Article
Biochemistry & Molecular Biology
Chloe Quignot, Guillaume Postic, Helene Bret, Julien Rey, Pierre Granger, Samuel Murail, Pablo Chacon, Jessica Andreani, Pierre Tuffery, Raphael Guerois
Summary: The InterEvDock3 protein docking server utilizes evolutionary constraints to generate structural models of protein assemblies, providing 10 candidate complexes and interface predictions. Three key innovations were implemented to improve model reliability, with server performance validated on large benchmark databases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Geochemistry & Geophysics
Dario Jozinovic, Valentino Lauciani, Sergio Bruni, Licia Faenza, Alberto Michelini
Summary: We present a web portal for promptly visualizing ground shaking maps generated by the U.S. Geological Survey ShakeMap version 4 software. The portal allows users to view the maps dynamically or statically, with different overlays for configurable information. The software can be installed on laptops or server computers, and users can choose between Docker image or installation after setting up a web server.
SEISMOLOGICAL RESEARCH LETTERS
(2022)
Review
Biochemistry & Molecular Biology
Haiyan Gong, Yi Yang, Sichen Zhang, Minghong Li, Xiaotong Zhang
Summary: This paper discusses the background, purpose, and methods of Hi-C data visualization analysis, covering topics such as 3D genome structure, A/B compartments, TADs, and loop detection, as well as its applications in cancer and cell differentiation research. Various issues in joint analyses based on Hi-C and other multi-omics data are also summarized to help researchers better understand the progress and applications of 3D genome technology.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Anna Klimovskaia Susmelj, Yani Ren, Yann Vander Meersche, Jean-Christophe Gelly, Tatiana Galochkina
Summary: In the era of increasing protein data, a relevant and interpretable visualization is crucial. Poincare disk projection has shown its efficiency in visualizing single-cell RNAseq data. Here, we introduce PoincareMSA, a new method for visualizing complex relationships between protein sequences using Poincare maps embedding. It demonstrates efficiency in visualizing protein family topology and annotating unknown sequences. PoincareMSA is implemented in open source Python code with available interactive Google Colab notebooks.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Sung-Joon Park, Kenta Nakai
Summary: Microorganisms infect and contaminate eukaryotic cells during biological experiments, influencing research conclusions. OpenContami is an online application providing a comprehensive overview of exogenous species in NGS datasets, aiding in understanding the impact of microbial contamination on biological and pathological traits.
Article
Statistics & Probability
Charlie Sire, Rodolphe Le Riche, Didier Rulliere, Jeremy Rohmer, Lucie Pheulpin, Yann Richet
Summary: Data visualization is crucial for assessing the risk of rare events like coastal or river flooding. The challenge lies in quantizing the probability law of these events, which becomes difficult when data is expensive and critical events are scarce. This article proposes a method that adapts Lloyd's algorithm to rare and costly-to-observe events, using importance sampling and Functional Principal Component Analysis combined with a Gaussian process.
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
(2023)
Article
Biochemical Research Methods
Bahareh Behkamal, Mahmoud Naghibzadeh, Andrea Pagnani, Mohammad Reza Saberi, Kamal Al Nasr
Summary: This article proposes a linear programming-based topology determination method to solve the secondary structure topology problem in three-dimensional geometrical space. It transforms the secondary structure matching problem into a complete weighted bipartite graph matching problem and uses linear programming algorithm to extract the true topology.
Article
Geography, Physical
Jan Drechsel, Nicole S. Khan, Alessio Rovere
Summary: PALEO-SEAL is a simple web interface for visualizing, querying and downloading Holocene sea-level datapoints formatted following the HOLSEA data template. The data is stored in a mySQL database, and the interface utilizes AngularJS. It can be easily deployed with basic knowledge of SQL and HTML, and is released in the open domain.
