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 20

System / cell line: complex ✕ Assay: molecular ✕ Clear

Solving structures of protein complexes by molecular replacement with Phaser.

PMID 17164524 · PMC2483468 · Acta crystallographica. Section D, Biological crystallography · 2007 · 7 claims · 4 setups

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Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components using a 'tree search with pruning' approach implemented in Phaser's automated MR mode.

β-lactamase rop antibody ap2 molecular
Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

PMID 19011008 · PMC2719557 · Investigative ophthalmology & visual science · 2009 · 6 claims · 5 setups

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TGFBIp (multiple molecular weight forms) is significantly overexpressed in FECD HCEC-DM complex compared to normal endothelium

pooled hcec-dm corneal 2-d western real-time
Structural effects of clinically observed mutations in JAK2 exons 13-15: comparison with V617F and exon 12 mutations.

PMID 19744331 · PMC2749040 · BMC structural biology · 2009 · 8 claims · 1 setups

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The simulation-derived JH1/JH2 interface provides a platform that explains the mutational effect of all tested mutants, including presumably benign controls, at the atomic level

homology-model-derived molecular
BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome.

PMID 19923229 · PMC2808957 · Nucleic acids research · 2010 · 6 claims · 5 setups

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BioDrugScreen is a web resource providing pre-docked and pre-scored receptor-ligand complexes for ranking molecules against human proteome targets

docked targets molecular binding continuum
Diet and DNA.

PMID 15174456 · PMC1315985 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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The tombusvirus CIRV p19 protein selectively binds short (21-22 nt) silencing siRNAs, using tryptophan residues Trp39 and Trp42 as molecular 'calipers' that stack with the ends of the siRNA duplex

cirv blood rice smokers x-ray site-directed mass
Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

PMID 16989739 · PMC3933161 · Journal of cellular and molecular medicine · 2006 · 6 claims · 8 setups

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Mutations in APP, PS1 and PS2 genes and polymorphisms in the APOE gene are implicated in AD pathogenesis

alzheimer brain alzheimer's presenilin-1 microarray proteomic transgenic
Methods for proteomic analysis of transcription factors.

PMID 19726046 · PMC2778203 · Journal of chromatography. A · 2009 · 8 claims · 8 setups

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Systematic oligonucleotide 'trapping' at nM DNA concentrations allows purification of TF-RE complexes in a highly purified state, exploiting the high specific affinity vs. low non-specific affinity of TFs for DNA

nuclear crude intact partially emsa southwestern systematic
Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.

PMID 19714203 · PMC2722018 · PLoS computational biology · 2009 · 8 claims · 8 setups

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Cancer mutations in ABL and EGFR activate kinases via a common multi-stage mechanism involving hydrophobic spine assembly, formation of a Src-like intermediate structure, and cooperative breakage/formation of characteristic salt bridges

abl egfr abl-sh2-sh3 homology molecular stability
Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

PMID 11119309 · PMC2448388 · Yeast (Chichester, England) · 2000 · 8 claims · 8 setups

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Celera sequenced a human genome to ~45-fold coverage from one donor and used high-quality sequence stretches to define ~6 million SNPs

homo saccharomyces nicotiana arabidopsis whole-genome oligonucleotide molecular
Harnessing the HGP of public health.

PMID 15176090 · PMC1241998 · Environmental health perspectives · 2004 · 8 claims · 7 setups

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The tombusvirus p19 protein selectively recognizes and sequesters short (21-22 nucleotide) silencing siRNAs, discriminating them from longer siRNAs by measuring siRNA length via tryptophan-mediated end-stacking interactions

carnation cirv blood rice x-ray site-directed mass
Coxiella burnetii genotyping.

PMID 16102309 · PMC3320512 · Emerging infectious diseases · 2005 · 8 claims · 5 setups

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Multispacer sequence typing (MST) is the first reliable method for typing Coxiella burnetii isolates

coxiella burnetii matrix sequence pcr molecular pcr-based
Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

PMID 16646632 · PMC1450327 · PLoS biology · 2006 · 8 claims · 5 setups

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The C-terminal domain of the gE ectodomain (CgE) is the minimal Fc-binding domain of gE-gI

recombinant selenomethionine-substituted ge-gi models surface x-ray computational
Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.

coli sds-page glutathione pepck-gst sds-page maldi-tof native
RNA interference in functional genomics and medicine.

PMID 12808314 · PMC3055057 · Journal of Korean medical science · 2003 · 8 claims · 7 setups

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RNAi is sequence-specific gene silencing induced by double-stranded RNA and is mediated by ~22-nt siRNAs generated from long dsRNA by the RNase III enzyme Dicer.

caenorhabditis drosophila mammalian postnatal dsrna biochemical synthetic
Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

PMID 18816392 · PMC2566984 · BMC evolutionary biology · 2008 · 7 claims · 7 setups

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Ultraconserved coding regions (UCRs, ≥120 nt with no synonymous or nonsynonymous substitutions) exist outside the homeobox in mammalian Hox genes

orthologous hox concatenated intronic sliding comparative molecular
Ethnic differences and functional analysis of MET mutations in lung cancer.

PMID 19723643 · PMC2767337 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 7 setups

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MET mutations identified in lung tumors are predominantly germline rather than somatic

tumor established recombinant cos-7 pcr elisa-based apoptosis
Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses.

PMID 33871355 · PMC8099432 · eLife · 2021 · 8 claims · 8 setups

Has reproduction · 89

IL-27 induces more sustained and higher-amplitude STAT1 phosphorylation than HypIL-6, while both induce comparable STAT3 phosphorylation

th-1 rpe1 t-cells expressing high-throughput dual-color single-molecule
Evolutionarily conserved human targets of adenosine to inosine RNA editing.

PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

panel brain chicken flna comparative rt-pcr homology
Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.

PMID 17318599 · PMC1915625 · Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2007 · 7 claims · 7 setups

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The T309V mutation shifts the CYP2D6 heme spin equilibrium toward the six-coordinate low-spin (6cLS) state, decreasing the five-coordinate high-spin (5cHS) fraction relative to wild type.

recombinant cyp2d6 computational resonance uv-vis sds-page
Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.

PMID 18616294 · PMC2646719 · Biochemistry · 2008 · 8 claims · 6 setups

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Both G[8,5-Me]T and T[5-Me,8]G intrastrand cross-links are strongly mutagenic in COS-7 and 293T mammalian cells

cos-7 293t synthetic pms2 shuttle primer steady-state

Experiments

Solving structures of protein complexes by molecular replacement with Phaser.

Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

Structural effects of clinically observed mutations in JAK2 exons 13-15: comparison with V617F and exon 12 mutations.

BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome.

Diet and DNA.

Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

Methods for proteomic analysis of transcription factors.

Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.

Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

Harnessing the HGP of public health.

Coxiella burnetii genotyping.

Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

RNA interference in functional genomics and medicine.

Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

Ethnic differences and functional analysis of MET mutations in lung cancer.

Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses.

Evolutionarily conserved human targets of adenosine to inosine RNA editing.

Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.

Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.