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).

• Interaction profile-based protein classification of death domain.

  PMID 15189571 · PMC459208 · BMC bioinformatics · 2004 · 7 claims · 6 setups

  Full-text index only

  An SVM-based classifier using Residue Pair Interaction Profiles (RPIPs) can classify death domain superfamily members into subfamilies with 89% average cross-validation accuracy

  homology-modeled death homology putative rigid-body homology model

• R2DT is a framework for predicting and visualising RNA secondary structure using templates.

  PMID 34108470 · PMC8190129 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 87

  R2DT is a template-based computational framework/pipeline that predicts and visualises RNA 2D structure in standardised, community-accepted layouts

  rnacentral query input aligned covariance trna-specific structure-guided

• Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.

  PMID 17537826 · PMC1933130 · Nucleic acids research · 2007 · 7 claims · 5 setups

  Full-text index only

  StSNP integrates dbSNP, PDB, KEGG, and NCBI Entrez data into a single web server for nsSNP analysis

  glutathione aldehyde sequences dbsnp comparative sequence-structure database

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand

• MODBASE: a database of annotated comparative protein structure models and associated resources.

  PMID 16381869 · PMC1347422 · Nucleic acids research · 2006 · 8 claims · 7 setups

  Full-text index only

  MODBASE is a database of automatically calculated comparative protein structure models covering all UniProt sequences matchable to a known structure

  uniprot non-redundant complexes saccharomyces comparative pairwise domain-domain

• Coverage of whole proteome by structural genomics observed through protein homology modeling database.

  PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.

  orfs predicted modeled representative homology transmembrane intrinsic

• Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

  PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

  Full-text index only

  Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

  genome functional registered omim comparative kendall's homology

• Prediction, syntax and semantic grounding in the brain and large language models.

  PMID 41807493 · PMC12979642 · Scientific reports · 2026 · 8 claims · 6 setups

  Has reproduction · 86

  Nouns show significant pre-onset neural activity, suggesting enhanced anticipatory processing of this word class.

  healthy cortex german pre-trained magnetoencephalography electroencephalography source

• Viral and host determinants of RNA virus vector replication and expression.

  PMID 15734041 · PMC7115378 · Vaccine · 2005 · 7 claims · 4 setups

  Full-text index only

  BMV RNA replication occurs in a virus-induced, membrane-bounded compartment rather than in the open cytoplasm.

  bmv saccharomyces wild-type immunogold genome-wide northern

• Predicting failure rate of PCR in large genomes.

  PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

  Full-text index only

  The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

  genomic genome pcr combined large-scale exact-match mismatch-tolerant

• Comparative genomics of fungal allergens and epitopes shows widespread distribution of closely related allergen and epitope orthologues.

  PMID 17029625 · PMC1613252 · BMC genomics · 2006 · 8 claims · 3 setups

  Full-text index only

  A database of 82 allergen sequences was compiled and used to search 22 fungal genomes for orthologues.

  fungal fumigatus enolase comparative epitope

• Assessing Bos taurus introgression in the UOA Bos indicus assembly.

  PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups

  Has reproduction · 86

  Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.

  cattle breed-pooled indian merged whole-genome snv template

• Evolutionary history of the UCP gene family: gene duplication and selection.

  PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

  Full-text index only

  The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

  vertebrate ucp human-mouse ucp1 sequence phylogenetic gene

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse

• Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

  PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

  genomes longin plant phytolongin iterative phylogenetic genomic