{"id":"https://openalex.org/W7117674792","doi":"https://doi.org/10.3390/cryst16010036","title":"Rational Engineering in Protein Crystallization: Integrating Physicochemical Principles, Molecular Scaffolds, and Computational Design","display_name":"Rational Engineering in Protein Crystallization: Integrating Physicochemical Principles, Molecular Scaffolds, and Computational Design","publication_year":2025,"publication_date":"2025-12-31","ids":{"openalex":"https://openalex.org/W7117674792","doi":"https://doi.org/10.3390/cryst16010036"},"language":"en","primary_location":{"id":"doi:10.3390/cryst16010036","doi":"https://doi.org/10.3390/cryst16010036","is_oa":true,"landing_page_url":"https://doi.org/10.3390/cryst16010036","pdf_url":"https://www.mdpi.com/2073-4352/16/1/36/pdf?version=1767191790","source":{"id":"https://openalex.org/S4210196485","display_name":"Crystals","issn_l":"2073-4352","issn":["2073-4352"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Crystals","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2073-4352/16/1/36/pdf?version=1767191790","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103173640","display_name":"S. ITO","orcid":"https://orcid.org/0000-0001-9899-7133","observed_orcids":["https://orcid.org/0000-0001-9899-7133"]},"institutions":[{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Sho Ito","raw_affiliation_strings":["Department of Biological Science and Technology , Faculty of Advanced Engineering , Tokyo University of Science , 6-3-1 Niijyuku , Katsushika , Tokyo , Japan 125-8585"],"raw_orcid":"https://orcid.org/0000-0001-9899-7133","affiliations":[{"raw_affiliation_string":"Department of Biological Science and Technology , Faculty of Advanced Engineering , Tokyo University of Science , 6-3-1 Niijyuku , Katsushika , Tokyo , Japan 125-8585","institution_ids":["https://openalex.org/I161296585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091369488","display_name":"Tatsuya Nishino","orcid":"https://orcid.org/0000-0001-8017-8762","observed_orcids":["https://orcid.org/0000-0001-8017-8762"]},"institutions":[{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Tatsuya Nishino","raw_affiliation_strings":["Department of Biological Science and Technology , Faculty of Advanced Engineering , Tokyo University of Science , 6-3-1 Niijyuku , Katsushika , Tokyo , Japan 125-8585"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Science and Technology , Faculty of Advanced Engineering , Tokyo University of Science , 6-3-1 Niijyuku , Katsushika , Tokyo , Japan 125-8585","institution_ids":["https://openalex.org/I161296585"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5091369488"],"corresponding_institution_ids":["https://openalex.org/I161296585"],"apc_list":{"value":2100,"currency":"CHF","value_usd":2534},"apc_paid":{"value":2100,"currency":"CHF","value_usd":2534},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.26457328,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"16","issue":"1","first_page":"36","last_page":"36"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.885699987411499,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.885699987411499,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11881","display_name":"Crystallization and Solubility Studies","score":0.09939999878406525,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.005100000184029341,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-crystallization","display_name":"protein crystallization","score":0.984000027179718},{"id":"https://openalex.org/keywords/contact-design","display_name":"contact design","score":0.6000000238418579},{"id":"https://openalex.org/keywords/heterogeneous-nucleation","display_name":"heterogeneous nucleation","score":0.9869999885559082},{"id":"https://openalex.org/keywords/gold-nanoparticles","display_name":"gold nanoparticles","score":0.722000002861023},{"id":"https://openalex.org/keywords/scaffold-design","display_name":"scaffold