Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 15

System / cell line: membrane ✕ Assay: prediction ✕ Clear

LOCATE: a mammalian protein subcellular localization database.

PMID 17986452 · PMC2238969 · Nucleic acids research · 2008 · 8 claims · 6 setups

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LOCATE is a curated, web-accessible database housing membrane organization and subcellular localization data for mouse and human proteins.

hela proteome indirect automated computational
Systematic prediction of human membrane receptor interactions.

PMID 19798668 · PMC3076061 · Proteomics · 2009 · 7 claims · 6 setups

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Predicting interactions specifically for membrane receptors, rather than deriving them from a general human interactome model, improves prediction performance for these proteins

cos-1 um-22a hep3b gst-egfr co-immunoprecipitation pulldown binding
A survey of integral alpha-helical membrane proteins.

PMID 19760129 · PMC2780624 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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An automated annotation pipeline defines the integral membrane genome and family associations for 21,379 proteins from 34 genomes, most belonging to 598 Pfam-derived membrane protein families.

pfam-a organisms 34-genome integral transmembrane comparative sequence
Aggregation propensity of the human proteome.

PMID 18927604 · PMC2557143 · PLoS computational biology · 2008 · 8 claims · 7 setups

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Long proteins have, on average, less intense/pronounced aggregation peaks than short proteins

proteome non-membrane proteins membrane sequence-based correlation statistical
Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

PMID 19842929 · PMC2923222 · Pharmacogenomics · 2009 · 8 claims · 8 setups

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Approximately 15-20% of nonsynonymous variants in membrane transporters exhibit reduced function

abc hek293 expressing sophie computational transporter transport
Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS.

PMID 19709643 · PMC3159575 · Journal of proteomics · 2009 · 7 claims · 5 setups

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Methanol-based solubilization, alone or combined with PPS, yields significantly higher membrane protein identification/enrichment than PPS alone in monocyte membrane proteomics

bacteriorhodopsin crude immuno-affinity lc-ms sds-page shotgun facs
A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups

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Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.

washed platelets tryptic hek293t lc-ms free longsage
Coverage of whole proteome by structural genomics observed through protein homology modeling database.

PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups

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FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.

orfs predicted modeled representative homology transmembrane intrinsic
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

PMID 15608166 · PMC540074 · Nucleic acids research · 2005 · 7 claims · 4 setups

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PA-GOSUB significantly extends the coverage of GO molecular function and subcellular localization annotations for 10 model organism proteomes compared with existing databases (GOA, Swiss-Prot).

sequences query swiss-prot naive-bayes blast feature
Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

PMID 37084271 · PMC10203375 · Bioinformatics (Oxford, England) · 2023 · 6 claims · 8 setups

Has reproduction · 85

AlphaFold2-derived structural features (solvent accessibility, amino acid network features, physicochemical environment, pLDDT) can be used to train a random forest classifier (AlphScore) that distinguishes proxy-benign from proxy-pathogenic missense variants.

gnomad alphafold2-predicted alphscore proteins machine secondary physicochemical
Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

PMID 15287975 · PMC507878 · Genome biology · 2004 · 8 claims · 6 setups

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3,848 Arabidopsis proteins were identified as likely plant-specific based on phylogenetic profiling and EST confirmation in multiple plant species

arabidopsis phylogenetic tblastn subcellular
Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

PMID 17062162 · PMC1635044 · Virology journal · 2006 · 8 claims · 6 setups

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VACV-DUKE is most similar to VACV-ACAM2000 and VACV-CLONE3, confirming it as a Dryvax-derived isolate

vacv-duke whole-genome phylogenetic comparative
Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains.

PMID 18560578 · PMC2409963 · PloS one · 2008 · 8 claims · 6 setups

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Ovarian cancer cells exhibit extensive shedding of extra-cellular domains from cell surface proteins into the extracellular milieu.

ovcar3 analysis lc-ms cell-surface silac
MitoP2: the mitochondrial proteome database--now including mouse data.

PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups

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MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping

saccharomyces yeast heart liver genome-wide single transcriptome
Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 78

73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.

triticum taiqd wheat promoter genome-wide phylogenetic synteny

Experiments

LOCATE: a mammalian protein subcellular localization database.

Systematic prediction of human membrane receptor interactions.

A survey of integral alpha-helical membrane proteins.

Aggregation propensity of the human proteome.

Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS.

A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

Coverage of whole proteome by structural genomics observed through protein homology modeling database.

PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains.

MitoP2: the mitochondrial proteome database--now including mouse data.

Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.