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Crauwels C, Díaz A, Vranken W. GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design. J Mol Biol 2025; 437:169164. [PMID: 40268234 DOI: 10.1016/j.jmb.2025.169164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 04/11/2025] [Accepted: 04/16/2025] [Indexed: 04/25/2025]
Abstract
G protein-coupled receptors (GPCRs) are membrane proteins crucial to numerous diseases, yet many remain poorly characterized and untargeted by drugs. Chimeric GPCRs have emerged as valuable tools for elucidating GPCR function by facilitating the identification of signaling pathways, resolving structures, and discovering novel ligands of poorly understood GPCRs. Such chimeric GPCRs are obtained by merging a well- and less-well-characterized GPCR at the intracellular limits of their transmembrane regions or intracellular loops, leveraging knowledge transfer from the well-characterized GPCR. However, despite the engineering of over 200 chimeric GPCRs to date, the design process remains largely trial-and-error and lacks a standardized approach. To address this gap, we introduce GPCRchimeraDB (https://www.bio2byte.be/gpcrchimeradb/), the first comprehensive database dedicated to chimeric GPCRs. It catalogs 212 chimeric receptors, identified through literature review, and includes 1,755 class A natural GPCRs, enabling connections between chimeras and their parent receptors while facilitating the exploration of novel parent combinations. Both chimeric and natural GPCR entries are extensively described at the sequence, structural, and biophysical level through a range of visualization tools, with annotations from resources like UniProt and GPCRdb and predictions from AlphaFold2 and b2btools. Additionally, GPCRchimeraDB offers a GPCR sequence aligner and a feature comparator to investigate differences between natural and chimeric receptors. It also provides design guidelines to support rational chimera engineering. GPCRchimeraDB is therefore a resource to facilitate and optimize the design of new chimeras, so helping to gain insights into poorly characterized receptors and contributing to advances in GPCR therapeutic development.
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Affiliation(s)
- Charlotte Crauwels
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium; AI Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Adrián Díaz
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium; AI Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium; AI Lab, Vrije Universiteit Brussel, Brussels, Belgium; Chemistry Department, Vrije Universiteit Brussel, Brussels, Belgium; Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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Donvil L, Housmans JAJ, Peeters E, Vranken W, Orlando G. In silico identification of archaeal DNA-binding proteins. Bioinformatics 2025; 41:btaf169. [PMID: 40315131 PMCID: PMC12065626 DOI: 10.1093/bioinformatics/btaf169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 03/17/2025] [Accepted: 03/31/2025] [Indexed: 05/04/2025] Open
Abstract
MOTIVATION The rapid advancement of next-generation sequencing technologies has generated an immense volume of genetic data. However, these data are unevenly distributed, with well-studied organisms being disproportionately represented, while other organisms, such as from archaea, remain significantly underexplored. The study of archaea is particularly challenging due to the extreme environments they inhabit and the difficulties associated with culturing them in the laboratory. Despite these challenges, archaea likely represent a crucial evolutionary link between eukaryotic and prokaryotic organisms, and their investigation could shed light on the early stages of life on Earth. Yet, a significant portion of archaeal proteins are annotated with limited or inaccurate information. Among the various classes of archaeal proteins, DNA-binding proteins are of particular importance. While they represent a large portion of every known proteome, their identification in archaea is complicated by the substantial evolutionary divergence between archaeal and the other better studied organisms. RESULTS To address the challenges of identifying DNA-binding proteins in archaea, we developed Xenusia, a neural network-based tool capable of screening entire archaeal proteomes to identify DNA-binding proteins. Xenusia has proven effective across diverse datasets, including metagenomics data, successfully identifying novel DNA-binding proteins, with experimental validation of its predictions. AVAILABILITY AND IMPLEMENTATION Xenusia is available as a PyPI package, with source code accessible at https://github.com/grogdrinker/xenusia, and as a Google Colab web server application at xenusia.ipynb.
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Affiliation(s)
- Linus Donvil
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels B-1050, Belgium
- Center for Neurosciences (C4N), Vrije Universiteit Brussel, Research Group Experimental Pharmacology (EFAR), Jette 1050, Belgium
| | - Joëlle A J Housmans
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Research Unit VEG-i-TEC, Ghent University, Kortrijk 8500, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels B-1050, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
- AI Lab, Vrije Universiteit Brussel, Brussels 1050, Belgium
- Department of Chemistry, Vrije Universiteit Brussel, Brussels 1050, Belgium
- Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Gabriele Orlando
- Laboratory of Pathogens and Host Immunity, University of Montpellier, CNRS and INSERM, Montpellier 34095, France
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Orlando G, Raimondi D, Codice F, Tabaro F, Vranken W. Prediction of disordered regions in proteins with recurrent Neural Networks and protein dynamics. J Mol Biol 2022; 434:167579. [DOI: 10.1016/j.jmb.2022.167579] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022]
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Orlando G, Raimondi D, Duran-Romaña R, Moreau Y, Schymkowitz J, Rousseau F. PyUUL provides an interface between biological structures and deep learning algorithms. Nat Commun 2022; 13:961. [PMID: 35181656 PMCID: PMC8857184 DOI: 10.1038/s41467-022-28327-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 01/18/2022] [Indexed: 11/09/2022] Open
Abstract
Structural bioinformatics suffers from the lack of interfaces connecting biological structures and machine learning methods, making the application of modern neural network architectures impractical. This negatively affects the development of structure-based bioinformatics methods, causing a bottleneck in biological research. Here we present PyUUL ( https://pyuul.readthedocs.io/ ), a library to translate biological structures into 3D tensors, allowing an out-of-the-box application of state-of-the-art deep learning algorithms. The library converts biological macromolecules to data structures typical of computer vision, such as voxels and point clouds, for which extensive machine learning research has been performed. Moreover, PyUUL allows an out-of-the box GPU and sparse calculation. Finally, we demonstrate how PyUUL can be used by researchers to address some typical bioinformatics problems, such as structure recognition and docking.
