Scholars@Duke
David C. Richardson

David C. Richardson

Professor Emeritus of Biochemistry
Biochemistry
dcr@kinemage.biochem.duke.edu
Duke Box 3711, Durham, NC 27710
132 Nanaline H Duke, Durham, NC 27710

Selected Publications

The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions.

Journal Article Acta Crystallogr D Struct Biol · December 1, 2023 Model building and refinement, and the validation of their correctness, are very effective and reliable at local resolutions better than about 2.5 Å for both crystallography and cryo-EM. However, at local resolutions worse than 2.5 Å both the procedures an ... Full text Link to item Cite

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

Journal Article Protein Sci · January 2022 We have curated a high-quality, "best-parts" reference dataset of about 3 million protein residues in about 15,000 PDB-format coordinate files, each containing only residues with good electron density support for a physically acceptable model conformation. ... Full text Open Access Link to item Cite

Improving SARS-CoV-2 structures: Peer review by early coordinate release.

Journal Article Biophys J · March 16, 2021 This work builds upon the record-breaking speed and generous immediate release of new experimental three-dimensional structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins and complexes, which are crucial to downstream vacc ... Full text Link to item Cite

Seeing the PDB.

Journal Article J Biol Chem · 2021 Ever since the first structures of proteins were determined in the 1960s, structural biologists have required methods to visualize biomolecular structures, both as an essential tool for their research and also to promote 3D comprehension of structural resu ... Full text Link to item Cite

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

Journal Article Protein Sci · January 2020 The MolProbity web service provides macromolecular model validation to help correct local errors, for the structural biology community worldwide. Here we highlight new validation features, and also describe how we are fighting back against outside developm ... Full text Link to item Cite

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

Journal Article Acta Crystallogr D Struct Biol · October 1, 2019 Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. Th ... Full text Link to item Cite

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.

Journal Article J Struct Biol · November 2018 We find that the overall quite good methods used in the CryoEM Model Challenge could still benefit greatly from several strategies for improving local conformations. Our assessments primarily use validation criteria from the MolProbity web service. Those c ... Full text Link to item Cite

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

Journal Article Acta Crystallogr D Struct Biol · February 1, 2018 Traditionally, validation was considered to be a final gatekeeping function, but refinement is smoother and results are better if model validation actively guides corrections throughout structure solution. This shifts emphasis from global to local measures ... Full text Link to item Cite

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

Journal Article Protein Sci · January 2018 This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, includin ... Full text Link to item Cite

Mismodeled purines: implicit alternates and hidden Hoogsteens.

Journal Article Acta Crystallogr D Struct Biol · October 1, 2017 Hoogsteen base pairs are seen in DNA crystal structures, but only rarely. This study tests whether Hoogsteens or other syn purines are either under-modeled or over-modeled, which are known problems for rare conformations. Candidate purines needing a syn/an ... Full text Link to item Cite

Alignment of 1000 Genomes Project reads to reference assembly GRCh38.

Journal Article Gigascience · July 1, 2017 The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on h ... Full text Link to item Cite

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

Journal Article J Mol Biol · May 5, 2017 Vicinal disulfides between sequence-adjacent cysteine residues are very rare and rather startling structural features which play a variety of functional roles. Typically discussed as an isolated curiosity, they have never received a general treatment cover ... Full text Link to item Cite

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.

Journal Article Genome Biol · January 26, 2017 BACKGROUND: A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability. RESULTS: We apply a novel analytical approach to measure and ... Full text Link to item Cite

The BLUEPRINT Data Analysis Portal.

Journal Article Cell Syst · November 23, 2016 The impact of large and complex epigenomic datasets on biological insights or clinical applications is limited by the lack of accessibility by easy, intuitive, and fast tools. Here, we describe an epigenomics comparative cyber-infrastructure (EPICO), an op ... Full text Link to item Cite

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.

Journal Article Cell · November 17, 2016 The International Human Epigenome Consortium (IHEC) coordinates the generation of a catalog of high-resolution reference epigenomes of major primary human cell types. The studies now presented (see the Cell Press IHEC web portal at http://www.cell.com/cons ... Full text Link to item Cite

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

Journal Article Cell · November 17, 2016 Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation. The vast majority of interactions are uncharted, constituting a major missing link in understanding genome control. Here, we use promoter c ... Full text Link to item Cite

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

Journal Article Cell · November 17, 2016 Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human ... Full text Link to item Cite

Molprobity's ultimate rotamer-library distributions for model validation.

