Proteins-Structure Function and Bioinformatics最新文献_第7页

Understanding the Role of RING-Between-RING E3 Ligase of the Human Malaria Parasite. 了解人疟原虫环间E3连接酶的作用。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-09-01 Epub Date: 2025-03-04 DOI: 10.1002/prot.26813

Varsha Kumari, Seema Vidyarthi, Aradhya Tripathi, Nirupa Chaurasia, Niharika Rai, Richa Shukla, Shagufa Nisrat Noorie, Girdhar Bhati, Simmi Anjum, Mohammad Anas, Shakil Ahmed, Niti Kumar

{"title":"Understanding the Role of RING-Between-RING E3 Ligase of the Human Malaria Parasite.","authors":"Varsha Kumari, Seema Vidyarthi, Aradhya Tripathi, Nirupa Chaurasia, Niharika Rai, Richa Shukla, Shagufa Nisrat Noorie, Girdhar Bhati, Simmi Anjum, Mohammad Anas, Shakil Ahmed, Niti Kumar","doi":"10.1002/prot.26813","DOIUrl":"10.1002/prot.26813","url":null,"abstract":"E3 ligases constitute an important component of proteostasis machinery, which plays a critical role in the survival of malaria parasites through post-translational modifications of their protein substrates. In contrast to humans, parasite E3 ligases have not been extensively studied. Here, we characterize a unique Plasmodium E3 ligase that has both RING and HECT-like features with zinc-coordinating domains. Plasmodium encodes a single RING-between-RING (RBR) E3 ligase that has evolutionarily diverged from human and other intracellular parasites. This RBR-E3 ligase is expressed throughout the erythrocytic phase of the P. falciparum lifecycle. Immunoprecipitation experiments showed that Pf RBR-E3 ligase catalyzes K6, K11, K48, and K63 mediated polyubiquitination, hinting towards its probable biological roles (DNA repair, proteasomal degradation, mitochondrial quality control). We observed that Pf RBR-E3 ligase interacts with UBCH5 and UBC13 family of E2-conjugating enzymes. Through mutational analysis in Pf RBR-E3 ligase, we identified residues in RING1 and RING2 domains that are critical for ubiquitination activity and its protein stability. Pf RBR-E3 ligase exhibits differences in immunofluorescence profile upon exposure of the parasite to different genotoxic (MMS) and proteotoxic (MG132, FCCP and artemisinin derivative) stress. Our study opens up avenues for exploring the client substrates of Pf RBR-E3 ligase and using this knowledge to design substrate-specific protein degradation-based alternative intervention strategies for malaria.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1436-1450"},"PeriodicalIF":2.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural and Functional Characterization of the 28 kDa Structured Core of BmSA1, the Major Surface Antigen of Babesia Microti. 微小巴贝斯虫主要表面抗原BmSA1 28 kDa结构核的结构与功能表征

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-09-01 Epub Date: 2025-05-09 DOI: 10.1002/prot.26836

Assia Mouhand, Joana Pissarra, Philippe Barthe, Christian Roumestand, Stéphane Delbecq

