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).

• BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.

  PMID 41266599 · PMC12635123 · Communications biology · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  BiRNA-BERT uses adaptive dual-tokenization that dynamically selects nucleotide-level (NUC) or byte-pair encoding (BPE) tokens based on input sequence length

  rfam plant lncrna-mirna sequences unsupervised mirna-lncrna length-binned

• Large-scale structural analysis of the core promoter in mammalian and plant genomes.

  PMID 16049029 · PMC1181242 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  DNA encodes at least two independent levels of functional information: protein/TF-binding sequence information and physical/structural properties of the molecule itself.

  core-promoter arabidopsis rice computational adaptive linear

• Structural organization and interactions of transmembrane domains in tetraspanin proteins.

  PMID 15985154 · PMC1190194 · BMC structural biology · 2005 · 8 claims · 5 setups

  Full-text index only

  TM1, TM2 and TM3 of human tetraspanins display a distinct heptad repeat motif (abcdefg)n, while TM4 lacks this motif.

  tetraspanin cd9 gfp single-cysteine sequence cross-species fluorescence

• Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.

  PMID 17349043 · PMC1829165 · BMC bioinformatics · 2007 · 8 claims · 6 setups

  Full-text index only

  A combined target-selection approach — pursuing both structurally uncharacterised domain families and additional targets from large structurally characterised superfamilies — is essential for comprehensive structural coverage of the genomes.

  sp-trembl hmm-based domain computational

• Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

  PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

  Full-text index only

  Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

  organisms cide cideb hmmer tblastn sequence

• A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation.

  PMID 19958498 · PMC2788387 · BMC genomics · 2009 · 8 claims · 4 setups

  Full-text index only

  Comparative homology modeling of wild-type and mutant α-mannosidase across human, cow, cat and guinea pig reveals a significant correlation between genotype severity and phenotype severity in α-mannosidosis

  lysosomal full-length pro-peptide bovine homology sequence weblogo

• nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

  PMID 15980516 · PMC1160133 · Nucleic acids research · 2005 · 6 claims · 4 setups

  Full-text index only

  nsSNPAnalyzer is a web server that predicts whether a query nsSNP is disease-associated or functionally neutral using a Random Forest classifier combining structural and evolutionary information

  curated homologous structure random structural secondary

• In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

  PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 95

  icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

  huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning

• Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

  PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

  Full-text index only

  Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

  genome genomic kinase psi-blast comparative genscan

• Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

  PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

  Full-text index only

  The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

  chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr

• Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

  PMID 16630345 · PMC1489951 · BMC bioinformatics · 2006 · 8 claims · 7 setups

  Full-text index only

  Sequence conservation (PSIC score difference) at the nsSNP position is the single most useful attribute for predicting deleterious vs neutral status.

  swissprot nssnp-containing nssnps machine single-attribute sequence

• The RCSB PDB information portal for structural genomics.

  PMID 16381872 · PMC1347482 · Nucleic acids research · 2006 · 7 claims · 5 setups

  Full-text index only

  The RCSB PDB Structural Genomics Information Portal integrates three resources: Structural Genomics Initiatives, Targets (TargetDB/PepcDB), and Structures (functional coverage analysis).

  structural nih genome sequence target production

• 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

• RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.

  PMID 31978147 · PMC6980424 · PloS one · 2020 · 8 claims · 6 setups

  Has reproduction · 71

  RNAmountAlign is the first RNA sequence/structure pairwise alignment algorithm based on incremental ensemble mountain distance, running in O(n^3) time and O(n^2) space for two sequences of length n.

  sequences sequence trna target pairwise global single

• 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

• A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

  PMID 17521420 · PMC1929158 · Genome biology · 2007 · 7 claims · 6 setups

  Full-text index only

  mtcPTM is a hierarchically organized database of human and mouse phosphosites that preserves experimental context, enabling comparison of phosphorylation patterns across conditions

  nonredundant database high-throughput homology

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

  Full-text index only

  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

  PMID 19969003 · PMC2822003 · Journal of molecular biology · 2010 · 7 claims · 7 setups

  Full-text index only

  PCP-consensus sequences of E protein show insertions/deletions that distinguish tick-borne, mosquito-borne, no-known-vector (NKV), and yellow fever virus (YFV) Flaviviruses

  natural aligned ns3 denv sequence pcp-consensus physicochemical

• 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

• Conservation, variability and the modeling of active protein kinases.

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

  Full-text index only

  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