QUATERNARY SCIENCE REVIEWS
(2021)
Article
Genetics & Heredity
Miaosen Liu, Jian Yang, Huilong Duan, Lan Yu, Dingwen Wu, Haomin Li
Summary: In this study, an automated pipeline called SNPMap was proposed to create an integrated visual SNP interpretation tool. SNPMap obtains relevant information from multiple databases through extraction, integration, and visualization, providing users with a lucid and detailed understanding of SNPs through keyword analysis and semantic relations.
FRONTIERS IN GENETICS
(2022)
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
Engineering, Civil
Qiang Zhang, Rui Shi, Chong-Yu Xu, Peng Sun, Huiqian Yu, Jiaqi Zhao
Summary: This study developed a new integrated remote sensing drought monitoring index that considers multiple factors such as precipitation, temperature, vegetation, and soil moisture. The performance of the index was compared and verified using real-world observed drought data. The results showed that the index performed better than other commonly used indices in describing the spatiotemporal characteristics of droughts.
JOURNAL OF HYDROLOGY
(2022)
Article
Computer Science, Information Systems
Julio Hernandez, Heidy M. Marin-Castro, Miguel Morales-Sandoval
Summary: The article proposes a new method based on linked data for combining individual web query interfaces into a single integrated WQI. By utilizing a domain-independent ontology to describe and integrate WQI elements, the approach successfully addresses the WQI integration problem.
Article
Computer Science, Information Systems
Guodao Sun, Zihao Zhu, Gefei Zhang, Chaoqing Xu, Yunchao Wang, Sujia Zhu, Baofeng Chang, Ronghua Liang
Summary: Mathematical optimization is used to find the best parameters in a search space and has been widely applied in computer science, engineering, operations research, and economics. It has also been extended to data visualization to improve data processing and exploration. However, there is a lack of comprehensive summarization of mathematical optimization in data visualization.
IEEE TRANSACTIONS ON BIG DATA
(2023)
Article
Geosciences, Multidisciplinary
Jiali Song, Hiroyuki Yamauchi, Takashi Oguchi, Takuro Ogura
Summary: This study examines the effectiveness of web hazard maps in disaster risk reduction (DRR) education compared to conventional paper hazard maps. The findings show that web hazard maps provide more accurate and user-friendly information for identifying risk areas. However, there are limitations in terms of usability and technological constraints, suggesting that a combination of online materials and paper maps is ideal for DRR education.
INTERNATIONAL JOURNAL OF DISASTER RISK REDUCTION
(2022)
Article
Computer Science, Information Systems
Jose E. Lozano-Rizk, Jose E. Gonzalez-Trejo, Raul Rivera-Rodriguez, Andrei Tchernykh, Salvador Villarreal-Reyes, Alejandro Galaviz-Mosqueda
Summary: This article introduces QoSS, an API web service that provides both Quality of Service and Security for applications through software-defined networks. Through a case study, it is shown that QoSS improves end-to-end application data transfer and supports dynamic path configuration based on application requirements.
Article
Biochemistry & Molecular Biology
Claudia Millan, Ronan M. Keegan, Joana Pereira, Massimo D. Sammito, Adam J. Simpkin, Airlie J. McCoy, Andrei N. Lupas, Marcus D. Hartmann, Daniel J. Rigden, Randy J. Read
Summary: This study introduces a new method (reLLG) for evaluating protein structure models that does not require diffraction data. Calibration against CASP14 targets showed that reLLG is a robust measure of model and group ranking. Additionally, refinements by CASP groups often lead to improved accuracy in models.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Lucy C. Ward, Hannah McCue, Daniel J. Rigden, Neil M. Kershaw, Chloe Ashbrook, Harry Hatton, Ellie Goulding, James R. Johnson, Andrew J. Carnell
Summary: Carboxyl methyltransferase enzymes from Aspergillus fumigatus showed high regioselectivity and good conversions in methylating a broad range of aromatic mono- and dicarboxylic acids. The second methylation of dicarboxylic acids exhibited strong pH dependence, with an optimum at pH 5.5-6. Potential for industrial biotechnology application was demonstrated in the production of a bioplastics precursor from bioderived 5-hydroxymethylfurfural.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Grzegorz Chojnowski, Adam J. Simpkin, Diego A. Leonardo, Wolfram Seifert-Davila, Dan E. Vivas-Ruiz, Ronan M. Keegan, Daniel J. Rigden
Summary: This article presents an automated pipeline for identifying protein sequences from cryo-EM reconstructions and crystallographic data. The method is applied to characterize the crystal structure of an unknown protein purified from snake venom, and it is shown that the approach can successfully identify protein sequences and validate sequence assignments in cryo-EM protein structures.
