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"citation": [
{
"text": "Barrera et al. (2016), Survey of variation in human transcription factors reveals prevalent DNA binding changes.",
"url": "https://doi.org/10.1126/science.aad2257"
},
{
"text": "Trabucco et al. (2022), Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization.",
"url": "https://arxiv.org/abs/2202.08450"
}
],
"context": [],
"dataset_id": "design-bench/tfbind8",
"default_split": "six6_ref_r1",
"description": "Complete canonical DNA 8-mer binding landscape for the SIX6 reference allele, PBM replicate 1.",
"inputs": [
{
"constraints": [
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"kind": "alphabet",
"symbols": [
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"C",
"G",
"T"
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{
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"minimum": 8
}
],
"description": "DNA sequence of exactly eight nucleotides.",
"name": "sequence"
}
],
"knowledge": {
"binding_affinity_and_thermodynamics": {
"description": "Equilibrium association and dissociation constants, occupancy, binding Gibbs energy, and kinetic rate constants.",
"media_type": "text/markdown",
"path": "knowledge/shared/binding-affinity-and-thermodynamics.md",
"title": "Binding Affinity and Thermodynamics"
},
"binding_sites_motifs_and_sequence_context": {
"description": "Binding sites, consensus sequences, PFM/PWM representations, strand orientation, and nucleotide dependencies.",
"media_type": "text/markdown",
"path": "knowledge/shared/binding-sites-motifs-and-sequence-context.md",
"title": "Binding Sites, Motifs, and Sequence Context"
},
"dna_structure_and_base_pairing": {
"description": "DNA strand direction, complementarity, canonical base pairing, grooves, and sequence-dependent duplex structure.",
"media_type": "text/markdown",
"path": "knowledge/shared/dna-structure-and-base-pairing.md",
"title": "DNA Structure and Base Pairing"
},
"protein_binding_microarrays": {
"description": "Universal PBM assay principles, word-level measurements, E-score calculation, and interpretive limitations.",
"media_type": "text/markdown",
"path": "knowledge/shared/protein-binding-microarrays.md",
"title": "Protein-Binding Microarrays"
},
"six_family_and_six6": {
"description": "SIX-family protein architecture and bounded biochemical evidence about SIX6 DNA recognition.",
"media_type": "text/markdown",
"path": "knowledge/design-bench/tfbind8/six-family-and-six6.md",
"title": "The SIX Family and SIX6"
},
"transcription_factor_dna_binding": {
"description": "Physical modes of DNA recognition and the distinctions among affinity, specificity, occupancy, and regulatory activity.",
"media_type": "text/markdown",
"path": "knowledge/shared/transcription-factor-dna-binding.md",
"title": "Transcription Factor\u2013DNA Binding"
}
},
"license": "other",
"schema_version": 1,
"source": [
{
"checksum": "sha256:30778471f1c5167698ac3d2b18fb54098ddaddbaa0550448afb25567e5075231",
"name": "Barrera et al. PBM TF binding landscapes",
"notes": "Published contiguous 8-mer landscape; redistribution terms are described in the dataset card.",
"url": "https://drive.google.com/file/d/1xS6N5qSwyFLC-ZPTADYrxZuPHjBkZCrj/view",
"version": "BAR15A"
},
{
"name": "Design-Bench TFBind8 preprocessing",
"revision": "e52939588421b5433f6f2e9b359cf013c542bd89",
"url": "https://github.com/brandontrabucco/design-bench/blob/e52939588421b5433f6f2e9b359cf013c542bd89/process/process_raw_tf_bind_8.py"
}
],
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"transcription_factor": "SIX6"
},
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"num_rows": 65536
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],
"description": "Published PBM enrichment score for the SIX6_REF_R1 condition.",
"name": "e_score"
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{
"constraints": [
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{
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}
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