Journal Article Proteins · September 2016 Here we describe the updated MolProbity rotamer-library distributions derived from an order-of-magnitude larger and more stringently quality-filtered dataset of about 8000 (vs. 500) protein chains, and we explain the resulting changes and improvements to m ... Full text Link to item Cite

Cover Image, Volume 84, Issue 9

Journal Article Proteins: Structure, Function and Bioinformatics · September 1, 2016 Full text Cite

Whole-genome fingerprint of the DNA methylome during human B cell differentiation.

Journal Article Nat Genet · July 2015 We analyzed the DNA methylome of ten subpopulations spanning the entire B cell differentiation program by whole-genome bisulfite sequencing and high-density microarrays. We observed that non-CpG methylation disappeared upon B cell commitment, whereas CpG m ... Full text Link to item Cite

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.

Journal Article Genome Res · April 2015 While analyzing the DNA methylome of multiple myeloma (MM), a plasma cell neoplasm, by whole-genome bisulfite sequencing and high-density arrays, we observed a highly heterogeneous pattern globally characterized by regional DNA hypermethylation embedded in ... Full text Link to item Cite

Computational Methods for RNA Structure Validation and Improvement.

Journal Article Methods Enzymol · 2015 With increasing recognition of the roles RNA molecules and RNA/protein complexes play in an unexpected variety of biological processes, understanding of RNA structure-function relationships is of high current importance. To make clean biological interpreta ... Full text Open Access Link to item Cite

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

Journal Article Nucleic Acids Res · November 10, 2014 The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of unc ... Full text Open Access Link to item Cite

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

Journal Article Structure · October 7, 2014 The Staphylococcus aureus virulence factor staphylococcal protein A (SpA) is a major contributor to bacterial evasion of the host immune system, through high-affinity binding to host proteins such as antibodies. SpA includes five small three-helix-bundle d ... Full text Open Access Link to item Cite

Transcriptional diversity during lineage commitment of human blood progenitors.

Journal Article Science · September 26, 2014 Blood cells derive from hematopoietic stem cells through stepwise fating events. To characterize gene expression programs driving lineage choice, we sequenced RNA from eight primary human hematopoietic progenitor populations representing the major myeloid ... Full text Link to item Cite

Biophysical highlights from 54 years of macromolecular crystallography.

Journal Article Biophys J · February 4, 2014 The United Nations has declared 2014 the International Year of Crystallography, and in commemoration, this review features a selection of 54 notable macromolecular crystal structures that have illuminated the field of biophysics in the 54 years since the f ... Full text Link to item Cite

Crystallographic model validation: from diagnosis to healing.

Journal Article Curr Opin Struct Biol · October 2013 Model validation has evolved from a passive final gatekeeping step to an ongoing diagnosis and healing process that enables significant improvement of accuracy. A recent phase of active development was spurred by the worldwide Protein Data Bank requiring d ... Full text Link to item Cite

Studying and polishing the PDB's macromolecules.

Journal Article Biopolymers · March 2013 Macromolecular crystal structures are among the best of scientific data, providing detailed insight into these complex and biologically important molecules with a relatively low level of error and subjectivity. However, there are two notable problems with ... Full text Link to item Cite

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

Journal Article Methods Enzymol · 2013 UNLABELLED: We have developed a suite of protein redesign algorithms that improves realistic in silico modeling of proteins. These algorithms are based on three characteristics that make them unique: (1) improved flexibility of the protein backbone, protei ... Full text Link to item Cite

Doing molecular biophysics: finding, naming, and picturing signal within complexity.

Journal Article Annu Rev Biophys · 2013 A macromolecular structure, as measured data or as a list of coordinates or even on-screen as a full atomic model, is an extremely complex and confusing object. The underlying rules of how it folds, moves, and interacts as a biological entity are even less ... Full text Link to item Cite

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

Journal Article Annu Rev Biophys · 2013 Advances in our understanding of macromolecular structure come from experimental methods, such as X-ray crystallography, and also computational analysis of the growing number of atomic models obtained from such experiments. The later analyses have made it ... Full text Link to item Cite

The zen of model anomalies - Correct most of them. Treasure the meaningful valid few. Live serenely with the rest!

