{"id":"https://openalex.org/W7220718258","doi":"https://doi.org/10.64898/2026.10.05.756905","title":"RGI-Toolkit: Differentiable Restraints for Controllable Biomolecular Structure Prediction","display_name":"RGI-Toolkit: Differentiable Restraints for Controllable Biomolecular Structure Prediction","publication_year":2026,"publication_date":"2026-10-06","ids":{"openalex":"https://openalex.org/W7220718258","doi":"https://doi.org/10.64898/2026.10.05.756905"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.05.756905","doi":"https://doi.org/10.64898/2026.10.05.756905","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.05.756905","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/06/2026.10.05.756905.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/06/2026.10.05.756905.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108915482","display_name":"Tatsuki Hori","orcid":"https://orcid.org/0009-0001-3991-8367","observed_orcids":["https://orcid.org/0009-0001-3991-8367"]},"institutions":[{"id":"https://openalex.org/I4405286394","display_name":"Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo","ror":"https://ror.org/0216tv790","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4400009020","https://openalex.org/I4405286394"]},{"id":"https://openalex.org/I4405286842","display_name":"Institute of Integrated Research, Institute of Science Tokyo","ror":"https://ror.org/038jk9m46","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4400009020","https://openalex.org/I4405286842"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tatsuki Hori","raw_affiliation_strings":["Department of Computational Drug Discovery and Design, Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan"],"raw_orcid":"https://orcid.org/0009-0001-3991-8367","affiliations":[{"raw_affiliation_string":"Department of Computational Drug Discovery and Design, Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan","institution_ids":["https://openalex.org/I4405286394","https://openalex.org/I4405286842"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077947736","display_name":"Yoshitaka Moriwaki","orcid":"https://orcid.org/0000-0003-0448-9790","observed_orcids":["https://orcid.org/0000-0003-0448-9790"]},"institutions":[{"id":"https://openalex.org/I4405286394","display_name":"Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo","ror":"https://ror.org/0216tv790","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4400009020","https://openalex.org/I4405286394"]},{"id":"https://openalex.org/I4405286842","display_name":"Institute of Integrated Research, Institute of Science Tokyo","ror":"https://ror.org/038jk9m46","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4400009020","https://openalex.org/I4405286842"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshitaka Moriwaki","raw_affiliation_strings":["Department of Computational Drug Discovery and Design, Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan","Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan"],"raw_orcid":"https://orcid.org/0000-0003-0448-9790","affiliations":[{"raw_affiliation_string":"Department of Computational Drug Discovery and Design, Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan","institution_ids":["https://openalex.org/I4405286394","https://openalex.org/I4405286842"]},{"raw_affiliation_string":"Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037440046","display_name":"Ryuichiro Ishitani","orcid":"https://orcid.org/0000-0002-4136-5685","observed_orcids":["https://orcid.org/0000-0002-4136-5685"]},"institutions":[{"id":"https://openalex.org/I4405286394","display_name":"Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo","ror":"https://ror.org/0216tv790","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4400009020","https://openalex.org/I4405286394"]},{"id":"https://openalex.org/I4405286842","display_name":"Institute of Integrated Research, Institute of Science Tokyo","ror":"https://ror.org/038jk9m46","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4400009020","https://openalex.org/I4405286842"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Ryuichiro Ishitani","raw_affiliation_strings":["Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan","Department of Computational Drug Discovery and Design, Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan"],"raw_orcid":"https://orcid.org/0000-0002-4136-5685","affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Department of Computational Drug Discovery and Design, Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan","institution_ids":["https://openalex.org/I4405286394","https://openalex.org/I4405286842"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5037440046"],"corresponding_institution_ids":["https://openalex.org/I4405286394","https://openalex.org/I4405286842","https://openalex.org/I74801974"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.00279999990016222,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/diffusion-based-model","display_name":"diffusion-based model","score":0.6690000295639038},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"protein structure prediction","score":0.5109999775886536},{"id":"https://openalex.org/keywords/conformational-bias","display_name":"conformational bias","score":0.6380000114440918},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"stereochemistry","score":0.5709999799728394},{"id":"https://openalex.org/keywords/alphafold-3","display_name":"AlphaFold3","score":0.6179999709129333},{"id":"https://openalex.org/keywords/python-library","display_name":"Python library","score":0.4880000054836273},{"id":"https://openalex.org/keywords/coordinate-optimization","display_name":"coordinate optimization","score":0.4059999883174896}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5472999811172485},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5286999940872192},{"id":"https://openalex.org/C202615002","wikidata":"https://www.wikidata.org/wiki/Q783507","display_name":"Differentiable