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).
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Prodepth: predict residue depth by support vector regression approach from protein sequences only.
PMID 19759917 · PMC2742725 · PloS one · 2009 · 8 claims · 8 setups
Residue depth can be reliably predicted solely from protein primary sequence using support vector regression on sequence-derived features.
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Evolutionary trace annotation of protein function in the structural proteome.
PMID 20036248 · PMC2831211 · Journal of molecular biology · 2010 · 8 claims · 7 setups
ET-ranked residue clusters can be used to build 3D templates that predict GO function in enzymes and non-enzymes alike, without prior knowledge of functional mechanism.
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Peptide bioinformatics: peptide classification using peptide machines.
PMID 19065810 · PMC7122642 · Methods in molecular biology (Clifton, N.J.) · 2008 · 8 claims · 4 setups
The bio-basis function, which converts peptides into numerical vectors using nongapped pairwise homology alignment scores against indicator peptides, can statistically quantify peptide similarity for classification.
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High-throughput crystallography for structural genomics.
PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups
SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues