Article
Geochemistry & Geophysics
Jian Kang, Ruben Fernandez-Beltran, Xian Sun, Jingen Ni, Antonio Plaza
Summary: To address missing annotations in ground-truth building mask layers due to delayed geospatial information updating, a new joint loss function is introduced to maximize F-1 scores of predicted building masks and preserve fine-grained structure of building boundaries.
IEEE GEOSCIENCE AND REMOTE SENSING LETTERS
(2022)
Article
Multidisciplinary Sciences
Preeti Choudhary, Stephen Anyango, John Berrisford, James Tolchard, Mihaly Varadi, Sameer Velankar
Summary: More than 61,000 proteins have correspondence between their amino acid sequence (UniProtKB) and 3D structures (PDB) through the SIFTS resource. SIFTS incorporates residue-level annotations from various biological resources and is maintained separately from the structure data in the PDB archive.
Article
Computer Science, Information Systems
Yi Zhong, Jia-Hui Pan, Haoxin Li, Wei-Shi Zheng
Summary: This paper proposes a weakly supervised method that uses global motion and local fine-grained features from current action videos to predict the next action label without the need for specific scene context labels.
FRONTIERS OF COMPUTER SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Evgeny M. Zdobnov, Dmitry Kuznetsov, Fredrik Tegenfeldt, Mose Manni, Matthew Berkeley, Evgenia Kriventseva
Summary: OrthoDB provides evolutionary and functional annotations of orthologs for a vast number of organisms, with a wide coverage of species and rich data content. The user interface has been enhanced, and features three views on the data, as well as online tools for interactive exploration and data download.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Ecology
R. Eugene Turner
Summary: White et al. measured land area in river diversion areas and concluded that there were beneficial or neutral effects, but failed to include reference sites for accurate comparisons. They highlighted the importance of using appropriate analysis methods and reference sites in evaluating environmental impacts. The omission of reference sites is a common problem that should be addressed to improve ecological intelligence.
ECOLOGICAL ENGINEERING
(2023)
Article
Biology
Miguel Romero, Felipe Kenji Nakano, Jorge Finke, Camilo Rocha, Celine Vens
Summary: With the development of new sequencing technologies, genomic data availability has increased rapidly. Previous studies have used this data to associate genes with biological functions, but often ignored the sparsity and noise in the datasets. This research proposes a method for detecting missing annotations in a hierarchical multi-label classification context, using function relations represented as a hierarchy. Experimental results on rice datasets demonstrate the accuracy and superiority of this method compared to current state-of-the-art approaches.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Federica Morani, Stefano Doccini, Daniele Galatolo, Francesco Pezzini, Rabah Soliymani, Alessandro Simonati, Maciej M. Lalowski, Federica Gemignani, Filippo M. Santorelli
Summary: The study proposes an integrative approach to understanding ARSACS and identifies disease-specific pathways and biological functions related to the condition. This provides a rationale for improving early diagnosis and treatment options.
Article
Computer Science, Software Engineering
Pedro Company, Jorge D. Camba, Stanislao Patalano, Ferdinando Vitolo, Antonio Lanzotti
Summary: Describing and supplementing geometric shapes and layouts with relevant information is crucial for successful product design communication. This paper introduces a functional classification of text annotations to shift traditional annotation practices towards the Model-Based Definition (MBD) paradigm. The proposed classification categorizes text annotations into four functional types and was tested with a group of users in a redesign task involving an annotated assembly model.
COMPUTER-AIDED DESIGN
(2023)
Article
Genetics & Heredity
Shaojun Wang, Ronghui You, Yunjia Liu, Yi Xiong, Shanfeng Zhu
Summary: NetGO 2.0 is an automated function prediction method that integrates multiple sources of information to improve performance. However, it does not leverage valuable information from a large number of unannotated proteins. Recently, protein language models have been proposed to learn informative representations from protein sequences. By incorporating this model into NetGO 2.0, researchers have developed NetGO 3.0, which significantly improves the performance of automated function prediction.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Plant Sciences
Ante Turudic, Zlatko Liber, Martina Grdisa, Jernej Jakse, Filip Varga, Zlatko Satovic
Summary: The development of bioinformatic solutions requires biological knowledge and often makes assumptions. In this study, we investigated the relationship between chloroplast sequence lengths and taxonomic proximity of species using RefSeq sequences from the asterid and rosid clades. We found that chloroplast length distributions are narrow at the family and genus levels, with outliers indicating possible inaccuracies in sequence assembly.