function","level":2,"score":0.5131000280380249},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.49630001187324524},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.40049999952316284},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.3921999931335449},{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.34860000014305115},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.322299987077713},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.3158000111579895},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.3149999976158142},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.31360000371932983},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3133000135421753},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.30469998717308044},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3005000054836273},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2946999967098236},{"id":"https://openalex.org/C108882727","wikidata":"https://www.wikidata.org/wiki/Q2991685","display_name":"Solid modeling","level":2,"score":0.2946000099182129},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.2922999858856201},{"id":"https://openalex.org/C99138194","wikidata":"https://www.wikidata.org/wiki/Q183427","display_name":"Hash function","level":2,"score":0.2732999920845032},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.27300000190734863},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.271699994802475},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.2689000070095062},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.26660001277923584},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.2655999958515167},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2655999958515167},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.26159998774528503},{"id":"https://openalex.org/C39920418","wikidata":"https://www.wikidata.org/wiki/Q11476","display_name":"Kinematics","level":2,"score":0.257099986076355},{"id":"https://openalex.org/C2989255885","wikidata":"https://www.wikidata.org/wiki/Q500256","display_name":"Molecular conformation","level":3,"score":0.2540000081062317}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.05.756905","doi":"https://doi.org/10.64898/2026.10.05.756905","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.05.756905","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/06/2026.10.05.756905.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.05.756905","doi":"https://doi.org/10.64898/2026.10.05.756905","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.05.756905","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/06/2026.10.05.756905.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7220718258.pdf","grobid_xml":"https://content.openalex.org/works/W7220718258.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W2970971581","https://openalex.org/W4214847177","https://openalex.org/W4400795417","https://openalex.org/W4404565424","https://openalex.org/W4406274436","https://openalex.org/W4411463597","https://openalex.org/W7133244780","https://openalex.org/W7153584620","https://openalex.org/W7163532908"],"related_works":["https://openalex.org/W2912932504","https://openalex.org/W7160532110","https://openalex.org/W7161109729","https://openalex.org/W7108208128","https://openalex.org/W7170581082","https://openalex.org/W2125042228","https://openalex.org/W2902192569","https://openalex.org/W4417183368","https://openalex.org/W3197845418","https://openalex.org/W7098455851"],"abstract_inverted_index":{"Abstract":[0],"Diffusion-based":[1],"models":[2],"have":[3],"substantially":[4],"advanced":[5],"biomolecular":[6,193],"structure":[7,65,188],"prediction.":[8],"Within":[9],"this":[10],"framework,":[11],"restraint-guided":[12],"inference":[13],"(RGI)":[14],"corrects":[15],"the":[16,47,97,149,164,169],"denoiser":[17],"output":[18],"at":[19],"each":[20],"reverse-diffusion":[21],"step":[22],"using":[23],"a":[24,35,53,62,80,88,93,125,176],"differentiable":[25],"restraint":[26,70],"loss,":[27],"allowing":[28],"available":[29,60],"experimental":[30,181],"information,":[31],"stereochemical":[32,199],"requirements,":[33],"or":[34],"specified":[36,123,170,196],"target":[37,171],"conformational":[38,197],"state":[39],"to":[40,87],"be":[41],"incorporated":[42],"into":[43,79,187],"predictions":[44],"without":[45],"retraining":[46],"model.":[48],"Here,":[49],"we":[50],"present":[51],"RGI-Toolkit,":[52],"general-purpose":[54],"Python":[55],"library":[56],"that":[57],"makes":[58],"RGI":[59],"for":[61,179,191],"range":[63],"of":[64],"predictors.":[66],"The":[67,129],"toolkit":[68,130],"consolidates":[69],"definition,":[71],"atom":[72],"selection,":[73],"loss":[74],"evaluation,":[75],"and":[76,92,104,111,145,152,159,183,190,198],"coordinate":[77],"optimization":[78],"shared,":[81],"backend-agnostic":[82],"engine,":[83],"limiting":[84],"predictor-specific":[85],"code":[86],"thin":[89],"preprocessing":[90],"adapter":[91],"single":[94],"hook":[95],"in":[96,124,148],"denoising":[98],"loop.":[99],"Restraints":[100],"on":[101,106,112],"distances,":[102],"angles,":[103],"dihedrals,":[105],"deviations":[107],"from":[108],"reference":[109],"structures,":[110],"user-defined":[113],"reaction":[114],"coordinates,":[115],"together":[116],"with":[117,195],"ligand":[118],"conformer":[119,141],"restraints,":[120],"are":[121],"all":[122,138],"common":[126],"configuration":[127],"format.":[128],"currently":[131],"supports":[132],"six":[133,139],"predictors,":[134,140],"including":[135],"AlphaFold3.":[136],"Across":[137],"restraints":[142,161],"eliminated":[143],"chirality":[144],"cis/trans":[146],"errors":[147],"predicted":[150],"ligands":[151],"improved":[153],"their":[154],"local":[155],"geometry,":[156],"while":[157],"geometric":[158,185],"custom":[160],"systematically":[162],"shifted":[163],"sampled":[165],"protein":[166],"conformations":[167],"toward":[168],"states.":[172],"RGI-Toolkit":[173],"thus":[174],"provides":[175],"unified":[177],"framework":[178],"integrating":[180],"information":[182],"prior":[184],"knowledge":[186],"prediction":[189],"generating":[192],"structures":[194],"properties.":[200]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-10-07T00:00:00"}
