Protein target highlights in CASP15: Analysis of models by structure providers
We present an in‐depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall abili...
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| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2023-12, Vol.91 (12), p.1571-1599 |
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| creator | Alexander, Leila T. Durairaj, Janani Kryshtafovych, Andriy Abriata, Luciano A. Bayo, Yusupha Bhabha, Gira Breyton, Cécile Caulton, Simon G. Chen, James Degroux, Séraphine Ekiert, Damian C. Erlandsen, Benedikte S. Freddolino, Peter L. Gilzer, Dominic Greening, Chris Grimes, Jonathan M. Grinter, Rhys Gurusaran, Manickam Hartmann, Marcus D. Hitchman, Charlie J. Keown, Jeremy R. Kropp, Ashleigh Kursula, Petri Lovering, Andrew L. Lemaitre, Bruno Lia, Andrea Liu, Shiheng Logotheti, Maria Lu, Shuze Markússon, Sigurbjörn Miller, Mitchell D. Minasov, George Niemann, Hartmut H. Opazo, Felipe Phillips, George N. Davies, Owen R. Rommelaere, Samuel Rosas‐Lemus, Monica Roversi, Pietro Satchell, Karla Smith, Nathan Wilson, Mark A. Wu, Kuan‐Lin Xia, Xian Xiao, Han Zhang, Wenhua Zhou, Z. Hong Fidelis, Krzysztof Topf, Maya Moult, John Schwede, Torsten |
| description | We present an in‐depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three‐dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology. |
| doi_str_mv | 10.1002/prot.26545 |
| format | Article |
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Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.</description><identifier>ISSN: 0887-3585</identifier><identifier>ISSN: 1097-0134</identifier><identifier>EISSN: 1097-0134</identifier><identifier>DOI: 10.1002/prot.26545</identifier><identifier>PMID: 37493353</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley & Sons, Inc</publisher><subject>CASP ; Computational Biology - methods ; cryo‐EM ; Life Sciences ; Models, Molecular ; Molecular biology ; Protein Conformation ; Protein structure ; protein structure prediction ; Proteins ; Proteins - chemistry ; X‐ray crystallography</subject><ispartof>Proteins, structure, function, and bioinformatics, 2023-12, Vol.91 (12), p.1571-1599</ispartof><rights>2023 The Authors. published by Wiley Periodicals LLC.</rights><rights>2023 The Authors. 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Hong ; Fidelis, Krzysztof ; Topf, Maya ; Moult, John ; Schwede, Torsten</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4835-9acb5a2bd630858c8f12c876d7f50d8c2f15adda19628c33a5778820d0145c073</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>CASP</topic><topic>Computational Biology - methods</topic><topic>cryo‐EM</topic><topic>Life Sciences</topic><topic>Models, Molecular</topic><topic>Molecular biology</topic><topic>Protein Conformation</topic><topic>Protein structure</topic><topic>protein structure prediction</topic><topic>Proteins</topic><topic>Proteins - chemistry</topic><topic>X‐ray crystallography</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Alexander, Leila T.</creatorcontrib><creatorcontrib>Durairaj, Janani</creatorcontrib><creatorcontrib>Kryshtafovych, Andriy</creatorcontrib><creatorcontrib>Abriata, Luciano A.</creatorcontrib><creatorcontrib>Bayo, Yusupha</creatorcontrib><creatorcontrib>Bhabha, Gira</creatorcontrib><creatorcontrib>Breyton, Cécile</creatorcontrib><creatorcontrib>Caulton, Simon G.</creatorcontrib><creatorcontrib>Chen, James</creatorcontrib><creatorcontrib>Degroux, Séraphine</creatorcontrib><creatorcontrib>Ekiert, Damian C.</creatorcontrib><creatorcontrib>Erlandsen, Benedikte S.</creatorcontrib><creatorcontrib>Freddolino, Peter L.</creatorcontrib><creatorcontrib>Gilzer, Dominic</creatorcontrib><creatorcontrib>Greening, Chris</creatorcontrib><creatorcontrib>Grimes, Jonathan M.</creatorcontrib><creatorcontrib>Grinter, Rhys</creatorcontrib><creatorcontrib>Gurusaran, Manickam</creatorcontrib><creatorcontrib>Hartmann, Marcus D.</creatorcontrib><creatorcontrib>Hitchman, Charlie J.</creatorcontrib><creatorcontrib>Keown, Jeremy R.</creatorcontrib><creatorcontrib>Kropp, Ashleigh</creatorcontrib><creatorcontrib>Kursula, Petri</creatorcontrib><creatorcontrib>Lovering, Andrew L.