Article
Biochemistry & Molecular Biology
Juan Mulero Hernandez, Jesualdo Tomas Fernandez-Breis
Summary: Gene regulation involves a complex network where transcription plays a key role, with enhancers playing an important role in regulating gene transcription. While research has made progress in understanding the relationship between enhancers and diseases, there are still challenges and gaps in the computational exploitation of enhancer data in current public databases.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Medicine, General & Internal
Jose Camara, Roberto Rezende, Ivan Miguel Pires, Antonio Cunha
Summary: Public databases provide color images of the optic papilla for research in glaucoma. However, the heterogeneous nature of the images and the lack of certain elements pose challenges. This study aims to improve the structure and content of public databases used for automated screening.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Tingting Liu, Feng Peng, Yunying Zhu, Xiao Cao, Qifan Wang, Fang Liu, Liwei Liu, Wei Xue
Summary: In this study, a series of myricetin derivatives containing quinazolinone sulfide were investigated for their antibacterial and antiviral activities. Two drug molecules, T5 and T15, exhibited strong effects against bacteria and viruses, with T15 showing promising potential in enhancing disease resistance in tobacco plants.
ARABIAN JOURNAL OF CHEMISTRY
(2022)
Article
Agronomy
Amira Aschi, Wassila Riah-Anglet, Sylvie Recous, Caroline Bailleul, Michael Aubert, Isabelle Trinsoutrot-Gattin
Summary: This study evaluated the response of soil microbial functions to the presence and placement of faba beans in crop rotations, combined with two tillage systems. The results showed that introducing faba beans as the crop preceding wheat significantly increased the total carbon and nitrogen content under reduced tillage. Enzyme activities, influenced by changes in soil physicochemical properties, significantly affected nitrogen fluxes.
Article
Genetics & Heredity
Elena G. Lara, Isabelle van der Windt, Douwe Molenaar, Marjon G. J. de Vos, Chrats Melkonian
Summary: A computational approach using metabolic gene annotation was used to rapidly predict putative interactions between members of urinary tract infection microbial communities, revealing that Enteroccus spp. were most complemented in its metabolism by other community members. Experimental supplementation of predicted metabolites confirmed the increase in population density of UTI Enterococcus isolates. This method shows promise as a rapid in silico screening tool for predicting metabolic interactions in microbial communities.
Article
Biochemistry & Molecular Biology
Rossana Zaru, Joseph Onwubiko, Antonio J. M. Ribeiro, Keeva Cochrane, Jonathan D. Tyzack, Venkatesh Muthukrishnan, Lukas Pravda, Janet M. Thornton, Claire O'Donovan, Sameer Velanker, Sandra Orchard, Andrew Leach, Maria J. Martin
Summary: Enzyme Portal serves as a free hub for researchers to easily access and explore enzyme-related information from various resources, addressing the challenge of time-consuming retrieval of scattered enzyme data.
Letter
Biochemical Research Methods
M. Michael Gromiha, Christine A. Orengo, Ramanathan Sowdhamini, Janet M. Thornton
Editorial Material
Biochemical Research Methods
David T. Jones, Janet M. Thornton
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P. Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D. Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S. Marks, Lennart Martens, Stuart A. McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C. E. Tosatto, Wim Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar
Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Roman A. Laskowski, Janet M. Thornton
Summary: The PDBsum web server offers structural analyses of Protein Data Bank entries, with recent additions focusing on SARS-CoV-2 virus proteins and AlphaFold models for human proteins. Users can easily compare predicted models against experimentally determined structures using the server.
