{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T01:15:28Z","timestamp":1774746928510,"version":"3.50.1"},"reference-count":86,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,1,4]],"date-time":"2024-01-04T00:00:00Z","timestamp":1704326400000},"content-version":"vor","delay-in-days":43,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFE0206400"],"award-info":[{"award-number":["2021YFE0206400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22220102001"],"award-info":[{"award-number":["22220102001"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["92370130"],"award-info":[{"award-number":["92370130"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81973281"],"award-info":[{"award-number":["81973281"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82373791"],"award-info":[{"award-number":["82373791"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["226-2022-00220"],"award-info":[{"award-number":["226-2022-00220"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Protein loops play a critical role in the dynamics of proteins and are essential for numerous biological functions, and various computational approaches to loop modeling have been proposed over the past decades. However, a comprehensive understanding of the strengths and weaknesses of each method is lacking. In this work, we constructed two high-quality datasets (i.e. the General dataset and the CASP dataset) and systematically evaluated the accuracy and efficiency of 13 commonly used loop modeling approaches from the perspective of loop lengths, protein classes and residue types. The results indicate that the knowledge-based method FREAD generally outperforms the other tested programs in most cases, but encountered challenges when predicting loops longer than 15 and 30 residues on the CASP and General datasets, respectively. The ab initio method Rosetta NGK demonstrated exceptional modeling accuracy for short loops with four to eight residues and achieved the highest success rate on the CASP dataset. The well-known AlphaFold2 and RoseTTAFold require more resources for better performance, but they exhibit promise for predicting loops longer than 16 and 30 residues in the CASP and General datasets. These observations can provide valuable insights for selecting suitable methods for specific loop modeling tasks and contribute to future advancements in the field.<\/jats:p>","DOI":"10.1093\/bib\/bbad486","type":"journal-article","created":{"date-parts":[[2024,1,4]],"date-time":"2024-01-04T01:20:44Z","timestamp":1704331244000},"source":"Crossref","is-referenced-by-count":14,"title":["Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency"],"prefix":"10.1093","volume":"25","author":[{"given":"Tianyue","family":"Wang","sequence":"first","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"given":"Langcheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pathology, New York University Medical Center , 550 First Avenue, New York, NY 10016 , USA"}]},{"given":"Xujun","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2783-5529","authenticated-orcid":false,"given":"Chao","family":"Shen","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"given":"Odin","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"given":"Jike","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"given":"Jialu","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"given":"Ruofan","family":"Jin","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"given":"Donghao","family":"Zhou","sequence":"additional","affiliation":[{"name":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, Guangdong , China"}]},{"given":"Shicheng","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"given":"Liwei","family":"Liu","sequence":"additional","affiliation":[{"name":"Advanced Computing and Storage Laboratory, Central Research Institute , 2012 Laboratories, Huawei Technologies Co., Ltd., Shenzhen 518129, Guangdong , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6893-2013","authenticated-orcid":false,"given":"Xiaorui","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology , Macao , China"}]},{"given":"Chang-Yu","family":"Hsieh","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"given":"Guangyong","family":"Chen","sequence":"additional","affiliation":[{"name":"Zhejiang Lab, Zhejiang University , Hangzhou 311121, Zhejiang , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1152-7759","authenticated-orcid":false,"given":"Peichen","family":"Pan","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0999-8802","authenticated-orcid":false,"given":"Yu","family":"Kang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7227-2580","authenticated-orcid":false,"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, Zhejiang , China"}]}],"member":"286","published-online":{"date-parts":[[2024,1,3]]},"reference":[{"key":"2024010401203025400_ref1","doi-asserted-by":"crossref","first-page":"e1003539","DOI":"10.1371\/journal.pcbi.1003539","article-title":"Fast protein loop sampling and structure prediction using distance-guided sequential chain-growth Monte Carlo method","volume":"10","author":"Tang","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2024010401203025400_ref2","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.crstbi.2021.07.002","article-title":"Current approaches to flexible loop modeling","volume":"3","author":"Barozet","year":"2021","journal-title":"Curr Res Struct Biol"},{"key":"2024010401203025400_ref3","doi-asserted-by":"crossref","first-page":"1584","DOI":"10.1002\/pro.2537","article-title":"Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction","volume":"23","author":"Rysavy","year":"2014","journal-title":"Protein Sci"},{"key":"2024010401203025400_ref4","doi-asserted-by":"crossref","first-page":"8106","DOI":"10.1093\/nar\/gku464","article-title":"G-quadruplex conformation and dynamics are determined by loop length and sequence","volume":"42","author":"Tippana","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref5","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1038\/s41594-017-0011-7","article-title":"Structure and dynamics of GPCR signaling complexes","volume":"25","author":"Hilger","year":"2018","journal-title":"Nat Struct Mol Biol"},{"key":"2024010401203025400_ref6","doi-asserted-by":"crossref","first-page":"6391","DOI":"10.1021\/acs.chemrev.5b00623","article-title":"The role of protein loops and linkers in conformational dynamics and allostery","volume":"116","author":"Papaleo","year":"2016","journal-title":"Chem Rev"},{"key":"2024010401203025400_ref7","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1016\/j.sbi.2010.09.005","article-title":"A role for flexible loops in enzyme catalysis","volume":"20","author":"Malabanan","year":"2010","journal-title":"Curr Opin Struct Biol"},{"key":"2024010401203025400_ref8","doi-asserted-by":"crossref","first-page":"12800","DOI":"10.1021\/acscatal.2c02258","article-title":"Flexibility regulation of loops surrounding the tunnel entrance in cytochrome P450 enhanced substrate access substantially","volume":"12","author":"Li","year":"2022","journal-title":"ACS Catalysis"},{"key":"2024010401203025400_ref9","doi-asserted-by":"crossref","first-page":"15889","DOI":"10.1021\/jacs.8b09378","article-title":"Loop motion in triosephosphate isomerase is not a simple open and shut case","volume":"140","author":"Liao","year":"2018","journal-title":"J Am Chem Soc"},{"key":"2024010401203025400_ref10","doi-asserted-by":"crossref","first-page":"7162","DOI":"10.1021\/acscatal.0c01623","article-title":"Methionine-rich loop of multicopper oxidase McoA follows open-to-close transitions with a role in enzyme catalysis","volume":"10","author":"Borges","year":"2020","journal-title":"ACS Catalysis"},{"key":"2024010401203025400_ref11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.physa.2018.12.039","article-title":"Investigating large-amplitude protein loop motions as extreme events using recurrence interval analysis","volume":"520","author":"Karain","year":"2019","journal-title":"Physica A Stat Mech Appl"},{"key":"2024010401203025400_ref12","first-page":"5126","article-title":"A defective flexible loop contributes to the processing and gating defects of the predominant cystic fibrosis-causing mutation","volume-title":"FASEB J","author":"Chen","year":"2019"},{"key":"2024010401203025400_ref13","doi-asserted-by":"crossref","first-page":"3830","DOI":"10.1021\/jacs.0c11806","article-title":"Loop dynamics and enzyme catalysis in protein tyrosine phosphatases","volume":"143","author":"Crean","year":"2021","journal-title":"J Am Chem Soc"},{"key":"2024010401203025400_ref14","doi-asserted-by":"crossref","first-page":"4368","DOI":"10.1021\/acs.jpclett.1c00778","article-title":"Protein loop conformational free energy changes via an alchemical path without reaction coordinates","volume":"12","author":"Arasteh","year":"2021","journal-title":"J Phys Chem Lett"},{"key":"2024010401203025400_ref15","first-page":"222","article-title":"Antibody H3 structure prediction, computational and structural","volume":"15","author":"Marks","year":"2017","journal-title":"Biotechnol J"},{"key":"2024010401203025400_ref16","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1515\/hsz-2018-0348","article-title":"Computational