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Databases, Protein

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  • A comparative analysis of HGSC and Celera human genome assemblies and gene sets  Academic Article
  • A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data  Academic Article
  • A general method to quantify quasi-equivalence in icosahedral viruses  Academic Article
  • A guide to the visual analysis and communication of biomolecular structural data  Academic Article
  • A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry  Academic Article
  • A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases  Academic Article
  • A proteomic glimpse into human ureter proteome  Academic Article
  • A semiempirical free energy force field with charge-based desolvation  Academic Article
  • A structural snapshot of CYP2B4 in complex with paroxetine provides insights into ligand binding and clusters of conformational states  Academic Article
  • A systematic approach to modeling, capturing, and disseminating proteomics experimental data  Academic Article
  • An automated procedure for detecting protein folds from sub-nanometer resolution electron density  Academic Article
  • An online resource for GPCR structure determination and analysis  Academic Article
  • Analyzing molecular interactions  Academic Article
  • Antibody modeling assessment II. Structures and models  Academic Article
  • Asia growth in membrane protein structure  Academic Article
  • Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications  Academic Article
  • Automated sequence-specific protein NMR assignment using the memetic algorithm match  Academic Article
  • Automatic annotation of matrix-assisted laser desorption/ionization n-glycan spectra  Academic Article
  • Automatic validation of phosphopeptide identifications from tandem mass spectra  Academic Article
  • Biogps: An extensible and customizable portal for querying and organizing gene annotation resources  Academic Article
  • Central limit theorem as an approximation for intensity-based scoring function  Academic Article
  • Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases  Academic Article
  • Classification of PDZ domains  Academic Article
  • Code developments to improve the efficiency of automated MS/MS spectra interpretation  Academic Article
  • Collecting and organizing systematic sets of protein data  Academic Article
  • Comparative assessment of large-scale proteomic studies of apoptotic proteolysis  Academic Article
  • Crystal structure of a conserved hypothetical protein (gi : 13879369) from Mouse at 1.90 A resolution reveals a new fold  Academic Article
  • Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 a resolution  Academic Article
  • Crystal structure of the C-terminal domain of mouse TLR9  Academic Article
  • Curation of the mammalian palmitoylome indicates a pivotal role for palmitoylation in diseases and disorders of the nervous system and cancers  Academic Article
  • DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs  Academic Article
  • Design and synthesis of a cell-permeable synthetic transcription factor mimic  Academic Article
  • Design, synthesis, and validation of a β-turn mimetic library targeting protein-protein and peptide-receptor interactions  Academic Article
  • Developing advanced X-ray scattering methods combined with crystallography and computation  Academic Article
  • Differential recovery of peptides from sample tubes and the reproducibility of quantitative proteomic data  Academic Article
  • Expanding the proteome: Disordered and alternatively folded proteins  Academic Article
  • Exploration of uncharted regions of the protein universe  Academic Article
  • Exploring icosahedral virus structures with VIPER  Academic Article
  • Extracting accurate precursor information for tandem mass spectra by raw converter  Academic Article
  • Functional analysis of hairpin ribozyme active site architecture  Academic Article
  • Genome pool strategy for structural coverage of protein families  Academic Article
  • Human Proteinpedia enables sharing of human protein data  Academic Article
  • Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry  Academic Article
  • Identification of direct residue contacts in protein-protein interaction by message passing  Academic Article
  • Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0  Academic Article
  • Integration of cardiac proteome biology and medicine by a specialized knowledgebase  Academic Article
  • Integrative illustration for coronavirus outreach  Academic Article
  • Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis  Academic Article
  • Large-scate database searching using tandem mass spectra: looking up the answer in the back of the book  Academic Article
  • Linking folding and binding  Academic Article
  • Liquid chromatography-fourier transform ion cyclotron resonance mass spectrometric characterization of protein kinase c phosphorylation  Academic Article
  • Loop modeling: sampling, filtering, and scoring  Academic Article