{"title":"Structural and Functional Characterization of the 28 kDa Structured Core of BmSA1, the Major Surface Antigen of Babesia Microti.","authors":"Assia Mouhand, Joana Pissarra, Philippe Barthe, Christian Roumestand, Stéphane Delbecq","doi":"10.1002/prot.26836","DOIUrl":"10.1002/prot.26836","url":null,"abstract":"Babesiosis is a tick-borne disease that poses a significant threat to animal health worldwide. In addition, climate change and the risk of human-to-human transmission through blood transfusion have made babesiosis an emerging disease in humans. Babesiosis is caused by the intraerythrocytic development of protozoan parasites from the genus Babesia, which belongs to the apicomplexan phylum that notably includes the more-widely studied causative agent of malaria, Plasmodium falciparum. Of the several hundred Babesia species identified so far, only a few are known to infect humans, with B. microti being the most prevalent and responsible for most of the clinical cases reported to date. There is no licensed vaccine for B. microti, and the development of a reliable serological diagnostic test would contribute to ensuring the safety of blood transfusions. The identification and characterization of parasite surface proteins are important steps in achieving this aim. One such protein is the GPI-anchored Major Surface Antigen BmSA1 (also known as BmGPI12), which is expressed at high levels at the surface of the merozoite. We present here the high-resolution solution structure of the 28 kDa structured core of BmSA1 (∆∆BmSA1) obtained through NMR spectroscopy. The structure of BmSA1 appears unrelated to the previously published structures of the major surface antigens of B. divergens (Bd37) or of B. canis (Bc28.1), which are thought to play a similar role in parasite invasion. We also define the erythrocyte binding function of ∆∆BmSA1, using NMR spectroscopy to map the binding interface. Finally, we used bioinformatic tools to map the potential epitopes of antibodies at the surface of the structured core of BmSA1.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1657-1671"},"PeriodicalIF":2.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12314584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144008018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure and Dynamics of Cannabinoid Binding to the GABA_A Receptor. 大麻素与GABAA受体结合的结构和动力学。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-09-01 Epub Date: 2025-04-24 DOI: 10.1002/prot.26831

Lautaro Damian Alvarez, N R Carina Alves

{"title":"Structure and Dynamics of Cannabinoid Binding to the GABAA Receptor.","authors":"Lautaro Damian Alvarez, N R Carina Alves","doi":"10.1002/prot.26831","DOIUrl":"10.1002/prot.26831","url":null,"abstract":"Research on medical cannabis is progressing, with several cannabinoids emerging as promising compounds for clinical use. The available evidence suggests that cannabinoids may modulate the glycine receptor (GlyR) and GABAA receptor, which are part of the pentameric ligand-gated ion channels (pLGICs) superfamily and facilitate chemical communication in the nervous system. In a previous study, we employed molecular dynamics (MD) simulations to elucidate the dynamics of the GlyR/Δ9-tetrahydrocannabinol (THC) complex and successfully identified a representative binding mode. Given the structural similarity between GlyR and GABAAR, we employed a similar strategy to investigate GABAAR-cannabinoid interactions. We initially assessed the binding mode of THC to GABAAR-α1β2γ2 at the equivalent binding site of the GlyR-that is, on its two α-subunits-as well as the impact of this binding on the channel's dimensions. Our results indicate, first, that the binding modes of THC to GABAAR and GlyR exhibit comparable characteristics and, second, that THC may function as a potentiator of GABA activity due to a significant opening of the channel pore. Additionally, we aimed to reduce the overall computational cost associated with exploring binding modes. To this end, we developed and validated a simplified model comprising a single-monomer system for cannabinoid binding studies. This model proved to be accurate and cost-effective, accelerating the in silico screening process and allowing for the study of GABAAR-cannabinoid binding through docking and MD simulations. Moreover, the analysis of different cannabinoids in this system suggests that cannabigerol (CBG) and cannabichromene (CBC) could act as ligands for GABAAR, opening unexplored avenues for research.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1613-1626"},"PeriodicalIF":2.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144014204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancing Enzyme Commission Number Prediction With Contrastive Learning and Agent Attention. 利用对比学习和智能体注意增强酶委托数预测。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-09-01 Epub Date: 2025-04-02 DOI: 10.1002/prot.26822

