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 9

System / cell line: structures ✕ Assay: same ✕ Clear

Oligomeric protein structure networks: insights into protein-protein interactions.

PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

non-redundant same known complexes structure hub comparison
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

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The Sequential Minimal Optimization (SMO) SVM algorithm was the best-performing classifier among 26 WEKA classifiers for predicting catalytic residues

benchmarking same pirsf pdb supervised wrapper sequence
Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

PMID 18769673 · PMC2518838 · PloS one · 2008 · 8 claims · 6 setups

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The protein sequence-structure map behaves as a noisy digital communication channel whose capacity C exceeds the transmission rate R for native structures, satisfying Shannon's noisy channel theorem

chains pdbselect25 same single-domain statistical channel negative
Structural evolution of the protein kinase-like superfamily.

PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

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All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

bank representative same kinase comparative manual structure-annotated
The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment.

PMID 25506420 · PMC4257144 · F1000Research · 2013 · 8 claims · 8 setups

Has reproduction · 42

The EPD between Cβ atoms of consecutive residues provides unique signatures of amino acid pair types and can discriminate native from decoy protein structures.

non-homologous same pisces structures finite-difference electrostatic sequence-distance
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
Conservation, variability and the modeling of active protein kinases.

PMID 17912359 · PMC1989141 · PloS one · 2007 · 7 claims · 5 setups

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A novel sequence-order independent (fold-independent) structural alignment algorithm was developed that maximizes side-chain similarity to produce a consensus kinase structure.

active-conformation same chak rio2 sequence-order pairwise structural
Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.

PMID 17264116 · PMC1851657 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Cruciform extrusion propensity of PATRRs depends on both length and central symmetry of the repeat.

plasmids same single-stranded patrr-containing cruciform endonuclease secondary
Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

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DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

coli plasmids plasmid white plasmid sequencing non-b

Experiments

Oligomeric protein structure networks: insights into protein-protein interactions.

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.

Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

Structural evolution of the protein kinase-like superfamily.

The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment.

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

Conservation, variability and the modeling of active protein kinases.

Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.

Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.