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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Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.
PMID 16790052 · PMC1534064 · BMC bioinformatics · 2006 · 8 claims · 7 setups
The Sequential Minimal Optimization (SMO) SVM algorithm was the best-performing classifier among 26 WEKA classifiers for predicting catalytic residues
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Wiggle-predicting functionally flexible regions from primary sequence.
PMID 16839194 · PMC1500818 · PLoS computational biology · 2006 · 7 claims · 6 setups
A GNM-derived, correlation-weighted 'FF score' can objectively define functionally flexible regions (FFRs) that match experimentally confirmed flexible/functional regions (hinges, recognition loops, catalytic loops).
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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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Sequence and structure signatures of cancer mutation hotspots in protein kinases.
PMID 19834613 · PMC2759519 · PloS one · 2009 · 8 claims · 6 setups
Developed CKMD (Composite Kinase Mutation Database), an integrated bioinformatics resource mapping genetic variation in protein kinase genes to sequence, structural, and functional data