Wendi Zhao, Qiaoling Han, Fan Yang, Yue Zhao

{"title":"Enhancing Enzyme Commission Number Prediction With Contrastive Learning and Agent Attention.","authors":"Wendi Zhao, Qiaoling Han, Fan Yang, Yue Zhao","doi":"10.1002/prot.26822","DOIUrl":"10.1002/prot.26822","url":null,"abstract":"The accurate prediction of enzyme function is crucial for elucidating disease mechanisms and identifying drug targets. Nevertheless, existing enzyme commission (EC) number prediction methods are limited by database coverage and the depth of sequence information mining, hindering the efficiency and precision of enzyme function annotation. Therefore, this study introduces ProteEC-CLA (Protein EC number prediction model with Contrastive Learning and Agent Attention). ProteEC-CLA utilizes contrastive learning to construct positive and negative sample pairs, which not only enhances sequence feature extraction but also improves the utilization of unlabeled data. This process helps the model learn the differences in sequence features, thereby enhancing its ability to predict enzyme function. Integrating the pre-trained protein language model ESM2, the model generates informative sequence embeddings for deep functional correlation analysis, significantly enhancing prediction accuracy. With the incorporation of the Agent Attention mechanism, ProteEC-CLA's ability to comprehensively capture local details and global features is enhanced, ensuring high-accuracy predictions on complex sequences. The results demonstrate that ProteEC-CLA performs exceptionally well on two independent and representative datasets. In the standard dataset, it achieves 98.92% accuracy at the EC4 level. In the more challenging clustered split dataset, ProteEC-CLA achieves 93.34% accuracy and an F1-score of 94.72%. With only enzyme sequences as input, ProteEC-CLA can accurately predict EC numbers up to the fourth level, significantly enhancing annotation efficiency and accuracy, which makes it a highly efficient and precise functional annotation tool for enzymology research and applications.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1507-1517"},"PeriodicalIF":2.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Homocysteine Thiolactone Modification of Ribonuclease A: Thermodynamics and Kinetics. 同半胱氨酸硫内酯修饰核糖核酸酶 A：热力学和动力学。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-09-01 Epub Date: 2025-04-04 DOI: 10.1002/prot.26824

Kabira Sabnam, Swagata Dasgupta

{"title":"Homocysteine Thiolactone Modification of Ribonuclease A: Thermodynamics and Kinetics.","authors":"Kabira Sabnam, Swagata Dasgupta","doi":"10.1002/prot.26824","DOIUrl":"10.1002/prot.26824","url":null,"abstract":"Homocysteine thiolactone is a metabolite associated with various diseases at elevated levels in humans. Lysine residues in proteins are modified through N-homocysteinylation and homocysteinylated proteins are prone to form dimers and oligomers through disulfide cross-linkages. This study investigates the effects of N-homocysteinylation on Ribonuclease A (RNase A). The formation of dimers and higher oligomers in RNase A have been confirmed by SDS-PAGE and MALDI-ToF. Agarose-gel assays revealed an altered ribonucleolytic activity due to Lys modification. Fluorescence spectroscopy indicates local changes in the Tyr microenvironment. CD melting studies reveal that β-sheet formation is slightly enhanced with a reduction in the α-helical content in case of modified RNase A. However, the similar melting temperature of both native and modified RNase A indicates overall structural integrity with local changes in secondary structural components. ITC and UV-visible kinetics show reduced ribonucleolytic activity in homocysteinylated RNase A compared to the unmodified enzyme. These findings provide insights into the structural and functional consequences of RNase A homocysteinylation, contributing to our understanding of hyperhomocysteinemia-related pathologies.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1518-1533"},"PeriodicalIF":2.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143782132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

β-ATPase of the Insect Panstrongylus megistus: Cloning, Bioinformatics Analysis, and Study of Its Interaction With Lipophorin. 昆虫大圆线虫β- atp酶的克隆、生物信息学分析及其与脂磷脂相互作用研究

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-09-01 Epub Date: 2025-04-23 DOI: 10.1002/prot.26830

Leonardo L Fruttero, Jimena Leyria, Rodrigo Ligabue-Braun, Pedro Clop, Pedro A Paglione, Maria A Perillo, Celia R Carlini, Estela Arrese, Lilián E Canavoso