design","score":0.6240000128746033},{"id":"https://openalex.org/keywords/alphafold","display_name":"AlphaFold","score":0.8330000042915344},{"id":"https://openalex.org/keywords/rfdiffusion","display_name":"RFdiffusion","score":0.9710000157356262},{"id":"https://openalex.org/keywords/crystallizability","display_name":"crystallizability","score":0.6399999856948853},{"id":"https://openalex.org/keywords/self-assembly","display_name":"self-assembly","score":0.6710000038146973}],"concepts":[{"id":"https://openalex.org/C53105671","wikidata":"https://www.wikidata.org/wiki/Q14777816","display_name":"Rational design","level":2,"score":0.5680000185966492},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4921000003814697},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.4912000000476837},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4077000021934509},{"id":"https://openalex.org/C153064111","wikidata":"https://www.wikidata.org/wiki/Q1281033","display_name":"Protein crystallization","level":3,"score":0.4034000039100647},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.375},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.36039999127388},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.3472999930381775},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.34610000252723694},{"id":"https://openalex.org/C2781285689","wikidata":"https://www.wikidata.org/wiki/Q21921428","display_name":"Crystal (programming language)","level":2,"score":0.3228999972343445},{"id":"https://openalex.org/C203036418","wikidata":"https://www.wikidata.org/wiki/Q284256","display_name":"Crystallization","level":2,"score":0.3197999894618988},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.3149999976158142},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.28209999203681946},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.2768999934196472},{"id":"https://openalex.org/C61048295","wikidata":"https://www.wikidata.org/wiki/Q909022","display_name":"Nucleation","level":2,"score":0.27549999952316284},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.26489999890327454},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.25609999895095825},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.25450000166893005},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.25119999051094055}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/cryst16010036","doi":"https://doi.org/10.3390/cryst16010036","is_oa":true,"landing_page_url":"https://doi.org/10.3390/cryst16010036","pdf_url":"https://www.mdpi.com/2073-4352/16/1/36/pdf?version=1767191790","source":{"id":"https://openalex.org/S4210196485","display_name":"Crystals","issn_l":"2073-4352","issn":["2073-4352"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Crystals","raw_type":"journal-article"},{"id":"doi:10.20944/preprints202512.1154.v1","doi":"https://doi.org/10.20944/preprints202512.1154.v1","is_oa":true,"landing_page_url":"https://doi.org/10.20944/preprints202512.1154.v1","pdf_url":"https://www.preprints.org/frontend/manuscript/f64e7a96296e6b863084f8bbbc660239/download_pub","source":{"id":"https://openalex.org/S6309402219","display_name":"Preprints.org","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"pmh:oai:doaj.org/article:8db4353609954bb1aa45c483648f19e2","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/8db4353609954bb1aa45c483648f19e2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Crystals, Vol 16, Iss 1, p 36 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/cryst16010036","doi":"https://doi.org/10.3390/cryst16010036","is_oa":true,"landing_page_url":"https://doi.org/10.3390/cryst16010036","pdf_url":"https://www.mdpi.com/2073-4352/16/1/36/pdf?version=1767191790","source":{"id":"https://openalex.org/S4210196485","display_name":"Crystals","issn_l":"2073-4352","issn":["2073-4352"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Crystals","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1258917961","display_name":"Structural analyses of the chromatin-like structure of histone-fold CENP-SX complex","funder_award_id":"23K05671","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7117674792.pdf","grobid_xml":"https://content.openalex.org/works/W7117674792.