Biochemistry & Molecular Biology

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Article Biochemistry & Molecular Biology

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 Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Zidek, Tim Green, Kathryn Tunyasuvunakool, Stig Petersen, John Jumper, Ellen Clancy, Richard Green, Ankur Vora, Mira Lutfi, Michael Figurnov, Andrew Cowie, Nicole Hobbs, Pushmeet Kohli, Gerard Kleywegt, Ewan Birney, Demis Hassabis, Sameer Velankar

Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Yasset Perez-Riverol, Jingwen Bai, Chakradhar Bandla, David Garcia-Seisdedos, Suresh Hewapathirana, Selvakumar Kamatchinathan, Deepti J. Kundu, Ananth Prakash, Anika Frericks-Zipper, Martin Eisenacher, Mathias Walzer, Shengbo Wang, Alvis Brazma, Juan Antonio Vizcaino

Summary: PRIDE is the largest data repository of mass spectrometry-based proteomics data in the world, with around 500 datasets submitted per month. In addition to continuous improvements in data pipelines and infrastructure, PRIDE has developed the Spectra Archive and MAGE-TAB file format to enhance sample metadata annotation and access to mass spectra.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

KEGG for taxonomy-based analysis of pathways and genomes

Minoru Kanehisa, Miho Furumichi, Yoko Sato, Masayuki Kawashima, Mari Ishiguro-Watanabe

Summary: KEGG is a manually curated database resource that integrates various biological objects classified into systems, genomic, chemical, and health information. Through the KEGG identifier and URL links, users can retrieve and browse information for different biological objects, including pathway maps, hierarchy, and genomes. KEGG has also improved KO assignment annotation and included more eukaryotic genomes for better representation of organisms in the taxonomic tree. The taxonomy mapping enables analysis of the conservation of functional and physical links among genes in different organism groups.

NUCLEIC ACIDS RESEARCH (2023)

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Article Biochemistry & Molecular Biology

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

Brad T. Sherman, Ming Hao, Ju Qiu, Xiaoli Jiao, Michael W. Baseler, H. Clifford Lane, Tomozumi Imamichi, Weizhong Chang

Summary: DAVID, a popular bioinformatics resource system, has undergone updates in 2021, including the rebuilding of the DAVID Gene system, increasing the number of gene-term records for annotation types, adding new annotations, assigning specific subgroups, and adding a species parameter for improved user experience.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Long-term cardiovascular outcomes of COVID-19

Yan Xie, Evan Xu, Benjamin Bowe, Ziyad Al-Aly

Summary: Individuals with COVID-19, even those who were not hospitalized during the acute phase of the infection, are at an increased long-term risk of various cardiovascular disorders. A study using national healthcare databases found that beyond the first 30 days after infection, individuals with COVID-19 have an elevated risk of developing cerebrovascular disorders, heart diseases, and other cardiovascular complications. The risk increases depending on the care setting during the acute phase.

NATURE MEDICINE (2022)

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Article Biochemistry & Molecular Biology

mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant

Wilfredo F. Garcia-Beltran, Kerri J. St Denis, Angelique Hoelzemer, Evan C. Lam, Adam D. Nitido, Maegan L. Sheehan, Cristhian Berrios, Onosereme Ofoman, Christina C. Chang, Blake M. Hauser, Jared Feldman, Alex L. Roederer, David J. Gregory, Mark C. Poznansky, Aaron G. Schmidt, A. John Iafrate, Vivek Naranbhai, Alejandro B. Balazs

Summary: Recent surveillance has identified the emergence of the SARS-CoV-2 Omicron variant, which carries up to 36 mutations in the spike protein and has the potential to evade vaccine-induced immunity. This study found that individuals vaccinated with mRNA vaccines exhibited strong neutralization of the Omicron variant, while most vaccinees had weak neutralization. The study also revealed that the Omicron variant infects more efficiently than other tested variants.

CELL (2022)

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Review Biochemistry & Molecular Biology

Age at onset of mental disorders worldwide: large-scale meta-analysis of 192 epidemiological studies

Marco Solmi, Joaquim Radua, Miriam Olivola, Enrico Croce, Livia Soardo, Gonzalo Salazar de Pablo, Jae Il Shin, James B. Kirkbride, Peter Jones, Jae Han Kim, Jong Yeob Kim, Andre F. Carvalho, Mary V. Seeman, Christoph U. Correll, Paolo Fusar-Poli

Summary: This study emphasizes the importance of promoting good mental health, prevention, and early intervention before the onset of mental disorders. It found that different types of mental disorders have different age at onset characteristics, providing valuable guidance for the timing of interventions for specific mental disorders.