Journal Article NATO Science for Peace and Security Series A: Chemistry and Biology · January 1, 2013 Historically, validation has been considered primarily as a gatekeeping function done at the end of a structure solution. Currently, the most interesting and important part of validation is the opportunity to correct diagnosed errors, provided mainly by lo ... Full text Cite

Graphical tools for macromolecular crystallography in PHENIX.

Journal Article J Appl Crystallogr · June 1, 2012 A new Python-based graphical user interface for the PHENIX suite of crystallography software is described. This interface unifies the command-line programs and their graphical displays, simplifying the development of new interfaces and avoiding duplication ... Full text Link to item Cite

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

Journal Article Acta Crystallogr D Biol Crystallogr · April 2012 Traditional methods for macromolecular refinement often have limited success at low resolution (3.0-3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge f ... Full text Link to item Cite

“The plot” thickens: More data, more dimensions, more uses

Journal Article · January 1, 2012 The scientific history of the Ramachandran plot is reviewed, emphasizing relationships to the title theme and to trends in current research. The growth and quality of macromolecular structure data have enabled the understanding of relationships with furthe ... Full text Cite

The role of local backrub motions in evolved and designed mutations.

Journal Article PLoS Comput Biol · 2012 Amino acid substitutions in protein structures often require subtle backbone adjustments that are difficult to model in atomic detail. An improved ability to predict realistic backbone changes in response to engineered mutations would be of great utility f ... Full text Link to item Cite

The Phenix software for automated determination of macromolecular structures.

Journal Article Methods · September 2011 X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutic ... Full text Link to item Cite

Alternate states of proteins revealed by detailed energy landscape mapping.

Journal Article J Mol Biol · January 14, 2011 What conformations do protein molecules populate in solution? Crystallography provides a high-resolution description of protein structure in the crystal environment, while NMR describes structure in solution but using less data. NMR structures display more ... Full text Link to item Cite

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

Journal Article Journal of applied crystallography · August 2010 phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available ... Full text Cite

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

Journal Article Acta Crystallogr D Biol Crystallogr · February 2010 Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpr ... Full text Link to item Cite

EuroPhenome: a repository for high-throughput mouse phenotyping data.

Journal Article Nucleic Acids Res · January 2010 The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPh ... Full text Link to item Cite

MolProbity: all-atom structure validation for macromolecular crystallography.

Journal Article Acta Crystallogr D Biol Crystallogr · January 2010 MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by opti ... Full text Link to item Cite

KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program.

Journal Article Protein Sci · November 2009 Proper visualization of scientific data is important for understanding spatial relationships. Particularly in the field of structural biology, where researchers seek to gain an understanding of the structure and function of biological macromolecules, it is ... Full text Link to item Cite

Recent developments in phasing and structure refinement for macromolecular crystallography.

Journal Article Curr Opin Struct Biol · October 2009 Central to crystallographic structure solution is obtaining accurate phases in order to build a molecular model, ultimately followed by refinement of that model to optimize its fit to the experimental diffraction data and prior chemical knowledge. Recent a ... Full text Link to item Cite

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

Journal Article J Struct Funct Genomics · March 2009 Misfit sidechains in protein crystal structures are a stumbling block in using those structures to direct further scientific inference. Problems due to surface disorder and poor electron density are very difficult to address, but a large class of systemati ... Full text Link to item Cite

KinImmerse: Macromolecular VR for NMR ensembles.

Journal Article Source Code Biol Med · February 17, 2009 BACKGROUND: In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience - to enhance intuition and communicate excitement - rather than as part of the actu ... Full text Link to item Cite

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

Journal Article Proteins · 2009 For template-based modeling in the CASP8 Critical Assessment of Techniques for Protein Structure Prediction, this work develops and applies six new full-model metrics. They are designed to complement and add value to the traditional template-based assessme ... Full text Link to item Cite

Algorithm for backrub motions in protein design.

Journal Article Bioinformatics · July 1, 2008 MOTIVATION: The Backrub is a small but kinematically efficient side-chain-coupled local backbone motion frequently observed in atomic-resolution crystal structures of proteins. A backrub shifts the C(alpha)-C(beta) orientation of a given side-chain by rigi ... Full text Link to item Cite

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

Journal Article RNA · March 2008 A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-fi ... Full text Link to item Cite

RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.

