CAID prediction portal: A comprehensive service for predicting intrinsic disorder and binding regions in proteins

Intrinsic disorder (ID) in proteins is well-established in structural biology, with increasing evidence for its involvement in essential biological processes. As measuring dynamic ID behavior experimentally on a large scale remains difficult, scores of published ID predictors have tried to fill this gap. Unfortunately, their heterogeneity makes it difficult to compare performance, confounding biologists wanting to make an informed choice. To address this issue, the Critical Assessment of protein Intrinsic Disorder (CAID) benchmarks predictors for ID and binding regions as a community blind-test in a standardized computing environment. Here we present the CAID Prediction Portal, a web server executing all CAID methods on user-defined sequences. The server generates standardized output and facilitates comparison between methods, producing a consensus prediction highlighting high-confidence ID regions. The website contains extensive documentation explaining the meaning of different CAID statistics and providing a brief description of all methods. Predictor output is visualized in an interactive feature viewer and made available for download in a single table, with the option to recover previous sessions via a private dashboard. The CAID Prediction Portal is a valuable resource for researchers interested in studying ID in proteins. The server is available at the URL: https://caid.idpcentral.org

Critical assessment of protein intrinsic disorder prediction (CAID) - Results of round 2

Protein intrinsic disorder (ID) is a complex and context-dependent phenomenon that covers a continuum between fully disordered states and folded states with long dynamic regions. The lack of a ground truth that fits all ID flavors and the potential for order-to-disorder transitions depending on specific conditions makes ID prediction challenging. The CAID2 challenge aimed to evaluate the performance of different prediction methods across different benchmarks, leveraging the annotation provided by the DisProt database, which stores the coordinates of ID regions when there is experimental evidence in the literature. The CAID2 challenge demonstrated varying performance of different prediction methods across different benchmarks, highlighting the need for continued development of more versatile and efficient prediction software. Depending on the application, researchers may need to balance performance with execution time when selecting a predictor. Methods based on AlphaFold2 seem to be good ID predictors but they are better at detecting absence of order rather than ID regions as defined in DisProt. The CAID2 predictors can be freely used through the CAID Prediction Portal, and CAID has been integrated into OpenEBench, which will become the official platform for running future CAID challenges

Platypalpus verbekei Grootaert & Chvala, 1992, nova espècie per Algèria i pel Nord d'Àfrica amb un catàleg de les espècies conegudes d'Algèria de la família Hybotidae (Diptera: Empidoidea: Hybotidae)

Based on the collections made in crop fields in Mostaganem (Algeria), an updated list of the Hybotidae species of Algeria is performed. The species Platypalpus verbekei Grootaert & Chvala, 1992 is here cited for the first time in North Africa. This species has a chromatic variation and a certain clypeus variation respect the European populations which are here detailed. In order to facilitate the recognition of this species it is included in this study a diagnosis (in Catalan) and a redescription (in English) based on the specimens collected from the Algerian population, showing the phenotypic variability of the species present in the two shores of the Mediterranean. In total 27 species distributed in 5 genera are known so far in Algeria, of which 4 are cited only in Algeria. Two species are excluded from the catalogue of the Algerian species giving the reasons for that decisio

Platypalpus verbekei Grootaert & Chvala, 1992, nova espècie per Algèria i pel Nord d'Àfrica amb un catàleg de les espècies conegudes d'Algèria de la família Hybotidae (Diptera: Empidoidea: Hybotidae)

Based on the collections made in crop fields in Mostaganem (Algeria), an updated list of the Hybotidae species of Algeria is performed. The species Platypalpus verbekei Grootaert & Chvala, 1992 is here cited for the first time in North Africa. This species has a chromatic variation and a certain clypeus variation respect the European populations which are here detailed. In order to facilitate the recognition of this species it is included in this study a diagnosis (in Catalan) and a redescription (in English) based on the specimens collected from the Algerian population, showing the phenotypic variability of the species present in the two shores of the Mediterranean. In total 27 species distributed in 5 genera are known so far in Algeria, of which 4 are cited only in Algeria. Two species are excluded from the catalogue of the Algerian species giving the reasons for that decisio

A Data Warehouse of Muscle Characteristics and Beef Quality in France and A Demonstration of Potential Applications

The BIF-Beef (Beef Integrated and Functional Biology) database contains animal, carcass, muscle and meat data (331,745 entries) collected from 43 experiments over the last 20 years and a great number of variables (621) characterising muscles (fat and collagen contents, cross-section and types of fibres, metabolic activity), making it a relevant tool to relate muscle characteristics to beef quality. Wide variation was observed in all described traits according to muscle type, sex and breed. The BIF-Beef database was mainly composed of data from young bulls of late-maturing beef breeds, which is why live weight and carcass weights of the animals were greater, and beef was leaner and lighter than results from other existing databases. Average cross-sectional area of fibres was greater in Semitendinosus than in Longissimus thoracis muscle and, for Longissimus, greater in steers than in young bulls. Intramuscular fat content was in descending order: Charolais > Limousin > Blond d’Aquitaine and females > steers > young bulls. Semitendinosus muscle was less oxidative and contained more collagen than Longissimus muscle. Collagen content in Longissimus was higher in Charolais than in Blond d’Aquitaine and Limousin young bulls. Within the Charolais breed, collagen content in Longissimus was higher in young bulls and steers than in females. Longissimus samples from young bulls were less tender than from females. Based on the above results, this database is a prerequisite for meta-analysis of relationships between muscle characteristics and beef quality in the European context