Article
Biochemistry & Molecular Biology
Ioannis G. Riziotis, Antonio J. M. Ribeiro, Neera Borkakoti, Janet M. Thornton
Summary: Conformational variation in catalytic residues can be captured as alternative snapshots in enzyme crystal structures. The study reveals that catalytic centers of enzymes can exhibit inherent rigidity or flexibility, with structural variability most often involving a subset of catalytic residues. Furthermore, it is found that active sites are predominantly flexible, with side chains being the main contributors. The goal of this work is to characterize the extent of flexibility in catalysis and relate it to enzyme evolution and substrate binding.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Charles A. Santana, Sandro C. Izidoro, Raquel C. De Melo-Minardi, Jonathan D. Tyzack, Antonio J. M. Ribeiro, Douglas E. Pires, Janet M. Thornton, Sabrina de A. Silveira
Summary: Proteins are important macromolecules for living systems, often interacting in binding sites with other molecules. GRaSP-web is a graph-based method using machine learning to predict putative ligand binding site residues, outperforming other state-of-the-art methods with a MCC of 0.61. It is scalable and quick, making consistent predictions for bound/unbound structures and a large dataset of proteins.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Ioannis G. Riziotis, Janet M. Thornton
Summary: Research explores methods to generate template libraries and algorithms to query conserved 3D motifs in protein functional sites, and introduces the concept of using multiple templates to represent flexible sites. Template-based functional site detection is predicted to be a powerful tool in characterizing a vast number of new protein models.
Article
Biochemistry & Molecular Biology
Neera Borkakoti, Janet M. Thornton
Summary: The drug discovery process involves designing compounds to selectively interact with their protein targets. Recent advancements in artificial intelligence have greatly improved the accuracy of protein structure prediction, making protein targets more accessible in the drug design process. In this perspective article, we highlight the importance of accurate protein structure prediction in various stages of small molecule drug discovery, discussing current capabilities and the potential impact of further evolution of predictive procedures.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Editorial Material
Chemistry, Multidisciplinary
Floriano P. Silva-Jr, Siva S. Panda, Carolina Horta Andrade, Nicholas Furnham
FRONTIERS IN CHEMISTRY
(2022)
Review
Biophysics
Antonio J. M. Ribeiro, Ioannis G. Riziotis, Jonathan D. Tyzack, Neera Borkakoti, Janet M. Thornton
Summary: Enzyme reactions occur in the active site through a series of catalytic steps that make up the enzyme mechanism. In natural evolution, new enzyme functions have been shown to emerge through adjusting existing mechanisms while keeping other steps intact. Studying the catalytic rules of enzymes can reveal similar catalytic steps between enzymes with different functions.
BIOPHYSICAL REVIEWS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Angus I. Lamond, Ivan Dikic, Andre Nussenzweig, Christoph W. Mueller, Janet M. Thornton, Michael B. Yaffe
Correction
Multidisciplinary Sciences
Ulas Isildak, Mehmet Somel, Janet M. Thornton, Handan Melike Donertas
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Ioannis G. Riziotis, Antonio J. M. Ribeiro, Neera Borkakoti, Janet M. Thornton
Summary: Enzyme catalysis is controlled by a limited set of residues and co-factors. By utilizing three-dimensional templates, recurring catalytic modules that are involved in metal ion, co-factor, and substrate binding can be identified. Some of these convergent modules perform specific catalytic functions, while enzymes that have diverged during evolution retain specific regions of their active site.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemical Research Methods
Antonio J. M. Ribeiro, Ioannis G. Riziotis, Jonathan D. Tyzack, Neera Borkakoti, Janet M. Thornton
Summary: The rich literature on enzyme reaction mechanisms can serve as the foundation for new knowledge-based approaches to investigate enzyme mechanisms. In this study, a tool called EzMechanism is presented, which can automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction based on catalytic rules compiled from a database of enzyme mechanisms. EzMechanism facilitates and improves the generation of hypotheses by considering relevant information derived from literature on both related and unrelated enzymes.
