Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.
David Sehnal,David Sehnal,David Sehnal,Sebastian Bittrich,Mandar Deshpande,Radka Svobodová,Radka Svobodová,Karel Berka,Václav Bazgier,Sameer Velankar,Stephen K. Burley,Stephen K. Burley,Jaroslav Koča,Jaroslav Koča,Alexander S. Rose +14 more
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TLDR
Mol* as mentioned in this paper is a web-native 3D visualization and streaming tool for macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations.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/.read more
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AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.
Mihaly Varadi,Stephen Anyango,Mandar Deshpande,Sreenath Nair,Cindy Natassia,Galabina Yordanova,David Yu Yuan,Oana Stroe,Gemma Wood,Agata Laydon,Augustin Žídek,Tim Green,Kathryn Tunyasuvunakool,Stig Petersen,John M. Jumper,Ellen Clancy,Richard E. Green,Ankur Vora,Mira Lutfi,Michael Figurnov,Andrew Cowie,Nicole Hobbs,Pushmeet Kohli,Gerard J. Kleywegt,Ewan Birney,Demis Hassabis,Sameer Velankar +26 more
TL;DR: The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions.
Journal ArticleDOI
InterPro in 2022
Typhaine Paysan-Lafosse,Matthias Blum,Sara Chuguransky,Tiago Daniel Pereira Grego,Beatriz Pinto,Gustavo A. Salazar,Maxwell L. Bileschi,Peer Bork,Alan Bridge,Lucy J. Colwell,Julian Gough,Daniel H. Haft,Ivica Letunic,Aron Marchler-Bauer,Huaiyu Mi,Darren A. Natale,Christine A. Orengo,Arun Prasad Pandurangan,Catherine Rivoire,Christian J. A. Sigrist,Ian Sillitoe,Narmada Thanki,Paul Thomas,Silvio C. E. Tosatto,Cathy H. Wu,Alex Bateman +25 more
TL;DR: The InterPro database as discussed by the authors provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites, and provides a more user friendly access to the data.
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Polyethylene Glycol Immunogenicity: Theoretical, Clinical, and Practical Aspects of Anti-Polyethylene Glycol Antibodies.
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Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.
Andrew D. Yates,James E. Allen,Ridwan M Amode,Andrey G Azov,Matthieu Barba,Andrés Becerra,Jyothish Bhai,Lahcen I. Campbell,Manuel Carbajo Martinez,Marc Chakiachvili,Kapeel Chougule,Mikkel B. Christensen,Bruno Contreras-Moreira,Alayne Cuzick,Luca Da Rin Fioretto,Paul Davis,Nishadi De Silva,Stavros Diamantakis,Sarah Dyer,Justin Elser,Carla Valeria Filippi,Carla Valeria Filippi,Carla Valeria Filippi,Astrid Gall,Dionysios Grigoriadis,Cristina Guijarro-Clarke,Parul Gupta,Kim E. Hammond-Kosack,Kevin L. Howe,Pankaj Jaiswal,Vinay Kaikala,Vivek Kumar,Sunita Kumari,Nick Langridge,Tuan Le,Manuel Luypaert,Gareth Maslen,Thomas Maurel,Benjamin Moore,Matthieu Muffato,Aleena Mushtaq,Guy Naamati,Sushma Naithani,Andrew Olson,Anne Parker,Michael Paulini,Helder Pedro,Emily Perry,Justin Preece,Mark Quinton-Tulloch,Faye H. Rodgers,Marc Rosello,Magali Ruffier,James Seager,Vasily Sitnik,Michal Szpak,John Tate,Marcela K. Tello-Ruiz,Stephen J. Trevanion,Martin Urban,Doreen Ware,Doreen Ware,Sharon Wei,Gary Williams,Andrea Winterbottom,Magdalena Zarowiecki,Robert D. Finn,Paul Flicek +67 more
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Journal ArticleDOI
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Robert Olson,Rida Assaf,Thomas Brettin,Neal Conrad,Clark Cucinell,James J. Davis,Donald M Dempsey,Allan W. Dickerman,Emily M. Dietrich,Ronald W. Kenyon,Mehmet Kuscuoglu,Elliot J. Lefkowitz,Jian Lu,Dustin Machi,Catherine A. Macken,Chunhong Mao,Anna Maria Niewiadomska,Marcus Nguyen,Gary J. Olsen,Jamie Overbeek,Bruce Parrello,Victoria A. Parrello,Jacob S Porter,Gordon D. Pusch,Maulik Shukla,Indresh Singh,Lucy Stewart,Gene S. Tan,Chris Thomas,Margo VanOeffelen,Veronika Vonstein,Zachary S Wallace,Andrew S. Warren,Alice R. Wattam,Fang Fang Xia,Hyunseung Yoo,Yu Zhang,Christian M. Zmasek,Richard H. Scheuermann,Rick Stevens +39 more
TL;DR: The BV-BRC as discussed by the authors merged the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center.
References
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TL;DR: The Pfam database is a widely used resource for classifying protein sequences into families and domains and the reintroduced Pfam-B which provides an automatically generated supplement to Pfam and contains 136 730 novel clusters of sequences that are not yet matched by a Pfam family.
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TL;DR: Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific ww PDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.
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