struct Biol (CryoEM Challenge special issue) 204 319-328 doi: 10.1016/j.jsb.2018.08.007



" Constructing atomic structural models into cryo-EM densities using molecular dynamics -- Pros and Cons "
Wang Y, Shekhar M, Thifault D, Williams C, Mcgreevy R, Richardson J, Singharoy A, Takhorshid E (2018) J Struct Biol (CryoEM Challenge special issue) 204 301-312 doi:10.1016/j.jsb.2018.08.003



" Model validation -- local diagnosis, correction, and when to quit "
Richardson JS, Williams CJ, Hintze BJ, Chen VB, Prisant MG, Videau LL, Richardson DC (2018) Acta Cryst D 74 132-142 from CCP4 Study Weekend 2017) PMC5947777



" Cis-nonPro peptides: Genuine occurrences and their functional roles "
Williams CJ,Videau LL, Hintze BJ, Richardson JS, Richardson DC (2018) https://www.biorxiv.org/content/early/2018/05/17/324517



" Mismodeled purines: Implicit alternates and hidden Hoogsteens "
Hintze BJ, Richardson JS, Richardson DC (2017) Acta Cryst D 73 852-859 doi: PMC5633910 (cover image)



" Broad analysis of vicinal disulfides: Occurrences, conformations with cis or with trans peptides, and functional roles including sugar binding "
Richardson JS, Videau LL, Williams CJ, Richardson DC (2017) J Mol Biol 429 1321-1335 "PMC5500257 (open access)



" MolProbity's ultimate rotamer-library distributions for model validation "
Hintze BJ, Lewis SM, Richardson JS, Richardson DC (2016) Proteins: Struc Func Bioinf 84 online since Mar 28 doi: 10.1002/prot.25039 (open access), PMC4983197



" Computational methods for RNA structure validation and improvement "
Jain S, Richardson DC, Richardson JS (2015) Chapter 7 in Structures of large RNA molecules and their complexes, Ed. Woodson S & Allain F, Methods Enzymol series 558 181-212



" New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey "
Zhou H, Hintze BJ, Kimsey IJ, Sathyamoorthy B, Yang S, Richardson JS, Al-Hashimi HM (2015) Nucl Acids Res 43 3420-3433 PMC4402545 doi: ??/??/?? (open access)



" New tools provide a second look at HDV ribozyme structure, dynamics and cleavage "
Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS (2014) Nucl Acids Res 42 12833-12846 doi: 10.1093/nar/gku992 (open access)



" Multiscale Conformational Heterogeneity in Staphylococcal Protein A: Possible Determinant of Functional Plasticity "
Deis LN, PembleIV CW, Qi Y, Hagarman A, Richardson DC, Richardson JS, Oas TG (2014) Structure 22 :1467-1477 doi:10.1016/j.str.2014.08.014 (open access)



" The Statistical Conformation of a Highly Flexible Protein: Small-Angle X-Ray Scattering of S. aureus Protein A "
Capp JoA, Hagarman A, Richardson DC, Oas TG (2014) Structure 22 :1184-1195 doi:10.1016/j.str.2014.6.011 (open access)

(F1000Prime recommendation by W Chazin doi:10.3410/f.718519299.793501063)



" Automated identification of elemental ions in macromolecular crystal structures "
Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD (2014) Acta Cryst D70 :1104-1114 doi:10.1107/S1399004714001308



" Biophysical Highlights from 54 Years of Macromolecular Crystallography "
Richardson JS, Richardson DC (2014) Biophysical Journal 106 :510-525 doi:10.1016/j.bpj.2014.01.001



" Recommendations of the wwPDB NMR Validation Task Force "
Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL (2013) Structure 21 :1563-1570 doi:10.1016/j.str.2013.07.021



" Crystallographic model validation: from diagnosis to healing "
Richardson JS, Prisant MG, Richardson DC (2013) Curr Op Struct Biol 23 :707-714 doi:10.1016/j.sbi.2013.06.004



"The Zen of model anomalies – Correct most of them. Treasure the meaningful valid few. Live serenely with the rest."
Richardson JS and Richardson DC (2013) In Advancing Methods in Biomolecular Crystallography, ed Read RJ, NATO conference volume from 2012 Erice crystallography school, Springer, (publ April 2013) pages:1-10 doi: 10.1007/978-94-007-6232-9



"Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems"
Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson JS, Terwilliger TC (2013) Ann. Rev. Biophys. 42:265-287 doi: 10.1146/annurev-biophys-083012-130253