design of structured loops for new protein functions","volume":"400","author":"Kundert","year":"2019","journal-title":"Biol Chem"},{"key":"2024010401203025400_ref17","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref18","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1110\/ps.9.9.1753","article-title":"Modeling of loops in protein structures","volume":"9","author":"Fiser","year":"2000","journal-title":"Protein Sci"},{"key":"2024010401203025400_ref19","doi-asserted-by":"crossref","first-page":"2920","DOI":"10.1002\/prot.23129","article-title":"Progress in super long loop prediction","volume":"79","author":"Zhao","year":"2011","journal-title":"Proteins"},{"key":"2024010401203025400_ref20","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/0022-2836(92)90553-V","article-title":"Taxonomy and conformational analysis of loops in proteins","volume":"224","author":"Ring","year":"1992","journal-title":"J Mol Biol"},{"key":"2024010401203025400_ref21","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1006\/jmbi.1996.0851","article-title":"Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling","volume":"267","author":"Rufino","year":"1997","journal-title":"J Mol Biol"},{"key":"2024010401203025400_ref22","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1471-2148-5-10","article-title":"Structural similarity of loops in protein families: toward the understanding of protein evolution","volume":"5","author":"Panchenko","year":"2005","journal-title":"BMC Evol Biol"},{"key":"2024010401203025400_ref23","doi-asserted-by":"crossref","first-page":"W390","DOI":"10.1093\/nar\/gkw297","article-title":"SL2: an interactive webtool for modeling of missing segments in proteins","volume":"44","author":"Ismer","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"2024010401203025400_ref24","doi-asserted-by":"crossref","first-page":"985","DOI":"10.3390\/biom12070985","article-title":"Benchmarking the accuracy of AlphaFold 2 in loop structure prediction","volume":"12","author":"Stevens","year":"2022","journal-title":"Biomolecules"},{"key":"2024010401203025400_ref25","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1002\/prot.24604","article-title":"Automated antibody structure prediction using Accelrys tools: results and best practices","volume":"82","author":"Fasnacht","year":"2014","journal-title":"Proteins"},{"key":"2024010401203025400_ref26","first-page":"e202200449","article-title":"Exploiting the innate plasticity of the programmed cell death-1 (PD1) receptor to design pembrolizumab H3 loop mimics**","volume-title":"ChemBioChem","author":"Richaud","year":"2022"},{"key":"2024010401203025400_ref27","doi-asserted-by":"crossref","first-page":"W423","DOI":"10.1093\/nar\/gkz403","article-title":"DaReUS-loop: a web server to model multiple loops in homology models","volume":"47","author":"Karami","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref28","doi-asserted-by":"crossref","first-page":"3013","DOI":"10.1093\/bioinformatics\/btz026","article-title":"KORP: knowledge-based 6D potential for fast protein and loop modeling","volume":"35","author":"L\u00f3pez-Blanco","year":"2019","journal-title":"Bioinformatics"},{"key":"2024010401203025400_ref29","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1002\/prot.10613","article-title":"A hierarchical approach to all-atom protein loop prediction","volume":"55","author":"Jacobson","year":"2004","journal-title":"Proteins"},{"key":"2024010401203025400_ref30","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1016\/S0022-2836(02)00470-9","article-title":"On the role of the crystal environment in determining protein side-chain conformations","volume":"320","author":"Jacobson","year":"2002","journal-title":"J Mol Biol"},{"key":"2024010401203025400_ref31","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1002\/prot.22658","article-title":"FREAD revisited: accurate loop structure prediction using a database search algorithm","volume":"78","author":"Choi","year":"2010","journal-title":"Proteins"},{"key":"2024010401203025400_ref32","first-page":"H3A 2R7","author":"Molecular Operating Environment (MOE), 2018.01","year":"2018"},{"key":"2024010401203025400_ref33","doi-asserted-by":"crossref","first-page":"3767","DOI":"10.1093\/bioinformatics\/btv438","article-title":"LoopIng: a template-based tool for predicting the structure of protein