ArticleProteins2021
Target highlights in CASP14: Analysis of models by structure providers.
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Article in Proteins, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18citing papers in PubMed
2.4field-weighted citation impact, top 10% of its field
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Who cites it
18 citing papers in PubMed, 38 citations in OpenAlex.
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- AlphaFold-guided molecular replacement for solving challenging crystal structures.Acta crystallographica. Section D, Structural biology · 2025Article
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- RNA target highlights in CASP15: Evaluation of predicted models by structure providers.Proteins · 2023Article
- More than just pattern recognition: Prediction of uncommon protein structure features by AI methods.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Deciphering Bacteriophage T5 Host Recognition Mechanism and Infection Trigger.Journal of virology · 2023Article
- Structural basis of bacteriophage T5 infection trigger andScience advances · 2023Article
- Exploring AlphaFold2's Performance on Predicting Amino Acid Side-Chain Conformations and Its Utility in Crystal Structure Determination of B318L Protein.International journal of molecular sciences · 2023Article
- eEF2K Inhibitor Design: The Progression of Exemplary Structure-Based Drug Design.Molecules (Basel, Switzerland) · 2023Review
- RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.Nucleic acids research · 2023Article
- Visualizing and accessing correlated SAXS data sets with Similarity Maps and Simple Scattering web resources.Methods in enzymology · 2023Article
- Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.Biomolecules · 2022Review
- Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps.BMC bioinformatics · 2022Article
- The accuracy of protein structures in solution determined by AlphaFold and NMR.Structure (London, England : 1993) · 2022Article
- Snowflake: A deep learning-based human leukocyte antigen matching algorithm considering allele-specific surface accessibility.Frontiers in immunology · 2022Article
- Article
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Authors and funding
38 authors at 20 institutions in 12 countries.
Leila T AlexanderBiozentrum, University of Basel, Basel, Switzerland.ORCID 0000-0002-7594-2110
Rosalba LeporeBarcelona Supercomputing Center (BSC), Barcelona, Spain.ORCID 0000-0002-9481-2557
Andriy KryshtafovychGenome Center, University of California, Davis, Davis, California, USA.ORCID 0000-0001-5066-7178
Athanassios AdamopoulosOncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Markus AlahuhtaBioscience Center, National Renewable Energy Laboratory, Golden, Colorado, USA.
Ann M ArvinDepartment of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.
Yannick J BombleBioscience Center, National Renewable Energy Laboratory, Golden, Colorado, USA.
Bettina BöttcherBiocenter and Rudolf Virchow Center, Julius-Maximilians Universität Würzburg, Würzburg, Germany.
Cécile BreytonUniv. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology, Grenoble, France.
Valerio ChiariniProgram in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.ORCID 0000-0002-3822-3336
Naga Babu ChinnamDepartment of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA.
Wah ChiuMicrobiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
Krzysztof FidelisGenome Center, University of California, Davis, Davis, California, USA.ORCID 0000-0002-8061-412X
Rhys GrinterInfection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.ORCID 0000-0002-8195-5348
Gagan D GuptaRadiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India.
Marcus D HartmannDepartment of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.ORCID 0000-0001-6937-5677
Christopher S HayesDepartment of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA.ORCID 0000-0002-2216-6445
Tatjana HeidebrechtOncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Andrea IlariInstitute of Molecular Biology and Pathology of the National Research Council of Italy (CNR), Rome, Italy.ORCID 0000-0002-7754-399X
Andrzej JoachimiakCenter for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
Youngchang KimCenter for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
Romain LinaresUniv. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology, Grenoble, France.
Andrew L LoveringSchool of Biosciences, University of Birmingham, Birmingham, UK.
Vladimir V LuninBioscience Center, National Renewable Energy Laboratory, Golden, Colorado, USA.
Andrei N LupasDepartment of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
Cihan MakbulBiocenter and Rudolf Virchow Center, Julius-Maximilians Universität Würzburg, Würzburg, Germany.
Karolina MichalskaCenter for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
John MoultDepartment of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA.ORCID 0000-0002-3012-2282
Prasun K MukherjeeNuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India.
William Sam NuttCenter for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
Stefan L OliverDepartment of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.ORCID 0000-0002-4614-7310
Anastassis PerrakisOncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Lucy StolsCenter for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
John A TainerDepartment of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA.