Journal Article J Math Biol · January 2008 Although accurate details in RNA structure are of great importance for understanding RNA function, the backbone conformation is difficult to determine, and most existing RNA structures show serious steric clashes (>or= 0.4 A overlap) when hydrogen atoms ar ... Full text Link to item Cite

Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.

Journal Article Nat Genet · September 2007 Nonsense-mediated mRNA decay (NMD) is of universal biological significance. It has emerged as an important global RNA, DNA and translation regulatory pathway. By systematically sequencing 737 genes (annotated in the Vertebrate Genome Annotation database) o ... Full text Link to item Cite

Mutations in the BRWD3 gene cause X-linked mental retardation associated with macrocephaly.

Journal Article Am J Hum Genet · August 2007 In the course of systematic screening of the X-chromosome coding sequences in 250 families with nonsyndromic X-linked mental retardation (XLMR), two families were identified with truncating mutations in BRWD3, a gene encoding a bromodomain and WD-repeat do ... Full text Link to item Cite

AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

Conference Bioinformatics · July 1, 2007 UNLABELLED: The undertaking of large-scale DNA sequencing screens for somatic variants in human cancers requires accurate and rapid processing of traces for variants. Due to their often aneuploid nature and admixed normal tissue, heterozygous variants foun ... Full text Link to item Cite

Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution.

Journal Article Acta Crystallogr Sect F Struct Biol Cryst Commun · July 1, 2007 The hypothetical protein PF0899 is a 95-residue peptide from the hyperthermophilic archaeon Pyrococcus furiosus that represents a gene family with six members. P. furiosus ORF PF0899 has been cloned, expressed and crystallized and its structure has been de ... Full text Link to item Cite

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

Journal Article Nucleic Acids Res · July 2007 MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle ... Full text Link to item Cite

Patterns of somatic mutation in human cancer genomes.

Journal Article Nature · March 8, 2007 Cancers arise owing to mutations in a subset of genes that confer growth advantage. The availability of the human genome sequence led us to propose that systematic resequencing of cancer genomes for mutations would lead to the discovery of many additional ... Full text Link to item Cite

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.

Journal Article J Struct Funct Genomics · March 2007 The open-reading frame PF0895 in the genome of the hyperthermophilic archaeon, Pyrococcus furiosus, encodes a 206-residue protein (M(R )23,152). The structure of the recombinant protein was solved by single isomorphous replacement with anomalous scattering ... Full text Link to item Cite

Mutations in CUL4B, which encodes a ubiquitin E3 ligase subunit, cause an X-linked mental retardation syndrome associated with aggressive outbursts, seizures, relative macrocephaly, central obesity, hypogonadism, pes cavus, and tremor.

Journal Article Am J Hum Genet · February 2007 We have identified three truncating, two splice-site, and three missense variants at conserved amino acids in the CUL4B gene on Xq24 in 8 of 250 families with X-linked mental retardation (XLMR). During affected subjects' adolescence, a syndrome emerged wit ... Full text Link to item Cite

Mutations in the gene encoding the Sigma 2 subunit of the adaptor protein 1 complex, AP1S2, cause X-linked mental retardation.

Journal Article Am J Hum Genet · December 2006 In a systematic sequencing screen of the coding exons of the X chromosome in 250 families with X-linked mental retardation (XLMR), we identified two nonsense mutations and one consensus splice-site mutation in the AP1S2 gene on Xp22 in three families. Affe ... Full text Link to item Cite

Mutation analysis of 24 known cancer genes in the NCI-60 cell line set.

Journal Article Mol Cancer Ther · November 2006 The panel of 60 human cancer cell lines (the NCI-60) assembled by the National Cancer Institute for anticancer drug discovery is a widely used resource. The NCI-60 has been characterized pharmacologically and at the molecular level more extensively than an ... Full text Link to item Cite

A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy.