loops","volume":"31","author":"Messih","year":"2015","journal-title":"Bioinformatics"},{"key":"2024010401203025400_ref34","doi-asserted-by":"crossref","first-page":"1935","DOI":"10.1093\/bioinformatics\/btu129","article-title":"Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design","volume":"30","author":"Bonet","year":"2014","journal-title":"Bioinformatics"},{"key":"2024010401203025400_ref35","doi-asserted-by":"crossref","first-page":"W173","DOI":"10.1093\/nar\/gkl113","article-title":"ArchPRED: a template based loop structure prediction server","volume":"34","author":"Fernandez-Fuentes","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref36","doi-asserted-by":"crossref","first-page":"W571","DOI":"10.1093\/nar\/gkp338","article-title":"SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins","volume":"37","author":"Hildebrand","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref37","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev.biophys.29.1.291","article-title":"Comparative protein structure modeling of genes and genomes","volume":"29","author":"Marti-Renom","year":"2000","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"2024010401203025400_ref38","doi-asserted-by":"crossref","first-page":"1656","DOI":"10.1021\/ci200143u","article-title":"Sampling multiple scoring functions can improve protein loop structure prediction accuracy","volume":"51","author":"Li","year":"2011","journal-title":"J Chem Inf Model"},{"key":"2024010401203025400_ref39","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1110\/ps.0242703","article-title":"Cyclic coordinate descent: a robotics algorithm for protein loop closure","volume":"12","author":"Canutescu","year":"2003","journal-title":"Protein Sci"},{"key":"2024010401203025400_ref40","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1038\/nmeth0809-551","article-title":"Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling","volume":"6","author":"Mandell","year":"2009","journal-title":"Nat Methods"},{"key":"2024010401203025400_ref41","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1002\/qua.20751","article-title":"Resultanta and loop closure","volume":"106","author":"Coutsias","year":"2006","journal-title":"Int J Quantum Chem"},{"key":"2024010401203025400_ref42","doi-asserted-by":"crossref","first-page":"e63090","DOI":"10.1371\/journal.pone.0063090","article-title":"Improvements to robotics-inspired conformational sampling in rosetta","volume":"8","author":"Stein","year":"2013","journal-title":"PloS One"},{"key":"2024010401203025400_ref43","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1002\/jcc.10416","article-title":"A kinematic view of loop closure","volume":"25","author":"Coutsias","year":"2004","journal-title":"J Comput Chem"},{"key":"2024010401203025400_ref44","doi-asserted-by":"crossref","first-page":"e113811","DOI":"10.1371\/journal.pone.0113811","article-title":"Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments","volume":"9","author":"Park","year":"2014","journal-title":"PloS One"},{"key":"2024010401203025400_ref45","doi-asserted-by":"crossref","first-page":"2500","DOI":"10.1093\/bioinformatics\/btg362","article-title":"ModLoop: automated modeling of loops in protein structures","volume":"19","author":"Fiser","year":"2003","journal-title":"Bioinformatics"},{"key":"2024010401203025400_ref46","doi-asserted-by":"crossref","first-page":"W210","DOI":"10.1093\/nar\/gkr352","article-title":"The FALC-loop web server for protein loop modeling","volume":"39","author":"Ko","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref47","doi-asserted-by":"crossref","first-page":"1821","DOI":"10.1021\/ct300977f","article-title":"Random coordinate descent with spinor-matrices and geometric filters for efficient loop closure","volume":"9","author":"Chys","year":"2013","journal-title":"J Chem Theory Comput"},{"key":"2024010401203025400_ref48","doi-asserted-by":"crossref","first-page":"1820","DOI":"10.1021\/ct300131p","article-title":"Protein loop modeling with optimized backbone potential functions","volume":"8","author":"Liang","year":"2012","journal-title":"J Chem Theory Comput"},{"key":"2024010401203025400_ref49","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1002\/jcc.23509","article-title":"LEAP: highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains","volume":"35","author":"Liang","year":"2014","journal-title":"J Comput Chem"},{"key":"2024010401203025400_ref50","doi-asserted-by":"crossref","first-page":"3158","DOI":"10.1093\/bioinformatics\/btt560","article-title":"Optimized atomic statistical potentials: assessment of protein interfaces and loops","volume":"29","author":"Dong","year":"2013","journal-title":"Bioinformatics"},{"key":"2024010401203025400_ref51","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1110\/ps.37601","article-title":"CODA: a combined algorithm for predicting