"Doing molecular biophysics: Finding, naming, and picturing signal within complexity"
Richardson JS and Richardson DC (2013) Ann. Rev. Biophys. 42:1-28 doi: 10.1146/annurev-biophys-083012-130353



"OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms"
Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen C-Y, Reza F, Anderson AC, Richardson DC, Richardson JS and Donald BR (2013) Meth Enzymol 523:87-107 doi: 10.1016/B978-0-12-394292-0.00005-9



"Scientific benchmarks for updating the Rosetta energy function"
Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, Baker D, Kuhlman B (2013) Meth Enzymol 523109-143 doi: 10.1016/B978-0-12-394292-0.00006-0



""The Plot" Thickens: More Data, More Dimensions, More Uses"
Richardson JS, Keedy DK, & Richardson DC (2013) Book Chapter: ISBN: 978-981-4449-15-1 (ebook)



"Studying and Polishing the PDB’s Macromolecules"
Richardson JS & Richardson DC (2012) Biopolymers 99(3)170-182. doi: 10.1002/bip.22108


(576 KB)

"The Role of Local Backrub Motions in Evolved and Designed Mutations."
Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, & Richardson JS (2012) PLoS Comp Biol 8(8). doi: 10.1371/journal.pcbi.1002629 (open access)



" Graphical tools for macromolecular crystallography in PHENIX"
Echols N, Grosse-Kunstleve RW, Afonine PV, Bunko ́czi G, Chen VB, Headd JJ, McCoy AJ, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, & Adams PD (2012) J. Appl. Cryst. 45:581-586. doi:10.1107/S0021889812017293 (open access)



"Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution"
Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, & Adams PD (2012) Acta Cryst D68:381-390. doi: 10.1107/S0907444911047834 (open access)



"A New Generation of Crystallographic Validation Tools for the Protein Data Bank"
Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, & Zwart PH (2011) Structure 19:1395-1412. doi: 10.1016/j.str.2011.08.006 (open access)



"The Phenix software for automated determination of macromolecular structures"
Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung L-W, Jain S, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2011) Methods 55:94-106. doi: 10.1016/j.ymeth.2011.07.005



"Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding"
Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, & Doudna Cate JH (2011) Science 332:981-984. doi: 10.1126/science.1202692



"Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping"
Tyka MD, Keedy DA, André I, DiMaio F, Song Y, Richardson DC, Richardson JS & David Baker D (2011) J Mol Biol 405(2):607-618. doi: /10.1016/j.jmb.2010.11.008 (open access)



"PHENIX: a comprehensive Python-based system for macromolecular structure solution"
Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) Acta Cryst D66:213-221. doi: 10.1107/S0907444909052925 (open access)



 "MolProbity: all-atom structure validation for macromolecular crystallography"
Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS & Richardson DC (2010)  Acta Cryst D66:12-21 doi: 10.1107/S0907444909042073 (open access)



 "Recent developments in phasing and structure refinement for macromolecular crystallography"
Adams PD, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS, Richardson DC & Terwilliger TC (2009)  Current Opinion in Structural Biology 19:566-572 doi: 10.1016/j.sbi.2009.07.014



 "KiNG (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program"
Chen VB, Davis IW & Richardson DC (2009)  Protein Sci 18:2403-2409 doi: 10.1002/pro.250 (open access)



 "The other 90% of the protein: Assessment beyond the Cαs for CASP8 template-based and high-accuracy models"
Keedy DA, Williams CJ, Headd JJ, Arendall WB, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC & Richardson JS (2009)  Proteins: Struc Func Bioinf 77(Suppl 9):29-49 doi: 10.1002/prot.22551


Book Link

" The Impact of Local Accuracy In Protein and RNA Structures: Validation As an Active Tool"
Richardson JS & Richardson DC (2009)  Chapter 15 in Structural Bioinformatics, 2nd Edition, ed. J. Gu and P. Bourne. Wiley (New York).



"KinImmerse: Macromolecular VR for NMR ensembles"
Block JN, Zielinski DJ, Chen VB, Davis IW, Vinson EC, Brady R, Richardson JS & Richardson DC (2009)  Source Code Biol Med 4:3. doi: 10.1186/1751-0473-4-3 (open access)



 "Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place"
Headd JJ, Immormino RM, Keedy DA, Emsley P, Richardson DC & Richardson JS  (2009)  J Struc Func Genomics 10:83-93. doi: 10.1007/s10969-008-9045-8 (open access)



 "Algorithm for backrub motions in protein design"
Georgiev I, Keedy DA, Richardson JS, Richardson DC & Donald BR (2008)  Bioinformatics 24:i196-i204. doi: 10.1093/bioinformatics/btn169 (open access)



