subject area of

• 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
• 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