the structurally variable regions of protein models","volume":"10","author":"Deane","year":"2001","journal-title":"Protein Sci"},{"key":"2024010401203025400_ref52","doi-asserted-by":"crossref","first-page":"1346","DOI":"10.1093\/bioinformatics\/btw823","article-title":"Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction","volume":"33","author":"Marks","year":"2017","journal-title":"Bioinformatics"},{"key":"2024010401203025400_ref53","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.aiopen.2022.10.001","article-title":"A survey of transformers","volume":"3","author":"Lin","year":"2022","journal-title":"AI Open"},{"key":"2024010401203025400_ref54","first-page":"596","article-title":"New deep learning methods for protein loop modeling","volume-title":"IEEE\/ACM Trans Comput Biol Bioinform","author":"Nguyen","year":"2019"},{"key":"2024010401203025400_ref55","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1162\/neco.1989.1.4.541","article-title":"Backpropagation applied to handwritten zip code recognition","volume":"1","author":"LeCun","year":"1989","journal-title":"Neural Comput"},{"key":"2024010401203025400_ref56","first-page":"84","article-title":"ImageNet classification with deep convolutional neural networks","volume-title":"Advances in Neural Information Processing Systems","author":"Krizhevsky","year":"2017"},{"key":"2024010401203025400_ref57","article-title":"DeepID-net: multi-stage and deformable deep convolutional neural networks for object detection","author":"Ouyang","year":"2014","journal-title":"arXiv:4093505"},{"key":"2024010401203025400_ref58","first-page":"834","volume-title":"Part-Based R-CNNs for Fine-Grained Category Detection","author":"Zhang","year":"2014"},{"key":"2024010401203025400_ref59","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1093\/bioinformatics\/btz684","article-title":"A reinforcement-learning-based approach to enhance exhaustive protein loop sampling","volume":"36","author":"Barozet","year":"2020","journal-title":"Bioinformatics"},{"key":"2024010401203025400_ref60","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2024010401203025400_ref61","first-page":"871","article-title":"Accurate prediction of protein structures and interactions using a three-track neural network","volume-title":"Science","author":"Baek","year":"2021"},{"key":"2024010401203025400_ref62","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref63","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/s41586-021-03828-1","article-title":"Highly accurate protein structure prediction for the human proteome","volume":"596","author":"Tunyasuvunakool","year":"2021","journal-title":"Nature"},{"key":"2024010401203025400_ref64","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac308","article-title":"Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors","volume":"23","author":"Lee","year":"2022","journal-title":"Brief Bioinform"},{"key":"2024010401203025400_ref65","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac152","article-title":"Differential performance of RoseTTAFold in antibody modeling","volume":"23","author":"Liang","year":"2022","journal-title":"Brief Bioinform"},{"key":"2024010401203025400_ref66","doi-asserted-by":"crossref","first-page":"2600","DOI":"10.1002\/pro.5560051223","article-title":"Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction","volume":"5","author":"Donate","year":"1996","journal-title":"Protein Sci"},{"key":"2024010401203025400_ref67","doi-asserted-by":"crossref","first-page":"3428","DOI":"10.1002\/prot.22849","article-title":"Protein loop modeling by using fragment assembly and analytical loop closure","volume":"78","author":"Lee","year":"2010","journal-title":"Proteins"},{"key":"2024010401203025400_ref68","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1093\/protein\/gzg119","article-title":"Loops in proteins (LIP)--a comprehensive loop database for homology modelling","volume":"16","author":"Michalsky","year":"2003","journal-title":"Protein Eng"},{"key":"2024010401203025400_ref69","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/1472-6807-6-15","article-title":"Saturating representation of loop conformational fragments in structure databanks","volume":"6","author":"Fernandez-Fuentes","year":"2006","journal-title":"BMC Struct Biol"},{"key":"2024010401203025400_ref70","doi-asserted-by":"crossref","first-page":"D315","DOI":"10.1093\/nar\/gkt1189","article-title":"ArchDB 2014: structural classification of loops in proteins","volume":"42","author":"Bonet","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref71","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1002\/jcc.26796","article-title":"Distance