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 10

System / cell line: in-silico ✕ Assay: x-ray ✕ Clear

Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry.

PMID 19788317 · PMC2764328 · Analytical chemistry · 2009 · 7 claims · 4 setups

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ProtMapMS automates data format conversion, mass spectrum interpretation, peptide detection/verification, modification site confirmation, and quantification of peptide oxidation extent from covalent labeling MS data

insulin oxidative enzymatic computational
In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach.

PMID 17559675 · PMC1913526 · BMC structural biology · 2007 · 8 claims · 4 setups

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A rigid-body docking-based approach can predict mutational effects on binding energetics for three structurally distinct enzyme-proteic inhibitor systems (hRI-Ang, Bn-Bs, BPTI-β-Trypsin)

ribonuclease barnase bovine hri-ang rigid-body cluster
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
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
Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

PMID 18787705 · PMC2527523 · PloS one · 2008 · 8 claims · 5 setups

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Reduction in V3's net positive charge makes V3 less variable due to limited positive selection

hiv-1 recombinant plasma gp120 sequence single-round v3-peptide-based
A restricted spectrum of NRAS mutations causes Noonan syndrome.

PMID 19966803 · PMC3118669 · Nature genetics · 2010 · 8 claims · 6 setups

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Germline NRAS mutations (T50I, G60E) cause a subset of Noonan syndrome cases via enhanced MAPK activation

cohort cos-7 recombinant nras mutation western ras
Common variants in FLNB/CRTAP, not ARHGEF3 at 3p, are associated with osteoporosis in southern Chinese women.

PMID 19727905 · PMC2946578 · Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA · 2010 · 7 claims · 6 setups

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Multiple SNPs and haplotypes in FLNB are significantly associated with BMD at lumbar spine, femoral neck, and total hip

southern same subjects genotype tag taqman dual-energy
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
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

Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry.

In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach.

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

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

Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

A restricted spectrum of NRAS mutations causes Noonan syndrome.

Common variants in FLNB/CRTAP, not ARHGEF3 at 3p, are associated with osteoporosis in southern Chinese women.

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

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.