  • MDB: The metalloprotein database and browser at The Scripps Research Institute  Academic Article
  • MS1, MS2, and SQT: three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications  Academic Article
  • Mass spectrometry in high-throughput proteomics: ready for the big time  Academic Article
  • Metabolomic data streaming for biology-dependent data acquisition  Academic Article
  • ModBase, a database of annotated comparative protein structure models and associated resources  Academic Article
  • Native atom types for knowledge-based potentials: application to binding energy prediction  Academic Article
  • NeuroPedia: neuropeptide database and spectral library  Academic Article
  • Outcome of a workshop on applications of protein models in biomedical research  Academic Article
  • Outcome of the first wwPDB Hybrid/Integrative Methods Task Force Workshop  Academic Article
  • PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data  Academic Article
  • PatternLab for proteomics: a tool for differential shotgun proteomics  Academic Article
  • PatternLab: from mass spectra to label-free differential shotgun proteomics  Academic Article
  • PepExplorer: a similarity-driven tool for analyzing de novo sequencing results  Academic Article
  • Pivotal role of computers and software in mass spectrometry - SEQUEST and 20 years of tandem MS database searching  Academic Article
  • ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity  Academic Article
  • Protein identification using 2D-LC-MS/MS  Academic Article
  • Proteome analysis of rhoptry-enriched fractions isolated from Plasmodium merozoites  Academic Article
  • Proteomic analysis of tumor necrosis factor-alpha (TNF-α)-induced L6 myotube secretome reveals novel TNF-α-dependent myokines in diabetic skeletal muscle  Academic Article
  • Quantitative proteomics of human fibroblasts with I1061T mutation in Niemann-Pick C1 (NPC1) protein provides insights into the disease pathogenesis  Academic Article
  • Quantitative proteomics of parotid saliva in primary Sjögren's syndrome  Academic Article
  • Recognition templates for predicting adenylate-binding sites in proteins  Academic Article
  • Refining homology models by combining replica-exchange molecular dynamics and statistical potentials  Academic Article
  • Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB  Academic Article
  • Revealing disease-associated pathways by network integration of untargeted metabolomics  Academic Article
  • Search engine processor: filtering and organizing peptide spectrum matches  Academic Article
  • Shotgun protein identification and quantification by mass spectrometry  Academic Article
  • Shotgun protein identification and quantification by mass spectrometry in neuroproteomics  Academic Article
  • Shotgun proteomics in neuroscience  Academic Article
  • Simicon: A web tool for protein-ligand model comparison through calculation of equivalent atomic contacts  Academic Article
  • Site-directed combinatorial construction of chimaeric genes: general method for optimizing assembly of gene fragments  Academic Article
  • Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases  Academic Article
  • Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast  Academic Article
  • The RCSB Protein Data Bank: views of structural biology for basic and applied research and education  Academic Article
  • The RCSB protein data bank: New resources for research and education  Academic Article
  • The RCSB protein data bank: Redesigned web site and web services  Academic Article
  • The cAMP binding domain: An ancient signaling module  Academic Article
  • The challenge of protein structure determination - lessons from structural genomics  Academic Article
  • The complete complement of C1q-domain-containing proteins in Homo sapiens  Academic Article
  • The gene wiki: Community intelligence applied to human gene annotation  Academic Article
  • The membrane protein data bank  Academic Article
  • The minimum information about a proteomics experiment (MIAPE)  Academic Article
  • The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation  Academic Article
  • The role of dynamic conformational ensembles in biomolecular recognition  Academic Article
  • The transcription factor encyclopedia  Academic Article
  • Understanding the enzymatic activity of 4-oxalocrotonate tautomerase and its mutant analogues: A computational study  Academic Article
  • VIPERdb(2): an enhanced and web API enabled relational database for structural virology  Academic Article
  • VIPERdb: a relational database for structural virology  Academic Article
  • Validation of tandem mass spectrometry database search results using DTASelect  Academic Article
  • XCMS2: Processing tandem mass spectrometry data for metabolite identification and structural characterization  Academic Article
  • bNAber: database of broadly neutralizing HIV antibodies  Academic Article
  • pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins  Academic Article

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