Article
Biochemical Research Methods
Adam J. Simpkin, Jens M. H. Thomas, Ronan M. Keegan, Daniel J. Rigden
Summary: Crystallographers have various search-model options for structure solution. The MrParse pipeline consolidates bioinformatic predictions and simplifies the decision process in molecular replacement (MR), providing rankings for experimental homologues and homologues in the EBI AlphaFold database. It also offers displays of predicted secondary structure, coiled-coil, and transmembrane regions to inform the choice of MR protocol.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Filomeno Sanchez Rodriguez, Grzegorz Chojnowski, Ronan M. Keegan, Daniel J. Rigden
Summary: This article introduces a new validation method based on deep learning prediction of inter-residue distances, which can accurately detect sequence-register errors in protein models.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Lucy C. Ward, Ellie Goulding, Daniel J. Rigden, Faye E. Allan, Alessandro Pellis, Harry Hatton, Georg M. Guebitz, Jesus Enrique Salcedo-Sora, Andrew J. Carnell
Summary: Mutation of the FtpM enzyme from Aspergillus fumigatus, named R166M, was reported to catalyze the quantitative conversion of bio-derived 2,5-furandicarboxylic acid (FDCA) to its dimethyl ester (FDME), the precursor of bioplastics. The AlphaFold 2 model revealed that the mutant had a highly electropositive active site, with 4 arginine residues facilitating the binding of the dicarboxylic acid over the intermediate monoester. The R166M mutation improved both binding and turnover of the monoester, allowing near quantitative conversion to the target dimethyl ester product, and showed improved activity for other diacids and monoacids.
Article
Biochemistry & Molecular Biology
Andriy Kryshtafovych, Daniel J. Rigden
Summary: This study describes the process of converting CASP15 targets into evaluation units (EUs) and assigning them to evolutionary-based prediction classes. The targets were divided into structural domains based on compactness and similarity. Models were evaluated on these domains and their combinations. If the performance on the combined units was similar to that on individual domains, the domains were joined to form larger EUs. Otherwise, if most predictors performed better on the individual domains, they were retained as EUs. As a result, 112 EUs were created from 77 tertiary structure prediction targets. These EUs were assigned to four prediction classes that roughly correspond to previous CASP difficulty categories.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Jon Agirre, Mihaela Atanasova, Haroldas Bagdonas, Charles B. Ballard, Arnaud Basle, James Beilsten-Edmands, Rafael J. Borges, David G. Brown, J. Javier Burgos-Marmol, John M. Berrisford, Paul S. Bond, Iracema Caballero, Lucrezia Catapano, Grzegorz Chojnowski, Atlanta G. Cook, Kevin D. Cowtan, Tristan I. Croll, Judit E. Debreczeni, Nicholas E. Devenish, Eleanor J. Dodson, Tarik R. Drevon, Paul Emsley, Gwyndaf Evans, Phil R. Evans, Maria Fando, James Foadi, Luis Fuentes-Montero, Elspeth F. Garman, Markus Gerstel, Richard J. Gildea, Kaushik Hatti, Maarten L. Hekkelman, Philipp Heuser, Soon Wen Hoh, Michael A. Hough, Huw T. Jenkins, Elisabet Jimenez, Robbie P. Joosten, Ronan M. Keegan, Nicholas Keep, Eugene B. Krissinel, Petr Kolenko, Oleg Kovalevskiy, Victor S. Lamzin, David M. Lawson, Andrey A. Lebedev, Andrew G. W. Leslie, Bernhard Lohkamp, Fei Long, Martin Maly, Airlie J. McCoy, Stuart J. McNicholas, Ana Medina, Claudia Millan, James W. Murray, Garib N. Murshudov, Robert A. Nicholls, Martin E. M. Noble, Robert Oeffner, Navraj S. Pannu, James M. Parkhurst, Nicholas Pearce, Joana Pereira, Anastassis Perrakis, Harold R. Powell, Randy J. Read, Daniel J. Rigden, William Rochira, Massimo Sammito, Filomeno Sanchez Rodriguez, George M. Sheldrick, Kathryn L. Shelley, Felix Simkovic, Adam J. Simpkin, Pavol Skubak, Egor Sobolev, Roberto A. Steiner, Kyle Stevenson, Ivo Tews, Jens M. H. Thomas, Andrea Thorn, Josep Trivino Valls, Ville Uski, Isabel Uson, Alexei Vagin, Sameer Velankar, Melanie Vollmar, Helen Walden, David Waterman, Keith S. Wilson, Martyn D. Winn, Graeme Winter, Marcin Wojdyr, Keitaro Yamashita