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Affiliation(s)
- Gabriele Orlando
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | | | - Ramon Duran-Romaña
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | | | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
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Kagami L, Roca-Martínez J, Gavaldá-García J, Ramasamy P, Feenstra KA, Vranken WF. Online biophysical predictions for SARS-CoV-2 proteins. BMC Mol Cell Biol 2021; 22:23. [PMID: 33892639 PMCID: PMC8062939 DOI: 10.1186/s12860-021-00362-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues for structure-based drug design. However, not all of the SARS-CoV-2 proteins, or regions thereof, have a well-defined three-dimensional structure, and as such might exhibit ambiguous, dynamic behaviour that is not evident from static structure representations, nor from molecular dynamics simulations using these structures. MAIN: We present a website ( https://bio2byte.be/sars2/ ) that provides protein sequence-based predictions of the backbone and side-chain dynamics and conformational propensities of these proteins, as well as derived early folding, disorder, β-sheet aggregation, protein-protein interaction and epitope propensities. These predictions attempt to capture the inherent biophysical propensities encoded in the sequence, rather than context-dependent behaviour such as the final folded state. In addition, we provide the biophysical variation that is observed in homologous proteins, which gives an indication of the limits of their functionally relevant biophysical behaviour. CONCLUSION The https://bio2byte.be/sars2/ website provides a range of protein sequence-based predictions for 27 SARS-CoV-2 proteins, enabling researchers to form hypotheses about their possible functional modes of action.
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Affiliation(s)
- Luciano Kagami
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium
| | - Joel Roca-Martínez
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- VIB Structural Biology Research Centre, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jose Gavaldá-García
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- VIB Structural Biology Research Centre, Pleinlaan 2, 1050, Brussels, Belgium
| | - Pathmanaban Ramasamy
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- VIB Structural Biology Research Centre, Pleinlaan 2, 1050, Brussels, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000, Ghent, Belgium
| | - K Anton Feenstra
- IBIVU - Center for Integrative Bioinformatics, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, 1081HV, The Netherlands
- AIMMS - Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, 1081HV, The Netherlands
| | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- VIB Structural Biology Research Centre, Pleinlaan 2, 1050, Brussels, Belgium.
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Orlando G, Raimondi D, Kagami LP, Vranken WF. ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values. Nucleic Acids Res 2020; 48:W36-W40. [PMID: 32459331 PMCID: PMC7319548 DOI: 10.1093/nar/gkaa391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy data provides valuable information on the behaviour of proteins in solution. The primary data to determine when studying proteins are the per-atom NMR chemical shifts, which reflect the local environment of atoms and provide insights into amino acid residue dynamics and conformation. Within an amino acid residue, chemical shifts present multi-dimensional and complexly cross-correlated information, making them difficult to analyse. The ShiftCrypt method, based on neural network auto-encoder architecture, compresses the per-amino acid chemical shift information in a single, interpretable, amino acid-type independent value that reflects the biophysical state of a residue. We here present the ShiftCrypt web server, which makes the method readily available. The server accepts chemical shifts input files in the NMR Exchange Format (NEF) or NMR-STAR format, executes ShiftCrypt and visualises the results, which are also accessible via an API. It also enables the ”biophysically-based” pairwise alignment of two proteins based on their ShiftCrypt values. This approach uses Dynamic Time Warping and can optionally include their amino acid code information, and has applications in, for example, the alignment of disordered regions. The server uses a token-based system to ensure the anonymity of the users and results. The web server is available at www.bio2byte.be/shiftcrypt.
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Affiliation(s)
- Gabriele Orlando
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, Brussels 1050, Belgium.,Switch Laboratory, VIB, Leuven, Belgium
| | - Daniele Raimondi
- ESAT-STADIUS, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium
| | - Luciano Porto Kagami
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, Brussels 1050, Belgium
| | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, Brussels 1050, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium.,VIB Structural Biology Research Centre, Pleinlaan 2, Brussels 1050, Belgium
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Zhang D, Guan ZX, Zhang ZM, Li SH, Dao FY, Tang H, Lin H. Recent Development of Computational Predicting Bioluminescent Proteins. Curr Pharm Des 2020; 25:4264-4273. [PMID: 31696804 DOI: 10.2174/1381612825666191107100758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022]
Abstract
Bioluminescent Proteins (BLPs) are widely distributed in many living organisms that act as a key role of light emission in bioluminescence. Bioluminescence serves various functions in finding food and protecting the organisms from predators. With the routine biotechnological application of bioluminescence, it is recognized to be essential for many medical, commercial and other general technological advances. Therefore, the prediction and characterization of BLPs are significant and can help to explore more secrets about bioluminescence and promote the development of application of bioluminescence. Since the experimental methods are money and time-consuming for BLPs identification, bioinformatics tools have played important role in fast and accurate prediction of BLPs by combining their sequences information with machine learning methods. In this review, we summarized and compared the application of machine learning methods in the prediction of BLPs from different aspects. We wish that this review will provide insights and inspirations for researches on BLPs.
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Affiliation(s)
- Dan Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zheng-Xing Guan
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zi-Mei Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Shi-Hao Li
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Fu-Ying Dao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hua Tang
- Department of Pathophysiology, Southwest Medical University, Luzhou 646000, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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