Journal Article Cancer Res · April 15, 2006 Malignant gliomas have a very poor prognosis. The current standard of care for these cancers consists of extended adjuvant treatment with the alkylating agent temozolomide after surgical resection and radiotherapy. Although a statistically significant incr ... Full text Link to item Cite

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

Journal Article Structure · February 2006 Surprisingly, the frozen structures from ultra-high-resolution protein crystallography reveal a prevalent, but subtle, mode of local backbone motion coupled to much larger, two-state changes of sidechain conformation. This "backrub" motion provides an infl ... Full text Link to item Cite

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

Journal Article Acta Crystallogr D Biol Crystallogr · July 2005 Recently, the demands of high-throughput macromolecular crystallography have driven continuous improvements in phasing methods, data-collection protocols and many other technologies. Single-wavelength anomalous scattering (SAS) phasing with chromium X-ray ... Full text Link to item Cite

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

Journal Article Acta Crystallogr D Biol Crystallogr · June 2005 Using a high degree of automation, the crystallography core at the Southeast Collaboratory for Structural Genomics (SECSG) has developed a high-throughput protein-to-structure pipeline. Various robots and automation procedures have been adopted and integra ... Full text Link to item Cite

RNA backbone rotamers--finding your way in seven dimensions.

Journal Article Biochem Soc Trans · June 2005 Despite the importance of local structural detail for a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been recalcitrant to analysis. There are too many variable dihedral angles per residue, and their raw em ... Full text Link to item Cite

Assessment of molecular construction in undergraduate biochemistry

Journal Article Journal of Chemical Education · January 1, 2005 Full text Cite

A test of enhancing model accuracy in high-throughput crystallography.

Journal Article J Struct Funct Genomics · 2005 The high throughput of structure determination pipelines relies on increased automation and, consequently, a reduction of time spent on interactive quality control. In order to meet and exceed current standards in model accuracy, new approaches are needed ... Full text Link to item Cite

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

Journal Article Nucleic Acids Res · July 1, 2004 MolProbity is a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules and can calcu ... Full text Link to item Cite

RNA backbone is rotameric.

Journal Article Proc Natl Acad Sci U S A · November 25, 2003 Despite the importance of local structural detail to a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been quite recalcitrant to analysis. There are too many variable torsion angles per residue, and their ra ... Full text Link to item Cite

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

Journal Article Proteins · February 15, 2003 Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information conta ... Full text Link to item Cite

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

Journal Article Proc Natl Acad Sci U S A · March 5, 2002 Featured Publication The fact that natural beta-sheet proteins are usually soluble but that fragments or designs of beta structure usually aggregate suggests that natural beta proteins must somehow be designed to avoid this problem. Regular beta-sheet edges are dangerous, beca ... Full text Link to item Cite

Teaching molecular 3-D literacy

Journal Article Biochemistry and Molecular Biology Education · January 1, 2002 Full text Cite

Exploring steric constraints on protein mutations using MAGE/PROBE.

Journal Article Protein Sci · November 2000 Featured Publication When planning a mutation to test some hypothesis, one crucial question is whether the new side chain is compatible with the existing structure; only if it is compatible can the interpretation of mutational results be straightforward. This paper presents a ... Full text Link to item Cite

The penultimate rotamer library.

Journal Article Proteins · August 15, 2000 Featured Publication All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors >/=40 or van der Waals overlaps >/=0.4 A) ... Link to item Cite

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

Journal Article J Mol Graph Model · June 2000 Featured Publication Experience has shown that protein redesigns (using the backbone from a known protein structure) are far more likely to produce well-ordered, native-like structures than are true de novo designs. Therefore, to design a four-helix bundle made of identical sh ... Full text Link to item Cite

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

Journal Article J Mol Biol · January 29, 1999 Featured Publication The technique of small-probe contact dot surfaces is described as a method for calculating and displaying the detailed atomic contacts inside or between molecules. It allows one both to measure and to visualize directly the goodness-of-fit of packing inter ... Full text Link to item Cite

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

Journal Article J Mol Biol · January 29, 1999 Small-probe contact dot surface analysis, with all explicit hydrogen atoms added and their van der Waals contacts included, was used to choose between the two possible orientations for each of 1554 asparagine (Asn) and glutamine (Gln) side-chain amide grou ... Full text Link to item Cite

Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering.