{"title":"β-ATPase of the Insect Panstrongylus megistus: Cloning, Bioinformatics Analysis, and Study of Its Interaction With Lipophorin.","authors":"Leonardo L Fruttero, Jimena Leyria, Rodrigo Ligabue-Braun, Pedro Clop, Pedro A Paglione, Maria A Perillo, Celia R Carlini, Estela Arrese, Lilián E Canavoso","doi":"10.1002/prot.26830","DOIUrl":"10.1002/prot.26830","url":null,"abstract":"Lipophorin is the main lipoprotein of the insect's hemolymph. Although its role in lipid metabolism has been extensively analyzed, the mechanisms of lipid delivery to target tissues mediated by lipophorin are not completely understood. It has been reported that the β-chain of the ATP synthase complex (β-ATPase) acts as a nonendocytic receptor for lipophorin in the hematophagous insect Panstrongylus megistus, and this function is relevant for the transfer of lipids. The aim of this study was to gather new information regarding the β-ATPase, including its sequence and interaction with lipophorin. A β-ATPase cDNA encoding a 521-amino acid protein was cloned from P. megistus. β-ATPase is highly conserved, and molecular phylogenetic analyses grouped the deduced amino acid sequences according to their respective taxa. Structural modeling of β-ATPase revealed a conserved folding pattern and three-dimensional architecture that allows docking with a modeled lipophorin, suggesting potential interaction between the two proteins. Recombinant β-ATPase (rβ-ATPase) was expressed in Escherichia coli, and the rβ-ATPase was purified by affinity chromatography. rβ-ATPase was combined with lipophorin at various ratios, and the sedimentation properties of these mixtures were analyzed by analytical ultracentrifugation. The changes in sedimentation behavior of the protein mixture compared to that of the individual proteins are consistent with binding between rβ-ATPase and lipophorin. This finding, which confirms the interaction of β-ATPase and lipophorin, provides additional support for the role of β-ATPase in the uptake of lipids by tissues.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1603-1612"},"PeriodicalIF":2.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12316553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Evolving Landscape of Amyloid Research. 淀粉样蛋白研究的发展前景。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-08-28 DOI: 10.1002/prot.70048

Bernardo Bonilauri

{"title":"The Evolving Landscape of Amyloid Research.","authors":"Bernardo Bonilauri","doi":"10.1002/prot.70048","DOIUrl":"https://doi.org/10.1002/prot.70048","url":null,"abstract":"The exponential growth of biomedical and life sciences literature, including research on amyloid biology, has made it increasingly challenging to track new discoveries and gain a comprehensive understanding of the evolution of specific research fields. Advances in natural language models (NLM) and artificial intelligence (AI) approaches now enable large-scale analysis of scientific publications, uncovering hidden patterns and facilitating data-driven insights. Here, a two-dimensional mapping of the global amyloid research landscape is presented, using the transformer-based large language model PubMedBERT, in combination with t-SNE and Latent Dirichlet Allocation (LDA), to analyze more than 140 000 abstracts from the PubMed database. This analysis provides a comprehensive visualization of the amyloid field, capturing key trends such as the historical progression of amyloid research, the emergence of dominant subfields, the distribution of contributing authors and their respective countries, and the identification of latent research topics over time, including chemicals and small molecules. By integrating AI-driven text analysis with large-scale bibliometric data, this study offers a novel perspective on the evolution of amyloid research, facilitating a deeper interdisciplinary understanding. This work serves as a valuable interactive resource for researchers while highlighting the potential of machine learning-driven literature mapping in identifying knowledge gaps and guiding future investigations.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MassiveFold Data for CASP16-CAPRI: A Systematic Massive Sampling Experiment. CASP16-CAPRI的海量数据：一个系统的海量采样实验。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-08-28 DOI: 10.1002/prot.70040