</creatorcontrib><creatorcontrib>Lemaitre, Bruno</creatorcontrib><creatorcontrib>Lia, Andrea</creatorcontrib><creatorcontrib>Liu, Shiheng</creatorcontrib><creatorcontrib>Logotheti, Maria</creatorcontrib><creatorcontrib>Lu, Shuze</creatorcontrib><creatorcontrib>Markússon, Sigurbjörn</creatorcontrib><creatorcontrib>Miller, Mitchell D.</creatorcontrib><creatorcontrib>Minasov, George</creatorcontrib><creatorcontrib>Niemann, Hartmut H.</creatorcontrib><creatorcontrib>Opazo, Felipe</creatorcontrib><creatorcontrib>Phillips, George N.</creatorcontrib><creatorcontrib>Davies, Owen R.</creatorcontrib><creatorcontrib>Rommelaere, Samuel</creatorcontrib><creatorcontrib>Rosas‐Lemus, Monica</creatorcontrib><creatorcontrib>Roversi, Pietro</creatorcontrib><creatorcontrib>Satchell, Karla</creatorcontrib><creatorcontrib>Smith, Nathan</creatorcontrib><creatorcontrib>Wilson, Mark A.</creatorcontrib><creatorcontrib>Wu, Kuan‐Lin</creatorcontrib><creatorcontrib>Xia, Xian</creatorcontrib><creatorcontrib>Xiao, Han</creatorcontrib><creatorcontrib>Zhang, Wenhua</creatorcontrib><creatorcontrib>Zhou, Z. Hong</creatorcontrib><creatorcontrib>Fidelis, Krzysztof</creatorcontrib><creatorcontrib>Topf, Maya</creatorcontrib><creatorcontrib>Moult, John</creatorcontrib><creatorcontrib>Schwede, Torsten</creatorcontrib><collection>Wiley Online Library Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Proteins, structure, function, and bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Alexander, Leila T.</au><au>Durairaj, Janani</au><au>Kryshtafovych, Andriy</au><au>Abriata, Luciano A.</au><au>Bayo, Yusupha</au><au>Bhabha, Gira</au><au>Breyton, Cécile</au><au>Caulton, Simon G.</au><au>Chen, James</au><au>Degroux, Séraphine</au><au>Ekiert, Damian C.</au><au>Erlandsen, Benedikte S.</au><au>Freddolino, Peter L.</au><au>Gilzer, Dominic</au><au>Greening, Chris</au><au>Grimes, Jonathan M.</au><au>Grinter, Rhys</au><au>Gurusaran, Manickam</au><au>Hartmann, Marcus D.</au><au>Hitchman, Charlie J.</au><au>Keown, Jeremy R.</au><au>Kropp, Ashleigh</au><au>Kursula, Petri</au><au>Lovering, Andrew L.</au><au>Lemaitre, Bruno</au><au>Lia, Andrea</au><au>Liu, Shiheng</au><au>Logotheti, Maria</au><au>Lu, Shuze</au><au>Markússon, Sigurbjörn</au><au>Miller, Mitchell D.</au><au>Minasov, George</au><au>Niemann, Hartmut H.</au><au>Opazo, Felipe</au><au>Phillips, George N.</au><au>Davies, Owen R.</au><au>Rommelaere, Samuel</au><au>Rosas‐Lemus, Monica</au><au>Roversi, Pietro</au><au>Satchell, Karla</au><au>Smith, Nathan</au><au>Wilson, Mark A.</au><au>Wu, Kuan‐Lin</au><au>Xia, Xian</au><au>Xiao, Han</au><au>Zhang, Wenhua</au><au>Zhou, Z. Hong</au><au>Fidelis, Krzysztof</au><au>Topf, Maya</au><au>Moult, John</au><au>Schwede, Torsten</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Protein target highlights in CASP15: Analysis of models by structure providers</atitle><jtitle>Proteins, structure, function, and bioinformatics</jtitle><addtitle>Proteins</addtitle><date>2023-12</date><risdate>2023</risdate><volume>91</volume><issue>12</issue><spage>1571</spage><epage>1599</epage><pages>1571-1599</pages><issn>0887-3585</issn><issn>1097-0134</issn><eissn>1097-0134</eissn><abstract>We present an in‐depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three‐dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. 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| fulltext | fulltext |
| identifier | ISSN: 0887-3585 |
| ispartof | Proteins, structure, function, and bioinformatics, 2023-12, Vol.91 (12), p.1571-1599 |
| issn | 0887-3585 1097-0134 1097-0134 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10792529 |
| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | CASP Computational Biology - methods cryo‐EM Life Sciences Models, Molecular Molecular biology Protein Conformation Protein structure protein structure prediction Proteins Proteins - chemistry X‐ray crystallography |
| title | Protein target highlights in CASP15: Analysis of models by structure providers |
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