{"id":"https://openalex.org/W4416283193","doi":"https://doi.org/10.3390/robotics14110167","title":"Sign Gradient Descent Algorithms for Accelerated Kinetostatic Protein Folding in Nanorobotics Design","display_name":"Sign Gradient Descent Algorithms for Accelerated Kinetostatic Protein Folding in Nanorobotics Design","publication_year":2025,"publication_date":"2025-11-17","ids":{"openalex":"https://openalex.org/W4416283193","doi":"https://doi.org/10.3390/robotics14110167"},"language":"en","primary_location":{"id":"doi:10.3390/robotics14110167","is_oa":true,"landing_page_url":"https://doi.org/10.3390/robotics14110167","pdf_url":"https://www.mdpi.com/2218-6581/14/11/167/pdf?version=1763393107","source":{"id":"https://openalex.org/S4210232487","display_name":"Robotics","issn_l":"2218-6581","issn":["2218-6581"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"Robotics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2218-6581/14/11/167/pdf?version=1763393107","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017956352","display_name":"Alireza Mohammadi","orcid":"https://orcid.org/0000-0002-1089-3872"},"institutions":[{"id":"https://openalex.org/I4210130704","display_name":"University of Michigan\u2013Dearborn","ror":"https://ror.org/035wtm547","country_code":"US","type":"education","lineage":["https://openalex.org/I4210130704"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alireza Mohammadi","raw_affiliation_strings":["Department Electrical & Computer Engineering, University of Michigan, Dearborn, MI 48128, USA","Department Electrical & Computer Engineering, University of Michigan, Dearborn, MI 48128 USA"],"affiliations":[{"raw_affiliation_string":"Department Electrical & Computer Engineering, University of Michigan, Dearborn, MI 48128, USA","institution_ids":["https://openalex.org/I4210130704"]},{"raw_affiliation_string":"Department Electrical & Computer Engineering, University of Michigan, Dearborn, MI 48128 USA","institution_ids":["https://openalex.org/I4210130704"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018629708","display_name":"Mohammad Al Saaideh","orcid":"https://orcid.org/0000-0003-1779-7012"},"institutions":[{"id":"https://openalex.org/I79817857","display_name":"University of Guelph","ror":"https://ror.org/01r7awg59","country_code":"CA","type":"education","lineage":["https://openalex.org/I79817857"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Mohammad Al Janaideh","raw_affiliation_strings":["Department Mechanical Engineering, University of Guelph, Guelph, ON N1G 2W1, Canada","Department Mechanical Engineering, University of Guelph, Guelph, ON N1G 2W1 Canada"],"affiliations":[{"raw_affiliation_string":"Department Mechanical Engineering, University of Guelph, Guelph, ON N1G 2W1, Canada","institution_ids":["https://openalex.org/I79817857"]},{"raw_affiliation_string":"Department Mechanical Engineering, University of Guelph, Guelph, ON N1G 2W1 Canada","institution_ids":["https://openalex.org/I79817857"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017956352"],"corresponding_institution_ids":["https://openalex.org/I4210130704"],"apc_list":{"value":1600,"currency":"CHF","value_usd":1732},"apc_paid":{"value":1600,"currency":"CHF","value_usd":1732},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.28050519,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"14","issue":"11","first_page":"167","last_page":"167"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.3093999922275543,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.3093999922275543,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.27160000801086426,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.13600000739097595,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.6625999808311462},{"id":"https://openalex.org/keywords/gradient-descent","display_name":"Gradient descent","score":0.6589999794960022},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.5917999744415283},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5486999750137329},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.541100025177002},{"id":"https://openalex.org/keywords/sign","display_name":"Sign (mathematics)","score":0.5059999823570251},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.47859999537467957},{"id":"https://openalex.org/keywords/nanorobotics","display_name":"Nanorobotics","score":0.4745999872684479}],"concepts":[{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6625999808311462},{"id":"https://openalex.org/C153258448","wikidata":"https://www.wikidata.org/wiki/Q1199743","display_name":"Gradient descent","level":3,"score":0.6589999794960022},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5917999744415283},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5486999750137329},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.541100025177002},{"id":"https://openalex.org/C139676723","wikidata":"https://www.wikidata.org/wiki/Q1193832","display_name":"Sign (mathematics)","level":2,"score":0.5059999823570251},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5002999901771545},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.48809999227523804},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.47859999537467957},{"id":"https://openalex.org/C187911381","wikidata":"https://www.wikidata.org/wiki/Q587024","display_name":"Nanorobotics","level":2,"score":0.4745999872684479},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.4205999970436096},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.420199990272522},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.3944999873638153},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.39329999685287476},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.34610000252723694},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.30140000581741333},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.30000001192092896},{"id":"https://openalex.org/C500300565","wikidata":"https://www.wikidata.org/wiki/Q925667","display_name":"Computer simulation","level":2,"score":0.2924000024795532},{"id":"https://openalex.org/C2776637919","wikidata":"https://www.wikidata.org/wiki/Q624380","display_name":"Descent (aeronautics)","level":2,"score":0.2849000096321106},{"id":"https://openalex.org/C47446073","wikidata":"https://www.wikidata.org/wiki/Q5165890","display_name":"Control theory (sociology)","level":3,"score":0.27730000019073486}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3390/robotics14110167","is_oa":true,"landing_page_url":"https://doi.org/10.3390/robotics14110167","pdf_url":"https://www.mdpi.com/2218-6581/14/11/167/pdf?version=1763393107","source":{"id":"https://openalex.org/S4210232487","display_name":"Robotics","issn_l":"2218-6581","issn":["2218-6581"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"Robotics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:e002f7708f6a450b8b7a2c57f02d568d","is_oa":true,"landing_page_url":"https://doaj.org/article/e002f7708f6a450b8b7a2c57f02d568d","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Robotics, Vol 14, Iss 11, p 167 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/robotics14110167","is_oa":true,"landing_page_url":"https://doi.org/10.3390/robotics14110167","pdf_url":"https://www.mdpi.com/2218-6581/14/11/167/pdf?version=1763393107","source":{"id":"https://openalex.org/S4210232487","display_name":"Robotics","issn_l":"2218-6581","issn":["2218-6581"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"Robotics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1965691274","display_name":null,"funder_award_id":"CMMI-2153744","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4173148126","display_name":null,"funder_award_id":"2153744","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5954070948","display_name":null,"funder_award_id":"CMMI-","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6755165505","display_name":null,"funder_award_id":"award","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337391","display_name":"Division of Civil, Mechanical and Manufacturing Innovation","ror":"https://ror.org/028yd4c30"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416283193.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Numerical":[0],"simulations":[1,187],"of":[2,8,47,64,77,91,104,117,132,145,171,188,191],"protein":[3,17,25,41,96,126,192],"folding":[4,29,39,56,153,190],"enable":[5],"the":[6,24,33,55,61,70,78,83,129,133,137,143,146,151,163,168],"design":[7],"protein-based":[9],"nanomachines":[10],"and":[11,22,30,54,159],"nanorobots":[12],"by":[13,51,60],"predicting":[14,124],"folded":[15,95,125,179],"three-dimensional":[16],"structures":[18],"with":[19,98],"high":[20],"accuracy":[21],"revealing":[23],"conformation":[26],"transitions":[27],"during":[28],"unfolding.":[31],"In":[32],"kinetostatic":[34,62,152],"compliance":[35],"method":[36],"(KCM)":[37],"for":[38,123],"simulations,":[40],"molecules":[42],"are":[43],"represented":[44],"as":[45],"ensembles":[46],"rigid":[48],"nano-linkages":[49],"connected":[50],"chemical":[52],"bonds,":[53],"process":[57],"is":[58,183],"driven":[59],"influence":[63],"nonlinear":[65],"interatomic":[66,105,172],"force":[67,106,173],"fields":[68],"until":[69],"system":[71],"converges":[72],"to":[73,93,149,156,177],"a":[74,115],"free-energy":[75,147],"minimum":[76],"protein.":[79],"Despite":[80],"its":[81],"strengths,":[82],"conventional":[84,134],"KCM":[85,135],"framework":[86],"demands":[87],"an":[88],"excessive":[89],"number":[90],"iterations":[92,131],"reach":[94,178],"conformations,":[97],"each":[99],"iteration":[100],"requiring":[101],"costly":[102],"computations":[103],"fields.":[107],"To":[108],"address":[109],"these":[110],"limitations,":[111],"this":[112],"work":[113],"introduces":[114],"family":[116],"sign":[118,144],"gradient":[119,148],"descent":[120],"(SGD)":[121],"algorithms":[122,140,166],"structures.":[127],"Unlike":[128],"heuristic-based":[130],"framework,":[136],"proposed":[138,164],"SGD":[139],"rely":[141],"on":[142],"guide":[150],"process.":[154],"Owing":[155],"their":[157],"faster":[158],"more":[160],"robust":[161],"convergence,":[162],"SGD-based":[165],"reduce":[167],"computational":[169],"burden":[170],"field":[174],"evaluations":[175],"required":[176],"conformations.":[180],"Their":[181],"effectiveness":[182],"demonstrated":[184],"through":[185],"numerical":[186],"KCM-based":[189],"backbone":[193],"chains.":[194]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-11-17T00:00:00"}