David C. Richardson

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