Summary: The Collaborative Computational Project No. 4 (CCP4) is an international collective led by the UK, dedicated to the development, testing, distribution, and promotion of software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs, unified by familiar execution routines, common libraries, and graphical interfaces. This article serves as a general literature citation for the use of the CCP4 software suite, providing an overview of its recent changes, new features, and future developments, while also highlighting the individual programs within the suite and providing up-to-date references for crystallographers worldwide.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Rhiju Das, Rachael C. Kretsch, Adam J. Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan M. Keegan, Maya Topf, Daniel J. Rigden, Zhichao Miao, Eric Westhof
Summary: This study reports the assessment of RNA structure predictions and highlights the performance of traditional methods compared to deep learning approaches. The evaluation, based on modeling and comparison with experimental data, shows that models generated by deep learning were worse than those generated by traditional methods. The study also demonstrates the potential utility of current RNA modeling approaches in RNA nanotechnology and structural biology.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Adam J. Simpkin, Shahram Mesdaghi, Filomeno Sanchez Rodriguez, Luc Elliott, David L. Murphy, Andriy Kryshtafovych, Ronan M. Keegan, Daniel J. Rigden
Summary: The results of tertiary structure assessment at CASP15 are reported, with many top groups achieving good predictions using methods like AlphaFold 2. Although there were some local differences between predictions and targets, a majority of groups produced high-quality predictions for most targets, which are valuable for tasks such as experimental structure determination and functional analysis.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Andriy Kryshtafovych, Gaetano T. Montelione, Daniel J. Rigden, Shahram Mesdaghi, Ezgi Karaca, John Moult
Summary: For the first time, the 2022 CASP community experiment added a section on computing multiple conformations for protein and RNA structures. The experiment had partial success in reproducing the ensembles for four out of nine targets, showing positive results. Enhanced sampling using variations of the AlphaFold2 deep learning method proved to be the most effective approach for protein structures. However, challenges remain in handling sparse or low-resolution experimental data and modeling RNA/protein complexes.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Adam J. Simpkin, Iracema Caballero, Stuart McNicholas, Kyle Stevenson, Elisabet Jimenez, Filomneno Sanchez Rodriguez, Maria Fando, Ville Uski, Charles Ballard, Grzegorz Chojnowski, Andrey Lebedev, Eugene Krissinel, Isabel Uson, Daniel J. Rigden, Ronan M. Keegan
Summary: The results of CASP14 showcased Deepmind's significant advancement in computational protein structure-prediction methodology, presenting both challenges and opportunities for experimental structural biology. The CCP4 suite introduces new utilities and enhanced applications to address the phase problem.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