 "RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature (an RNA Ontology Consortium contribution)"
Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, David Micallef d, Westbrook J & Berman HM (2008)  RNA 14 :465-481. doi: 10.1261/rna.657708 (open access)



 "RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone"
Wang X, Kapral GJ, Murray LW, Richardson DC, Richardson JS & Snoeyink J (2008) J Math Biol 56:253-278. doi: 10.1007/s00285-007-0082



"MolProbity: all-atom contacts and structure validation for proteins and nucleic acids"
Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS & Richardson DC (2007) Nucleic Acids Res 35 W375-W383. doi:10.1093/nar/gkm216 (open access)


SuppData &
hi-res img

"The backrub motion: How protein backbone shrugs when a sidechain dances"
Davis IW, Arendall WB, Richardson DC, & Richardson JS (2006) Structure 14, 265-274. doi:10.1016/j.str.2005.10.007 (Supplementary data available also.)



"The RNA Ontology Consortium: An Open Invitation to the RNA Community"
Leontis NB, Altman R, Berman HM, Brenner SE, Brown J, Engelke D, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR & Westhof E (2006) RNA 12, 533-541. doi:10.1261/rna.2343206 (open access)



"A test of enhancing model accuracy in high-throughput crystallography"
Arendall WB, Tempel W, Richardson JS, Zhou W, Wang S, Davis IW, Liu Z-J, Rose JP, Carson WM, Luo M, Richardson DC, & Wang B-C. (2005) J Struc Func Genomics 6, 1-11. doi:10.1007/s10969-005-3138-4



"MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes"
Davis IW, Murray LW, Richardson JS, & Richardson DC. (2004) . Nucleic Acids Res 32 W615-619. doi:10.1093/nar/gkh398 (open access)



"The Cis Pro Touch-Turn: A Rare Motif Preferred at Functional Sites"
Videau LL, Arendall WB, & Richardson JS. (2004) Proteins: Struc Func Bioinf 56, 298-309. doi:10.1002/prot.20101



"Kinetic Role of Helix Caps in Protein Folding is Context-Dependent"
Kapp GT, Richardson JS, & Oas TG. (2004) Biochemistry 43, 3814-3823. doi:10.1021/bi035683k



"RNA Backbone Is Rotameric"
Murray LW, Arendall WB, Richardson DC, & Richardson JS (2003) PNAS-USA 100, 13904-13909. doi:10.1073/pnas.1835769100



"Structure Validation by Cα Geometry: φ,ψ and Cβ Deviation."
Lovell SC, Davis IW, Arendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS, & Richardson DC (2003) Proteins: Struc Func Genet 50, 437-450. doi:10.1002/prot.10286



"New Tools and Data for Improving Structures, Using All-Atom Contacts. "
Richardson JS, Arendall WB, & Richardson DC (2003) Chapter in Methods in Enzymology: Macromolecular Crystallography, Part D, ed. C.W. Carter, Jr and R.M. Sweet. Academic Press (San Diego)374, 385-412.



"Natural β-Sheet Proteins Use Negative Design to Avoid Edge-to-Edge Aggregation."
Richardson JS & Richardson DC (2002) PNAS-USA 99, 2754-2759. doi:10.1073/pnas.052706099



"Teaching Molecular 3-D Literacy."
Richardson DC, Richardson JS (2002) Biochem Molec Biol Educ 30, 21-26. doi:10.1002/bmb.2002.494030010005

 2001Volume F

"MAGE, PROBE, and Kinemages."
Richardson DC & Richardson JS (2001) In International Tables for Crystallography, ed. Rossmann MG, Arnold E vol. F, chapter 25.2.8.,, 727-730 Kluwer Publ



"The Penultimate Rotamer Library."
Lovell SC, Word JM, Richardson JS, Richardson DC (2000) Proteins: Struc Func Genet 40, 389-408. doi: 10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2

20th Century Classics



"Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogen Atoms."
Word MJ, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, & Richardson DC (1999) J Mol Biol 285, 1711-33. doi:10.1006/jmbi.1998.2400



"Asparagine and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-chain Amide Orientation."
Word MJ, Lovell SC, Richardson JS, & Richardson DC (1999) J Mol Biol 285, 1735-47. doi:10.1006/jmbi.1998.2401


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link to anatax docs

"The Anatomy and Taxonomy of Protein Structure" (and updates)
Richardson JS (1981 & 2004-2006) In Advances in Protein Chemistry, ed. Anfinsen CB, Edsall JT, Richards FM. (updates & original on our website) 34, 167-339 Academic Press.

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