Does Learning Protein Folding Generalize to Broader Reasoning?
Paper • 2609.38879 • Published • 122
id stringlengths 16 16 | messages listlengths 3 3 | metadata dict |
|---|---|---|
foldbench:5sbj_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "5sbj_A",
"pdb": "5sbj",
"chain": "A",
"assembly_name": "5sbj-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 26,
"length_bin": "short",
"foldbench_manifest_sequence": "YCSDCGADXSQVRGGYCTNCGASXDRIR",
"foldbench_manifest_length": 28,
"cif_parsed_sequence":... |
foldbench:7pv5_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "7pv5_A",
"pdb": "7pv5",
"chain": "A",
"assembly_name": "7pv5-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 75,
"length_bin": "short",
"foldbench_manifest_sequence": "EIFKVEVKNMGYFGIGEFKKLLRNTLKFDVTKIKAPTRKEFAFVXFRSQEDQQRALEILNGYKWKGKVLKAHVAK",
"foldbench... |
foldbench:7qp5_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "7qp5_A",
"pdb": "7qp5",
"chain": "A",
"assembly_name": "7qp5-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 241,
"length_bin": "long",
"foldbench_manifest_sequence": "QDPTLAQAVRATIAKHREHLLEFIRLDEPAPLNAMTLAQWSSPNVLSSLLAVYSDHIYRNQPMMIRENKPLISLWAQWYIGLMVPPLMLA... |
foldbench:7qsj_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "7qsj_A",
"pdb": "7qsj",
"chain": "A",
"assembly_name": "7qsj-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 346,
"length_bin": "long",
"foldbench_manifest_sequence": "LDAVPGVPGVLTPEQCRQTAQAIADAQEPSGALPWFEGGHTDPWDHVENAMALTVAGLLEPARAAFDWCRTTQRPDGSWPIQIRNGVVED... |
foldbench:7t9r_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "7t9r_A",
"pdb": "7t9r",
"chain": "A",
"assembly_name": "7t9r-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 38,
"length_bin": "short",
"foldbench_manifest_sequence": "SYYSTLQCRNNHGHCRRLCFHGEQWIGNCNGRHQHCCK",
"foldbench_manifest_length": 38,
"cif_parsed_... |
foldbench:7tlh_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "7tlh_A",
"pdb": "7tlh",
"chain": "A",
"assembly_name": "7tlh-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 124,
"length_bin": "medium",
"foldbench_manifest_sequence": "ACRPCSDAELLLAACTSDFVIHGTIHGVAHDTELQESVITVVVARVIRQTLPLFKEGSSEGQGRASIRTLLRCGVRPGPGSFLFMGWS... |
foldbench:7tjb_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "7tjb_A",
"pdb": "7tjb",
"chain": "A",
"assembly_name": "7tjb-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 222,
"length_bin": "long",
"foldbench_manifest_sequence": "WKQGTEAAAVRSGDKVFFAGDSLMQGVAPFVQKSLKQQYGIESANLSKQSTGLSYPSFFDWPKTIEETLKKHPEISVLAVFLGPNDPWDF... |
foldbench:7uba_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "7uba_A",
"pdb": "7uba",
"chain": "A",
"assembly_name": "7uba-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 187,
"length_bin": "long",
"foldbench_manifest_sequence": "PDIECECDLLCPITSTRIKQCKNCRKFVHSLCYGNKPGPKVDKCISCVYGPMFDPSSSEFKDLMMLRKCYRFLSRNKGFPPSIKEFTNSI... |
foldbench:7uk8_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "7uk8_A",
"pdb": "7uk8",
"chain": "A",
"assembly_name": "7uk8-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 383,
"length_bin": "xlong",
"foldbench_manifest_sequence": "HHHHMERVSITERPDWREKAHEYGFNFHTMYGEPYWCEDAYYKLTLAQVEKLEEVTAELHQMCLKVVEKVIASDELMTKFRIPKHTWSF... |
foldbench:7ur2_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "7ur2_A",
"pdb": "7ur2",
"chain": "A",
"assembly_name": "7ur2-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 160,
"length_bin": "medium",
"foldbench_manifest_sequence": "DAFFRTGSFRNDGLKASDVLPILKEKVAFVSGGRDKRGGPILTFPARHDRIRQEDLRKLVTYLASVPSEDVCKRGFTVIIDMRGSKWD... |
foldbench:7ur7_A | [
{
"role": "system",
"content": "You predict protein backbone structures from sequence, MSA and template-derived constraints. Output only a valid BB4Q10 structure block; do not add explanations."
},
{
"role": "user",
"content": "<protein_folding_input version=\"foldbench-monomer-v1\">\n<sequence ... | {
"source_id": "7ur7_A",
"pdb": "7ur7",
"chain": "A",
"assembly_name": "7ur7-assembly1",
"source_dataset": "FoldBench/monomer_protein",
"sequence_length": 63,
"length_bin": "short",
"foldbench_manifest_sequence": "SEVKELLEEFLKRNKPVRIHHKNGEEIKVRITHIGEDTVEFELNGRTHRINIKDILDVKEWLE",
"foldbench_manifest_le... |
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FoldBench334 processed snapshot
The exact 334-protein BB4Q10 target records used for Fold2Reason structural
readout. target_manifest.json describes the evaluated target cohort. This is
a processed snapshot for the paper, not a replacement for the official FoldBench.
from datasets import load_dataset
targets = load_dataset("GENTEL-Lab/FoldBench334", split="test")
Paper: https://huggingface.co/papers/2609.38879
Code and evaluation protocol: https://github.com/GENTEL-lab/Fold2Reason
Upstream FoldBench: https://github.com/BEAM-Labs/FoldBench
Source: project dataset.zip, SHA-256 97ef38130fec0b7caaa323022d5b7bef620e7b26dfa42a1da4713066806dd90b. Original files are
unchanged; see SOURCE_PROVENANCE.json for file hashes.
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