geometry and protein loop modeling","volume":"43","author":"Labiak","year":"2022","journal-title":"J Comput Chem"},{"key":"2024010401203025400_ref72","doi-asserted-by":"crossref","first-page":"W94","DOI":"10.1093\/nar\/gki402","article-title":"PISCES: recent improvements to a PDB sequence culling server","volume":"33","author":"Wang","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref73","doi-asserted-by":"crossref","first-page":"D364","DOI":"10.1093\/nar\/gku1028","article-title":"A series of PDB-related databanks for everyday needs","volume":"43","author":"Touw","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref74","doi-asserted-by":"crossref","first-page":"D376","DOI":"10.1093\/nar\/gkz1064","article-title":"The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures","volume":"48","author":"Andreeva","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref75","doi-asserted-by":"crossref","first-page":"D310","DOI":"10.1093\/nar\/gkt1242","article-title":"SCOP2 prototype: a new approach to protein structure mining","volume":"42","author":"Andreeva","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"Suppl 1","key":"2024010401203025400_ref76","article-title":"Critical assessment of methods of protein structure prediction (CASP)-round XII","volume":"86","author":"Moult","year":"2018","journal-title":"Proteins"},{"key":"2024010401203025400_ref77","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1002\/prot.25823","article-title":"Critical assessment of methods of protein structure prediction (CASP)-round XIII","volume":"87","author":"Kryshtafovych","year":"2019","journal-title":"Proteins"},{"key":"2024010401203025400_ref78","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/j.jmb.2007.07.050","article-title":"Protein-protein docking with backbone flexibility","volume":"373","author":"Wang","year":"2007","journal-title":"J Mol Biol"},{"key":"2024010401203025400_ref79","doi-asserted-by":"crossref","first-page":"e23294","DOI":"10.1371\/journal.pone.0023294","article-title":"Generalized fragment picking in Rosetta: design, protocols and applications","volume":"6","author":"Gront","year":"2011","journal-title":"PloS One"},{"key":"2024010401203025400_ref80","doi-asserted-by":"crossref","first-page":"e24109","DOI":"10.1371\/journal.pone.0024109","article-title":"RosettaRemodel: a generalized framework for flexible backbone protein design","volume":"6","author":"Huang","year":"2011","journal-title":"PloS One"},{"key":"2024010401203025400_ref81","first-page":"430","author":"Yang","year":"2010"},{"key":"2024010401203025400_ref82","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1107\/S0567739478001680","article-title":"A discussion of the solution for the best rotation to relate two sets of vectors","volume":"34","author":"Kabsch","year":"1978","journal-title":"Acta Crystallogr A"},{"key":"2024010401203025400_ref83","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1107\/S0567739476001873","article-title":"A solution for the best rotation to relate two sets of vectors","volume":"32","author":"Kabsch","year":"1976","journal-title":"Acta Crystallogr A"},{"key":"2024010401203025400_ref84","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.1093\/nar\/gki524","article-title":"TM-align: a protein structure alignment algorithm based on the TM-score","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2024010401203025400_ref85","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1006\/jmbi.1999.2826","article-title":"New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification","volume":"289","author":"Wojcik","year":"1999","journal-title":"J Mol Biol"},{"key":"2024010401203025400_ref86","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1002\/prot.10376","article-title":"The nature of the turn in omega loops of proteins","volume":"51","author":"Pal","year":"2003","journal-title":"Proteins"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/1\/bbad486\/54943752\/bbad486.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/1\/bbad486\/54943752\/bbad486.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,4]],"date-time":"2024-01-04T01:21:22Z","timestamp":1704331282000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbad486\/7505239"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,22]]},"references-count":86,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,11,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbad486","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,1,1]]},"published":{"date-parts":[[2023,11,22]]},"article-number":"bbad486"}}