Journal Article Proc Natl Acad Sci U S A · January 19, 1999 Featured Publication Previous rotamer libraries showed little significant clustering for asparagine chi2 or glutamine chi3 values, but none of those studies corrected amide orientations or omitted disordered side chains. The current survey used 240 proteins at Full text Link to item Cite

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

Journal Article Pac Symp Biocomput · 1996 Puzzle pieces are defined as small packing units which make up the unique tertiary interactions in proteins. Anti-parallel and perpendicular helix-helix contacts were broken down into basic puzzle-piece pairs in order to study the traits of such contacts: ... Link to item Cite

Defining, computing, and visualizing molecular interfaces

Journal Article Proceedings of the IEEE Visualization Conference · December 1, 1995 A parallel, analytic approach for defining and computing the inter- and intra-molecular interfaces in three dimensions is described. The molecular interface surfaces are derived from approximations to the power-diagrams over the participating molecular uni ... Cite

The Alacoil: a very tight, antiparallel coiled-coil of helices.

Journal Article Protein Sci · November 1995 Featured Publication The Alacoil is an antiparallel (rather than the usual parallel) coiled-coil of alpha-helices with Ala or another small residue in every seventh position, allowing a very close spacing of the helices (7.5-8.5 A between local helix axes), often over four or ... Full text Link to item Cite

An algorithm for smoothly tessellating beta-sheet structures in proteins.

Journal Article J Mol Graph · February 1995 An algorithm is presented for tiling the surface of beta-sheet structures, smoothed both along the strands and perpendicular to them. The algorithm is intended for creating graphical representations of beta structure within the three-dimensional context of ... Full text Link to item Cite

The tyrosine corner: a feature of most Greek key beta-barrel proteins.

Journal Article Protein Sci · November 1994 The Tyr corner is a conformation in which a tyrosine (residue "Y") near the beginning or end of an antiparallel beta-strand makes an H bond from its side-chain OH group to the backbone NH and/or CO of residue Y - 3, Y - 4, or Y - 5 in the nearby connection ... Full text Link to item Cite

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

Journal Article Proc Natl Acad Sci U S A · September 13, 1994 How an amino acid sequence encodes the information necessary for a protein to adopt a unique tertiary structure remains unresolved. We are addressing this problem by designing "from scratch" protein molecules that will adopt predetermined three-dimensional ... Full text Link to item Cite

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.

Journal Article Protein Sci · February 1994 Featured Publication We describe a new paradigm for modeling proteins in interactive computer graphics systems--continual maintenance of a physically valid representation, combined with direct user control and visualization. This is achieved by a fast algorithm for energy mini ... Full text Link to item Cite

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

Journal Article Proceedings of the 20th Annual Conference on Computer Graphics and Interactive Techniques, SIGGRAPH 1993 · September 1, 1993 VIEW is an exploratory visualization system for studying the structures of molecules. The system supports a high degree of complex user interaction with the image. Visualizations are constructed by selecting drawing tools from a library. Each tool uses par ... Full text Cite

A common arch structure in beta sandwich proteins: The tyrosine turn

Journal Article Protein Engineering, Design and Selection · January 1, 1993 Full text Cite

Structural characteristics of felix, a designed protein

Journal Article Protein Engineering, Design and Selection · January 1, 1993 Full text Cite

Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992.

Journal Article Biophys J · November 1992 Looking at proteins is an active process of interpretation and selection, emphasizing some features and deleting others. Multiple representations are needed, for such purposes as showing motions or conveying both the chain connectivity and the three-dimens ... Link to item Cite

The kinemage: a tool for scientific communication.

Journal Article Protein Sci · January 1992 Featured Publication A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond within a fraction of a second: the entire image can be rotated in real time, parts of the display can be tu ... Full text Link to item Cite

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

Journal Article Science · August 24, 1990 Featured Publication The protein Felix was designed de novo to fold into an antiparallel four-helix bundle of specific topology. Its sequence of 79 amino acid residues is not homologous to any known protein sequence, but is "native-like" in that it is nonrepetitive and contain ... Full text Link to item Cite

Bitewing radiographs of children taken with and without a film-holding device.

Journal Article Dentomaxillofac Radiol · August 1989 To help minimize radiation exposure, all dental radiographs must yield maximum diagnostic information. Film-holding devices have been recommended as a means of improving the diagnostic yield. Our study compared the diagnostic quality of bitewing radiograph ... Full text Link to item Cite

The de novo design of protein structures.

