Databases, Protein

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  Subject Areas on Research

  • A mass spectrometry-based proteomic approach to study Marek's Disease Virus gene expression. 
  • A new generation of crystallographic validation tools for the protein data bank. 
  • A proteogenomic survey of the Medicago truncatula genome. 
  • A test of enhancing model accuracy in high-throughput crystallography. 
  • Accelerating crystal structure determination with iterative AlphaFold prediction. 
  • All-atom contacts: a new approach to structure validation. 
  • 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. 
  • Bayesian inference for genomic data integration reduces misclassification rate in predicting protein-protein interactions. 
  • Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. 
  • BioWarehouse: a bioinformatics database warehouse toolkit. 
  • Bioinformatic challenges in targeted proteomics. 
  • Crystallographic model validation: from diagnosis to healing. 
  • DIG--a system for gene annotation and functional discovery. 
  • Decision tree classification of proteins identified by mass spectrometry of blood serum samples from people with and without lung cancer. 
  • Design and application of a data-independent precursor and product ion repository. 
  • Development of human protein reference database as an initial platform for approaching systems biology in humans. 
  • Discovering the landscape of protein modifications. 
  • Discovery and verification of protein differences between Er positive/Her2/neu negative breast tumor tissue and matched adjacent normal breast tissue. 
  • EuroPhenome: a repository for high-throughput mouse phenotyping data. 
  • Evaluating the quality of NMR structures by local density of protons. 
  • Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences. 
  • High-throughput identification of IMCD proteins using LC-MS/MS. 
  • Identification and validation of a potential lung cancer serum biomarker detected by matrix-assisted laser desorption/ionization-time of flight spectra analysis. 
  • Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. 
  • Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors. 
  • LETM1, a gene deleted in Wolf-Hirschhorn syndrome, encodes an evolutionarily conserved mitochondrial protein. 
  • Mining database for the expression and gene regulation network of JAK2 in skin cutaneous melanoma. 
  • MolProbity: More and better reference data for improved all-atom structure validation. 
  • Molprobity's ultimate rotamer-library distributions for model validation. 
  • New tools and data for improving structures, using all-atom contacts. 
  • PACES: Protein sequential assignment by computer-assisted exhaustive search. 
  • Protein imperfections: separating intrinsic from extrinsic variation of torsion angles. 
  • Protein loop closure using orientational restraints from NMR data. 
  • Protein-Protein Docking Benchmark 2.0: an update. 
  • Protein-protein docking: overview and performance analysis. 
  • Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale. 
  • Proteomic profiling of a layered tissue reveals unique glycolytic specializations of photoreceptor cells. 
  • Recommendations of the wwPDB NMR Validation Task Force. 
  • Reverse engineering gene regulatory networks. 
  • Seeing the PDB. 
  • SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization. 
  • Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms. 
  • Studying and polishing the PDB's macromolecules. 
  • The Gene Ontology in 2010: extensions and refinements. 
  • The cis-Pro touch-turn: a rare motif preferred at functional sites. 
  • The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues. 
  • The metabolomics standards initiative. 
  • The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. 
  • YbiV from Escherichia coli K12 is a HAD phosphatase. 
  • ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. 
  • ZPLD1 gene is disrupted in a patient with balanced translocation that exhibits cerebral cavernous malformations. 
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  Keywords of People

  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Richardson, David C., Professor Emeritus of Biochemistry, Biochemistry