Nessim Raouraoua, Marc F Lensink, Guillaume Brysbaert

{"title":"MassiveFold Data for CASP16-CAPRI: A Systematic Massive Sampling Experiment.","authors":"Nessim Raouraoua, Marc F Lensink, Guillaume Brysbaert","doi":"10.1002/prot.70040","DOIUrl":"https://doi.org/10.1002/prot.70040","url":null,"abstract":"Massive sampling with AlphaFold2 has become a widely used approach in protein structure prediction. Here we present the MassiveFold CASP16-CAPRI dataset, a systematic, large-scale sampling of both monomeric and multimeric protein targets. By exploiting maximal parallelization, we produced up to 8040 models per target and shared them with the community for collaborative selection and scoring. This collective effort minimizes redundant computation and environmental impact, while granting resource-limited groups - especially those focused on scoring - access to high quality structures. In our analysis, we define an interface-difficulty classification based on DockQ metrics, showing that massive sampling yields the greatest gains on most of the challenging interfaces. Crucially, this classification can be predicted from the median ipTM scores of a routine AF2 run, enabling users to selectively deploy massive sampling only when it is most needed. Combined with a reduction of the massive sampling from 8040 to 2475 predictions, such targeted strategies dramatically cut computation time and resource use with minimal loss of accuracy. Finally, we underscore the persistent challenge of choosing optimal models from massive sampling datasets, emphasizing the need for more robust scoring methods. The MassiveFold datasets, together with AlphaFold ranking scores and CASP and CAPRI assessment metrics, are publicly available at https://github.com/GBLille/CASP16-CAPRI_MassiveFold_Data to accelerate further progress in protein structure prediction and assembly modeling.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Markovian Timescales of Intramolecular Disulfide Pairing in Cyclotides. 环核苷酸分子内二硫配对的马尔可夫时间尺度。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-08-28 DOI: 10.1002/prot.70041

Jayapriya Venkatesan, Durba Roy

引用次数: 0

Critical Assessment of Protein Intrinsic Disorder Round 3 - Predicting Disorder in the Era of Protein Language Models. 蛋白质内在紊乱的关键评估第3轮-在蛋白质语言模型时代预测紊乱。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-08-26 DOI: 10.1002/prot.70045

Mahta Mehdiabadi, Alessio Del Conte, Maria Victoria Nugnes, Maria Cristina Aspromonte, Silvio C E Tosatto, Damiano Piovesan

{"title":"Critical Assessment of Protein Intrinsic Disorder Round 3 - Predicting Disorder in the Era of Protein Language Models.","authors":"Mahta Mehdiabadi, Alessio Del Conte, Maria Victoria Nugnes, Maria Cristina Aspromonte, Silvio C E Tosatto, Damiano Piovesan","doi":"10.1002/prot.70045","DOIUrl":"https://doi.org/10.1002/prot.70045","url":null,"abstract":"Intrinsic disorder (ID) in proteins is a complex phenomenon, encompassing a continuum from entirely disordered regions to structured domains with flexible segments. The absence of a ground truth for all forms of disorder, combined with the possibility of structural transitions between ordered and disordered states under specific conditions, makes accurate prediction of ID especially challenging. The Critical Assessment of Protein Intrinsic Disorder (CAID) evaluates ID prediction methods using diverse benchmarks derived from DisProt, a manually curated database of experimentally validated annotations. This paper presents findings from the third (CAID3), in which 24 new methods were assessed along with the predictors from previous rounds. Compared to CAID2, the top-performing methods in CAID3 demonstrated significant gains in average precision: over 31% improvement in predicting linker regions, and 15% in disorder prediction. This round introduces a new binding sub-challenge focused on identifying binding regions within known IDR boundaries. The results indicate that this task remains challenging, highlighting the potential for improvement. The top-performing methods in CAID3 are mostly new and commonly used embeddings from protein language models (pLMs), underscoring the growing impact of pLMs in tackling the complexities of disordered proteins and advancing ID prediction.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0