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            "name": "MolStar",
            "description": "Mol* is a web application for visualization of biomacromolecular structures including experimental data (for example electron densities) and annotations. Can visualize also molecular dynamics.",
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                        "title": "Mol∗Viewer: Modern web app for 3D visualization and analysis of large biomolecular structures",
                        "abstract": "Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol∗ development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol∗ Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol∗ Viewer is open source and freely available at https://molstar.org/.",
                        "date": "2021-07-02T00:00:00Z",
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                        "authors": [
                            {
                                "name": "Sehnal D."
                            },
                            {
                                "name": "Bittrich S."
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                            {
                                "name": "Deshpande M."
                            },
                            {
                                "name": "Svobodova R."
                            },
                            {
                                "name": "Berka K."
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                            {
                                "name": "Bazgier V."
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                            {
                                "name": "Velankar S."
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                            {
                                "name": "Burley S.K."
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                            {
                                "name": "Koca J."
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                            {
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            "description": "The PlantRNA database compiles tRNA gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms.",
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                        "title": "PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes",
                        "abstract": "PlantRNA (http://plantrna.ibmp.cnrs.fr/) is a comprehensive database of transfer RNA (tRNA) gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. In the first release (PlantRNA 1.0), tRNA genes from 11 organisms were annotated. In this second version, the annotation was implemented to 51 photosynthetic species covering the whole phylogenetic tree of photosynthetic organisms, from the most basal group of Archeplastida, the glaucophyte Cyanophora paradoxa, to various land plants. tRNA genes from lower photosynthetic organisms such as streptophyte algae or lycophytes as well as extremophile photosynthetic species such as Eutrema parvulum were incorporated in the database. As a whole, about 37 000 tRNA genes were accurately annotated. In the frame of the tRNA genes annotation from the genome of the Rhodophyte Chondrus crispus, non-canonical splicing sites in the D- or T-regions of tRNA molecules were identified and experimentally validated. As for PlantRNA 1.0, comprehensive biological information including 5′- and 3′-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences and tRNA mitochondrial import are included.",
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                            {
                                "name": "Cognat V."
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                            {
                                "name": "Pawlak G."
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                            {
                                "name": "Pflieger D."
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                            {
                                "name": "Drouard L."
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                    "metadata": {
                        "title": "PlantRNA, a database for tRNAs of photosynthetic eukaryotes",
                        "abstract": "PlantRNA database (http://plantrna.ibmp.cnrs.fr/) compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. The set of annotated tRNA gene sequences has been manually curated for maximum quality and confidence. The novelty of this database resides in the inclusion of biological information relevant to the function of all the tRNAs entered in the library. This includes 5′- and 3′-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Finally, data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA-binding proteins are also included. The current annotation concerns complete genomes from 11 organisms: five flowering plants (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula and Brachypodium distachyon), a moss (Physcomitrella patens), two green algae (Chlamydomonas rein-hardtii and Ostreococcus tauri), one glaucophyte (Cyanophora paradoxa), one brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). The database will be regularly updated and implemented with new plant genome annotations so as to provide extensive information on tRNA biology to the research community. © The Author(s) 2012.",
                        "date": "2013-01-01T00:00:00Z",
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                        "authors": [
                            {
                                "name": "Cognat V."
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                            {
                                "name": "Pawlak G."
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                            {
                                "name": "Duchene A.-M."
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                            {
                                "name": "Daujat M."
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                            {
                                "name": "Gigant A."
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                            {
                                "name": "Salinas T."
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                            {
                                "name": "Michaud M."
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                            {
                                "name": "Gutmann B."
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                            {
                                "name": "Giege P."
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                            {
                                "name": "Gobert A."
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                            {
                                "name": "Marechal-Drouard L."