Journal Article Trends Biochem Sci · July 1989 Full text Link to item Cite

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

Journal Article Science · June 17, 1988 Featured Publication A definition based on alpha-carbon positions and a sample of 215 alpha helices from 45 different globular protein structures were used to tabulate amino acid preferences for 16 individual positions relative to the helix ends. The interface residue, which i ... Full text Link to item Cite

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

Journal Article Proteins · 1988 The DNA-binding helix pairs in gene repressor and activator proteins were compared with other approximately perpendicular pairs of adjacent helices in the known protein structures. Two other examples of closely matching conformations were found in cytochro ... Full text Link to item Cite

The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase.

Journal Article J Biol Chem · August 5, 1986 Featured Publication Isolated hemoprotein subunits of Escherichia coli NADPH:sulfite reductase catalyze the 6-electron reduction of SO2-3 to S2-. The prosthetic groups of the hemoprotein, a siroheme and a Fe4S4 cluster, have been shown by spectroscopy to be tightly coupled. We ... Link to item Cite

The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase

Journal Article Journal of Biological Chemistry · January 1, 1986 Isolated hemoprotein subunits of Escherichia coli NADPH:sulfite reductase catalyze the 6-electron reduction of SO32- to S2-. The prosthetic groups of the hemoprotein, a siroheme and a Fe4S4 cluster, have been shown by spectroscopy to be tightly coupled. We ... Cite

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

Journal Article J Mol Biol · April 5, 1985 Crystals of the acyl carrier protein of Escherichia coli have been grown and analyzed by X-ray diffraction. The crystals grow in space group C2 with unit cell dimensions a = 46.8 A, b = 52.1 A, c = 47.3 A and beta = 93.2 degrees. An isomorphous derivative, ... Full text Link to item Cite

Interpretation of electron density maps.

Journal Article Methods Enzymol · 1985 Full text Link to item Cite

Protein engineering: Design and synthesis of a protein

Journal Article Federation Proceedings · January 1, 1984 Cite

Structure and mechanism of copper, zinc superoxide dismutase.

Journal Article Nature · November 17, 1983 Copper, zinc superoxide dismutase (SOD) catalyses the very rapid two-step dismutation of the toxic superoxide radical (O-2) to molecular oxygen and hydrogen peroxide through the alternate reduction and oxidation of the active-site copper. We report here th ... Full text Link to item Cite

Electrostatic recognition between superoxide and copper, zinc superoxide dismutase.

Journal Article Nature · November 17, 1983 Electrostatic forces have been implicated in a variety of biologically important molecular interactions including drug orientation by DNA, protein folding and assembly, substrate binding and catalysis and macromolecular complementarity with inhibitors, dru ... Full text Link to item Cite

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

Journal Article J Mol Biol · September 15, 1982 Featured Publication Full text Link to item Cite

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

Journal Article Proc Natl Acad Sci U S A · June 1978 A beta bulge is a region between two consecutive beta-type hydrogen bonds which includes two residues (positions 1 and 2) on one strand opposite a single residue (position x) on the other strand. Compared to regular beta structure, a beta bulge puts the us ... Full text Link to item Cite

Metal sites of copper-zinc superoxide dismutase.

Journal Article Biochemistry · May 3, 1977 Silver-copper and silver-cobalt proteins have been prepared in which Ag+ resides in the native copper site of superoxide dismutase and either Cu2+ of Co2+ reside in the zinc site. The electron paramagnetic resonance (EPR) spectrum of the copper and the vis ... Full text Link to item Cite

Alpha-carbon coordinates for bovine Cu,Zn superoxide dismutase.

Journal Article Biochem Biophys Res Commun · April 21, 1975 Full text Link to item Cite

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

Journal Article Proc Natl Acad Sci U S A · April 1975 An electron density map at 3 angstrom resolution has been calculated for Cu2+, Zn2+ superoxide dismutase from bovine erythrocytes, and the course of the main chain has been traced. The dominant structural feature is an 8-stranded barrel of antiparallel bet ... Full text Link to item Cite

Two crystal forms of bovine superoxide dismutase.

Journal Article J Biol Chem · October 10, 1972 Link to item Cite

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

Journal Article Proc Natl Acad Sci U S A · October 1969 Independent 4 A electron density maps calculated for the extracellular nuclease of Staphylococcus aureus (based on data from three heavy-atom derivatives) and for a nuclease-thymidine-3',5'-diphosphate-calcium ion complex (based on a single isomorphous der ... Full text Link to item Cite