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 18

System / cell line: crystal ✕ Assay: x-ray ✕ Clear

Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction.

PMID 19690369 · PMC2733880 · Acta crystallographica. Section D, Biological crystallography · 2009 · 8 claims · 7 setups

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A COP-based microfluidics system (SpinX cards, 500 chambers of 320 nl each) was established for protein crystallization and in situ X-ray diffraction.

chicken bovine p53 arabidopsis microbatch situ vapour-diffusion
Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

PMID 19031011 · PMC2756966 · Journal of structural and functional genomics · 2009 · 8 claims · 6 setups

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A discovery-oriented pipeline using standardized single-condition methods (one expression system, one detergent, one SEC buffer) can efficiently triage large numbers of eukaryotic IMP targets to identify well-behaved candidates for crystallization

cerevisiae ddm-solubilized sec-included tmhmm ligase-independent small-scale
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
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
International research networks in viral structural proteomics: again, lessons from SARS.

PMID 18054092 · PMC2793675 · Antiviral research · 2008 · 8 claims · 8 setups

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International research networks (SPINE, VIZIER, FSPS, SEPSDA, SARS-DTV) coordinated a global effort to structurally characterize the SARS-CoV proteome

sars-cov x-ray nmr genome
International sequencing consortium.

PMID 15174459 · PMC1315987 · Environmental health perspectives · 2004 · 8 claims · 6 setups

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The p19 viral silencing-suppressor protein selectively recognizes short (21-22 nt) silencing siRNAs by measuring duplex length, using tryptophan residues (Trp39, Trp42) as molecular calipers that stack against the siRNA end base pairs.

cirv blood sampled rice x-ray site-directed mass
Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

PMID 19028587 · PMC2686088 · Journal of structural biology · 2009 · 8 claims · 8 setups

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Nucleotide-bound (ADP and ANP/AMP-PNP) Mer kinase domain adopts an autoinhibited DFG-Asp-in/αC-Glu-out conformation with an activation-loop residue inserted into the active site

recombinant phosphorylated mer x-ray positional differential
Structural genomics and drug discovery for infectious diseases.

PMID 19860716 · PMC2789569 · Infectious disorders drug targets · 2009 · 7 claims · 4 setups

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CSGID applies high-throughput X-ray crystallography structural genomics to NIAID category A-C pathogen proteins to enable structure-aided drug discovery, with a goal of 400 protein/protein-ligand structures

selenomethionine-substituted recombinant genes x-ray high-throughput purification
The role of medical structural genomics in discovering new drugs for infectious diseases.

PMID 19855826 · PMC2756625 · PLoS computational biology · 2009 · 8 claims · 6 setups

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Structure-based drug design using X-ray/NMR protein structures has contributed to the development of numerous approved and improved therapeutics.

bacteria plasmodium candidate burkholderia high-throughput animal compound-target
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

PMID 19758473 · PMC2745591 · BMC bioinformatics · 2009 · 8 claims · 8 setups

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None of 39 tested structural properties can be used as a sole classification criterion to separate neutral SNPs from disease mutations.

ensembl swissprot same structural foldx side
Prediction of specificity-determining residues for small-molecule kinase inhibitors.

PMID 19032760 · PMC2655090 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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S-Filter is a novel method combining sequence and structural information (within PFAAT) to predict specificity-determining residues and selectivity profiles for small-molecule kinase inhibitors

panel kinase-inhibitor sequence erk2 caliper radiometric solvent
Glycoprotein structural genomics: solving the glycosylation problem.

PMID 17355862 · PMC1885966 · Structure (London, England : 1993) · 2007 · 8 claims · 5 setups

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Transiently expressing glycoproteins in HEK293T cells with kifunensine or swainsonine allows correct folding while retaining endo H sensitivity, solving the glycosylation problem for structural genomics

s19a srptpμ hek293t maldi-tof endoglycosidase x-ray
High-throughput crystallography for structural genomics.

PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups

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SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues

recombinant recalcitrant hundred family hydrogen situ site-directed
SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

PMID 16381914 · PMC1347399 · Nucleic acids research · 2006 · 8 claims · 8 setups

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SGCEdb is a flexible, reusable database and web interface for reporting and analyzing structural genomics experiment results, focused on C. elegans

elegans expressed soluble crystallized recombinant solubility purification
The VIZIER project: preparedness against pathogenic RNA viruses.

PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups

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Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.

viruses virus coli soluble large-scale bioinformatic recombinant
Assembling a jigsaw puzzle with 20,000 parts.

PMID 12801408 · PMC193613 · Genome biology · 2003 · 8 claims · 8 setups

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Re-routing the intracellular interaction domains of receptor tyrosine kinases can redirect their signaling output, e.g. converting a growth signal into an apoptosis signal.

yeast caenorhabditis escherichia proteome-wide microarray yeast rnai
Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

PMID 16522644 · PMC1390679 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Align-GVGD predicts loss of transactivation activity with high specificity (~88%) but lower sensitivity (67.9-71.2%) for neutral mutants

p53 tp53 yeast-based sequence align-gvgd
A novel matrix metalloproteinase 2 (MMP2) terminal hemopexin domain mutation in a family with multicentric osteolysis with nodulosis and arthritis with cardiac defects.

PMID 18985071 · PMC2721823 · European journal of human genetics : EJHG · 2009 · 7 claims · 8 setups

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A novel homozygous frameshift mutation (1732delA) in exon 11 of MMP2 causes MONA in this Turkish family by deleting the terminal (third and fourth) hemopexin domains.

blood-derived patient-derived serum genomic direct rt-pcr gelatin

Experiments

Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction.

Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

Harnessing the HGP of public health.

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

International research networks in viral structural proteomics: again, lessons from SARS.

International sequencing consortium.

Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

Structural genomics and drug discovery for infectious diseases.

The role of medical structural genomics in discovering new drugs for infectious diseases.

Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

Prediction of specificity-determining residues for small-molecule kinase inhibitors.

Glycoprotein structural genomics: solving the glycosylation problem.

High-throughput crystallography for structural genomics.

SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

The VIZIER project: preparedness against pathogenic RNA viruses.

Assembling a jigsaw puzzle with 20,000 parts.

Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

A novel matrix metalloproteinase 2 (MMP2) terminal hemopexin domain mutation in a family with multicentric osteolysis with nodulosis and arthritis with cardiac defects.