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                        "journal": "Nucleic Acids Research"
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                    "name": "Valerie Cognat",
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        {
            "name": "PyMut",
            "description": "PyMut is a Python3 module that fills the gap between machine learning and bioinformatics, providing methods that help in the prediction of pathology in protein mutations.",
            "homepage": "http://mmb.irbbarcelona.org/PMut/pymut",
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                            "uri": "http://edamontology.org/operation_3661",
                            "term": "SNP annotation"
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                            "term": "Variant classification"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3092",
                            "term": "Protein feature detection"
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                    ],
                    "input": [
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                            "data": {
                                "uri": "http://edamontology.org/data_2974",
                                "term": "Protein sequence (raw)"
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                                    "uri": "http://edamontology.org/format_2200",
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                    "url": "https://mmb.irbbarcelona.org/PMut/help",
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                    "doi": "10.1093/nar/gkx313",
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                        "title": "PMut: A web-based tool for the annotation of pathological variants on proteins, 2017 update",
                        "abstract": "We present here a full update of the PMut predictor, active since 2005 and with a large acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine has been renewed, and converted into a fully featured standalone training and prediction engine that not only powers PMut web portal, but that can generate custom predictors with alternative training sets or validation schemas. PMut Web portal allows the user to perform pathology predictions, to access a complete repository of pre-calculated predictions, and to generate and validate new predictors. The default predictor performs with good quality scores (MCC values of 0.61 on 10-fold cross validation, and 0.42 on a blind test with SwissVar 2016 mutations).",
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                            {
                                "name": "Lopez-Ferrando V."
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                            {
                                "name": "Gazzo A."
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                            {
                                "name": "De La Cruz X."
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                            {
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                            {
                                "name": "Gelpi J.L."
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                        "journal": "Nucleic Acids Research"
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                    "term": "Mobile genetic elements"
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                }
            ],
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            "documentation": [
                {
                    "url": "http://integronfinder.readthedocs.org/",
                    "type": [
                        "General"
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                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/nar/gkw319",
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                    "metadata": {
                        "title": "Identification and analysis of integrons and cassette arrays in bacterial genomes",
                        "abstract": "Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program-IntegronFinder-to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.",
                        "date": "2016-06-02T00:00:00Z",
                        "citationCount": 193,
                        "authors": [
                            {
                                "name": "Cury J."
                            },
                            {
                                "name": "Jove T."
                            },
                            {
                                "name": "Touchon M."
                            },
                            {
                                "name": "Neron B."
                            },
                            {
                                "name": "Rocha E.P."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.3390/microorganisms10020224",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": "2.0.1",
                    "note": null,
                    "metadata": {
                        "title": "Integron Functionality and Genome Innovation: An Update on the Subtle and Smart Strategy of Integrase and Gene Cassette Expression Regulation",
                        "abstract": "Integrons are considered hot spots for bacterial evolution, since these platforms allow one-step genomic innovation by capturing and expressing genes that provide advantageous novelties, such as antibiotic resistance. The acquisition and shuffling of gene cassettes featured by integrons enable the population to rapidly respond to changing selective pressures. However, in order to avoid deleterious effects and fitness burden, the integron activity must be tightly controlled, which happens in an elegant and elaborate fashion, as discussed in detail in the present review. Here, we aimed to provide an up‐to‐date overview of the complex regulatory networks that permeate the expression and functionality of integrons at both transcriptional and translational levels. It was possible to compile strong shreds of evidence clearly proving that these versatile platforms include functions other than acquiring and expressing gene cassettes. The well‐balanced mechanism of integron expression is intricately related with environmental signals, host cell physiology, fitness, and survival, ultimately leading to adaptation on the demand.",
                        "date": "2022-02-01T00:00:00Z",
                        "citationCount": 9,
                        "authors": [
                            {
                                "name": "Fonseca E.L."
                            },
                            {
                                "name": "Vicente A.C."
                            }
                        ],
                        "journal": "Microorganisms"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Institut Pasteur",
                    "email": null,
                    "url": "http://www.pasteur.fr/en",
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                    "name": "C3BI",
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                {
                    "name": "Jean Cury",
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                    "name": "Bertrand Neron",
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                    "note": "CNRS - UMR 352"
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                    "name": "Jean Cury",
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        {
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                    "metadata": {
                        "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench",
                        "abstract": "Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. © 2009 The Author(s).",
                        "date": "2009-05-07T00:00:00Z",
                        "citationCount": 6580,
                        "authors": [
                            {
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                            },
                            {
                                "name": "Procter J.B."
                            },
                            {
                                "name": "Martin D.M.A."
                            },
                            {
                                "name": "Clamp M."
                            },
                            {
                                "name": "Barton G.J."
                            }
                        ],
                        "journal": "Bioinformatics"
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    ]
}