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 23

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

The RCSB PDB information portal for structural genomics.

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

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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
MutDB: update on development of tools for the biochemical analysis of genetic variation.

PMID 17827212 · PMC2238958 · Nucleic acids research · 2008 · 7 claims · 5 setups

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MutDB integrates dbSNP and Swiss-Prot genetic variation data with protein structural information, functional disruption prediction scores, and clinical phenotype links (OMIM, dbGAP)

proteins mutdb nonsynonymous genes sequence web functional
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
nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

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

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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
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

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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
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

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Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

identified cst csts comparative coding exon
Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

PMID 19842929 · PMC2923222 · Pharmacogenomics · 2009 · 8 claims · 8 setups

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Approximately 15-20% of nonsynonymous variants in membrane transporters exhibit reduced function

abc hek293 expressing sophie computational transporter transport
Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

PMID 11879542 · PMC128918 · Arthritis research · 2002 · 8 claims · 6 setups

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Antibody sequences that violate normal ontogenic/developmental constraints indicate a failure of B-cell regulation

peripheral diseased rheumatoid autoimmune immunoglobulin single-cell cloning
Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

PMID 18654622 · PMC2447880 · PLoS computational biology · 2008 · 8 claims · 5 setups

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Bongo identifies mutations causing local and global structural effects with a remarkably low false positive rate

p53 1bpi mutations disease-associated graph correlation structural
Genome bioinformatic analysis of nonsynonymous SNPs.

PMID 17708757 · PMC1978506 · BMC bioinformatics · 2007 · 8 claims · 8 setups

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Structure- and sequence-based prediction tools can generally distinguish disease-causing mutations from neutral ones

gene modelled nssnps automated fold relative
Tissue compartment analysis for biomarker discovery by gene expression profiling.

PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

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TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

kidney pure serial rt-pcr sage histo-morphometry
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

reference unigene ensembl normal tandem polymorphism gene
MODBASE, a database of annotated comparative protein structure models and associated resources.

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

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

sequences chains template chain comparative pairwise ligand
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

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

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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
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

families genes individuals kidney genome-wide sanger resequencing
Unraveling the Causal Linkages of RBP7 and SCGB3A1 on Pelvic Organ Prolapse: Multifaceted Insights From Genome-Wide Mendelian Randomization, Single-Cell RNA Analysis, and Network Pharmacology.

PMID 41497737 · PMC12765987 · BioMed research international · 2026 · 8 claims · 7 setups

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High RBP7 expression causally increases POP risk

vaginal gwas rbp7 key single-cell mendelian protein-protein
Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.

PMID 41547856 · PMC12917120 · Nature communications · 2026 · 8 claims · 8 setups

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GARDEN identifies and characterizes rare pathogenic cell populations/regions in spatial omics by embedding graph-based dynamic attention into a spatially-aware graph fusion contrastive model

breast anterior brain olfactory 10x starmap slide-seqv2
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups

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InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM

saccharomyces homo bank computational yeast tandem
Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.

PMID 41800382 · PMC12967217 · Bioinformatics advances · 2026 · 6 claims · 8 setups

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Annotation tools show substantial variation in isoform detection, structural completeness, splicing classification, and handling of 5' read truncation when applied to plant dRNA-seq data.

barley extracted tool novel nanopore illumina transcriptome
The macrophage entry mechanism of SARS-CoV-2 mediated by surface CD98/TMPRSS11E complex is associated with the cellular tropism toward proinflammatory M1 and pathogenesis.

PMID 41877147 · PMC13137717 · Respiratory research · 2026 · 8 claims · 8 setups

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CD98 (CD98hc/SLC3A2) is a novel receptor for the SARS-CoV-2 Spike protein

thp-1-derived 293t structures thp-1 co-ip co-immunoprecipitation molecular

Experiments

The RCSB PDB information portal for structural genomics.

MutDB: update on development of tools for the biochemical analysis of genetic variation.

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

nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

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

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

Genome bioinformatic analysis of nonsynonymous SNPs.

Tissue compartment analysis for biomarker discovery by gene expression profiling.

Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

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

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

Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

Unraveling the Causal Linkages of RBP7 and SCGB3A1 on Pelvic Organ Prolapse: Multifaceted Insights From Genome-Wide Mendelian Randomization, Single-Cell RNA Analysis, and Network Pharmacology.

Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.

InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.

The macrophage entry mechanism of SARS-CoV-2 mediated by surface CD98/TMPRSS11E complex is associated with the cellular tropism toward proinflammatory M1 and pathogenesis.