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1963829486","https://openalex.org/W1976033992","https://openalex.org/W1983234357","https://openalex.org/W1985699483","https://openalex.org/W1991208570","https://openalex.org/W1993492122","https://openalex.org/W2001338150","https://openalex.org/W2006431107","https://openalex.org/W2010280142","https://openalex.org/W2015526636","https://openalex.org/W2020601776","https://openalex.org/W2025608974","https://openalex.org/W2044637791","https://openalex.org/W2048935540","https://openalex.org/W2055145326","https://openalex.org/W2056790687","https://openalex.org/W2069529679","https://openalex.org/W2078983417","https://openalex.org/W2087543902","https://openalex.org/W2093666200","https://openalex.org/W2100059462","https://openalex.org/W2104477830","https://openalex.org/W2111417089","https://openalex.org/W2123363094","https://openalex.org/W2131011009","https://openalex.org/W2135451205","https://openalex.org/W2166033246","https://openalex.org/W2170667639","https://openalex.org/W2567180700","https://openalex.org/W2620636699","https://openalex.org/W2916966936","https://openalex.org/W3114528330","https://openalex.org/W3164247752","https://openalex.org/W3177828909","https://openalex.org/W3183475563","https://openalex.org/W3195806082","https://openalex.org/W3202105508","https://openalex.org/W4213379039","https://openalex.org/W4214951334","https://openalex.org/W4224307055","https://openalex.org/W4288060491","https://openalex.org/W4296031103","https://openalex.org/W4302343761","https://openalex.org/W4383957026","https://openalex.org/W4387208815","https://openalex.org/W4387673953","https://openalex.org/W4396721167","https://openalex.org/W4408783694"],"related_works":[],"abstract_inverted_index":{"X-ray":[0],"crystallography":[1],"remains":[2],"the":[3,66,102,133],"gold":[4,97],"standard":[5],"for":[6,105,131],"high-resolution":[7],"structural":[8],"biology,":[9],"yet":[10],"obtaining":[11],"diffraction-quality":[12],"crystals":[13],"continues":[14],"to":[15,21,35,57,100,120,159],"pose":[16],"a":[17,29,41,47],"major":[18],"bottleneck":[19],"due":[20],"inherently":[22],"low":[23],"success":[24],"rates.":[25],"This":[26],"review":[27],"advocates":[28],"paradigm":[30],"shift":[31],"from":[32,124,163],"probabilistic":[33],"screening":[34],"rational":[36],"engineering,":[37],"reframing":[38],"crystallization":[39,122],"as":[40,155],"controllable":[42],"self-assembly":[43],"process.":[44],"We":[45,108],"provide":[46],"comprehensive":[48],"overview":[49],"of":[50,69,78,135],"strategies":[51,88,168],"that":[52,89,173],"connect":[53],"fundamental":[54],"physicochemical":[55,87],"principles":[56,130],"practical":[58],"applications,":[59],"beginning":[60],"with":[61,177],"contact":[62],"design,":[63,112,149],"which":[64,150],"involves":[65],"active":[67],"engineering":[68],"crystal":[70,106,161],"contacts":[71],"through":[72],"surface":[73],"entropy":[74],"reduction":[75],"(SER),":[76],"introduction":[77],"electrostatic":[79],"patches.":[80],"Complementing":[81],"these":[82,167],"molecular":[83],"approaches,":[84],"we":[85,128,144],"discuss":[86],"exploit":[90],"heterogeneous":[91],"nucleation":[92],"on":[93,139],"functionalized":[94],"surfaces":[95],"and":[96,117,157],"nanoparticles":[98],"(AuNPs)":[99],"lower":[101],"energy":[103],"barrier":[104],"formation.":[107],"also":[109],"address":[110],"scaffold":[111],"utilizing":[113],"rigid":[114],"fusion":[115],"partners":[116],"polymer-forming":[118],"chaperones":[119],"promote":[121],"even":[123],"low-concentration":[125],"solutions.":[126],"Furthermore,":[127],"highlight":[129],"controlling":[132],"behavior":[134],"multi-component":[136],"complexes,":[137],"based":[138],"our":[140],"experimental":[141],"experience.":[142],"Finally,":[143],"examine":[145],"de":[146],"novo":[147],"lattice":[148],"leverages":[151],"AI":[152],"tools":[153],"such":[154],"AlphaFold":[156],"RFdiffusion":[158],"program":[160],"lattices":[162],"first":[164],"principles.":[165],"Together,":[166],"establish":[169],"an":[170],"integrated":[171],"workflow":[172],"links":[174],"thermodynamic":[175],"stability":[176],"crystallizability.":[178]},"counts_by_year":[],"updated_date":"2026-10-08T09:06:37.294493","created_date":"2025-12-31T00:00:00"}