Maya TopfInstitute of Structural and Molecular Biology, Birkbeck, University College London, London, UK.
Susan E TsutakawaMolecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA.ORCID 0000-0002-4918-4571
Mauricio Valdivia-DelgadoSchool of Biosciences, University of Birmingham, Birmingham, UK.
Torsten SchwedeBiozentrum, University of Basel, Basel, Switzerland.ORCID 0000-0003-2715-335X
Argonne National Laboratory · USNational Laboratory of the Rockies · USThe Netherlands Cancer Institute · NLBhabha Atomic Research Centre · INCentre National de la Recherche Scientifique · FRMax Planck Institute for Developmental Biology · DESIB Swiss Institute of Bioinformatics · CHStanford University · USThe University of Texas MD Anderson Cancer Center · USUniversity of Birmingham · GBUniversity of California, Davis · USUniversity of Würzburg · DEBarcelona Supercomputing Center · ESDiscovery Institute · USInstitute of Molecular Biology and Pathology · ITInstitute of Structural and Molecular Biology · GBLawrence Berkeley National Laboratory · USResearch Institute for Bioscience and Biotechnology · NPSLAC National Accelerator Laboratory · USUniversity of California, Santa Barbara · US
Funding
Transcription-Coupled & Replication-Associated Excision RepairP01CA092584 · NCI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI John A. Tainer · 2001 to 2026
$89.6M3 D ELECTRON MICROSCOPY OF MACROMOLECULES (5P41RR002250-27)P41GM103832 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2012 to 2019
$15.1MUnified Data Resource for Large Complexes Determined by Cryo-Electron MicroscopyR01GM079429 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2007 to 2021
$11.6MProspective analysis to determine model accuracy performance and boundaries in the post-AlphaFold2 environmentR01GM100482 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI FIDELIS, KRZYSZTOF A · 2012 to 2025
$11.1MResource for Biocomputing Visualization and InformaticsP41GM103311 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2012 to 2017
$8.2MMesoscale and Nanoscale Technologies Integrated by Structures for DNA Repair Complexes (MANTIS-DRC)R35CA220430 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI John A. Tainer · 2018 to 2026
$7.6MVaricella-Zoster Virus: T Cell/Skin Tropisms &ImmunityR01AI020459 · NIAID · STANFORD UNIVERSITY · PI OLIVER, STEFAN LYNE · 1985 to 2023
$6.4MMolecular Mechanisms of anti-bacterial contact-dependent growth inhibition (CDI)R01GM117930 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI HAYES, CHRISTOPHER S. · 2016 to 2023
$3.0MAcquisition of a 300 kV Electron Microscope for Structural BiologyS10OD021600 · OD · STANFORD UNIVERSITY · PI CHIU, WAH · 2016 to 2016
$2.0MVaricella-Zoster Virus: T Cell/Skin Tropisms & ImmunityR37AI020459 · NIAID · STANFORD UNIVERSITY · PI ARVIN, ANN · 2016 to 2020
$2.0MVaricella zoster virus: molecular controls of cell fusion-dependent pathogenesisR01AI102546 · NIAID · STANFORD UNIVERSITY · PI ARVIN, ANN · 2012 to 2016
$1.9MTowards Accurate Protein Structure Predictions with SAXS Technology (TAPESTRY)R01GM137021 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI TSUTAKAWA, SUSAN EMIKO · 2020 to 2023
$1.6MNCI NIH HHS P01 CA092584NCI NIH HHS R35 CA220430NIAID NIH HHS HHSN272201700060CNIAID NIH HHS R01 AI020459NIAID NIH HHS R01 AI102546NIAID NIH HHS R37 AI020459NIGMS NIH HHS P41 GM103311NIGMS NIH HHS P41 GM103832NIGMS NIH HHS R01 GM079429NIGMS NIH HHS R01 GM100482NIGMS NIH HHS R01 GM117373NIGMS NIH HHS R01 GM117930NIGMS NIH HHS R01 GM137021NIH HHS S10 OD021600Wellcome Trust 209437/Z/17/Z
Abstract
The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.
Indexed as
Models, MolecularProtein ConformationSoftwareAmino Acid SequenceComputational BiologyCryoelectron MicroscopyCrystallography, X-RayProteinsSequence Analysis, ProteinProteinsCASPcommunity-wide experimentcryo-EMprotein structure predictionX-ray crystallography
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