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 4

System / cell line: pdb ✕ Assay: case-study ✕ Clear

Columba: an integrated database of proteins, structures, and annotations.

PMID 15801979 · PMC1087474 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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COLUMBA physically integrates data from twelve protein structure-related databases (PDB, KEGG, Swiss-Prot, CATH, SCOP, Gene Ontology, ENZYME, etc.) into a single PostgreSQL data warehouse.

pdb database sequence secondary
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
MACSIMS: multiple alignment of complete sequences information management system.

PMID 16792820 · PMC1539025 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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MACSIMS is a multiple alignment-based information management system combining knowledge-based database mining with ab initio sequence predictions

balibase-derived sequences same query automatic database initio
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

PMID 17980028 · PMC2186358 · BMC bioinformatics · 2007 · 7 claims · 3 setups

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The DAVID Gene Concept, a single-linkage algorithm, merges gene clusters from Entrez Gene, UniRef100, and PIR-NREF100 that share protein IDs and species into unified DAVID gene clusters, improving cross-referencing between NCBI and UniProt systems

members entire usp8 sequence annotation

Experiments

Columba: an integrated database of proteins, structures, and annotations.

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

MACSIMS: multiple alignment of complete sequences information management system.

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.