MOLECULAR PSYCHIATRY (2022)

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Article Biochemistry & Molecular Biology

Ensembl 2022

Fiona Cunningham, James E. Allen, Jamie Allen, Jorge Alvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Jose Gonzalez Martinez, Cristina Guijarro-Clarke, Arthur Gymer, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Thomas Juettemann, Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Carlos Marugan, Shamika Mohanan, Aleena Mushtaq, Marc Naven, Denye N. Ogeh, Anne Parker, Andrew Parton, Malcolm Perry, Ivana Pilizota, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, Jose G. Perez-Silva, William Stark, Emily Steed, Kyosti Sutinen, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Michal Szpak, Anja Thormann, Francesca Floriana Tricomi, David Urbina-Gomez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Natalie Willhoft, Andrea Winterbottom, Elizabeth Wass, Marc Chakiachvili, Bethany Flint, Adam Frankish, Stefano Giorgetti, Leanne Haggerty, Sarah E. Hunt, Garth R. IIsley, Jane E. Loveland, Fergal J. Martin, Benjamin Moore, Jonathan M. Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, John Tate, David Thybert, Stephen J. Trevanion, Sarah Dyer, Peter W. Harrison, Kevin L. Howe, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek

Summary: Ensembl is unique in its flexible infrastructure for access to genomic data and annotation. They have focused on expediting annotation of new assemblies via the Ensembl Rapid Release platform, with the greatest annual number of newly annotated genomes released. They also developed a new method for comparative analyses and annotated non-vertebrate eukaryotes for the first time.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

The Omicron variant is highly resistant against antibody-mediated neutralization: Implications for control of the COVID-19 pandemic

Markus Hoffmann, Nadine Krueger, Sebastian Schulz, Anne Cossmann, Cheila Rocha, Amy Kempf, Inga Nehlmeier, Luise Graichen, Anna-Sophie Moldenhauer, Martin S. Winkler, Martin Lier, Alexandra Dopfer-Jablonka, Hans-Martin Jaeck, Georg M. N. Behrens, Stefan Poehlmann

Summary: The Omicron variant of SARS-CoV-2 is spreading rapidly and shows resistance to most therapeutic antibodies. It also evades neutralization by antibodies induced by infection or vaccination more efficiently than the Delta variant. This suggests that therapeutic antibodies may not be effective against the Omicron variant, and double vaccination with BNT162b2 may not provide adequate protection against severe disease caused by this variant.

CELL (2022)

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Article Biochemistry & Molecular Biology

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

Wanwisa Dejnirattisai, Jiandong Huo, Daming Zhou, Jiri Zahradnik, Piyada Supasa, Chang Liu, Helen M. E. Duyvesteyn, Helen M. Ginn, Alexander J. Mentzer, Aekkachai Tuekprakhon, Rungtiwa Nutalai, Beibei Wang, Aiste Dijokaite, Suman Khan, Ori Avinoam, Mohammad Bahar, Donal Skelly, Sandra Adele, Sile Ann Johnson, Ali Amini, Thomas G. Ritter, Chris Mason, Christina Dold, Daniel Pan, Sara Assadi, Adam Bellass, Nicola Omo-Dare, David Koeckerling, Amy Flaxman, Daniel Jenkin, Parvinder K. Aley, Merryn Voysey, Sue Ann Costa Clemens, Felipe Gomes Naveca, Valdinete Nascimento, Fernanda Nascimento, Cristiano Fernandes da Costa, Paola Cristina Resende, Alex Pauvolid-Correa, Marilda M. Siqueira, Vicky Baillie, Natali Serafin, Gaurav Kwatra, Kelly Da Silva, Shabir A. Madhi, Marta C. Nunes, Tariq Malik, Peter J. M. Openshaw, J. Kenneth Baillie, Malcolm G. Semple, Alain R. Townsend, Kuan-Ying A. Huang, Tiong Kit Tan, Miles W. Carroll, Paul Klenerman, Eleanor Barnes, Susanna J. Dunachie, Bede Constantinides, Hermione Webster, Derrick Crook, Andrew J. Pollard, Teresa Lambe, Neil G. Paterson, Mark A. Williams, David R. Hall, Elizabeth E. Fry, Juthathip Mongkolsapaya, Jingshan Ren, Gideon Schreiber, David Stuart, Gavin R. Screaton

Summary: On November 24, 2021, the sequence of a new SARS-CoV-2 variant, Omicron-B.1.1.529, was announced. Compared to previous variants, Omicron has a higher number of mutations in the Spike (S) protein. Serum neutralization of Omicron by individuals vaccinated or previously infected with Alpha, Beta, Gamma, or Delta variants is significantly reduced or ineffective. Third vaccine doses can boost neutralization titers against Omicron, and high titers are observed in both vaccinated individuals and those infected with the Delta variant. Most potent monoclonal antibodies and antibodies under development are unable to effectively neutralize Omicron due to mutations in its Spike protein. Omicron has structural changes compared to earlier viruses and utilizes mutations that enhance its binding to ACE2, allowing for immune escape. This results in a large number of mutations in the ACE2 binding site and a rebalancing of receptor affinity similar to earlier pandemic viruses.

CELL (2022)

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Article Biochemistry & Molecular Biology

The carbohydrate-active enzyme database: functions and literature

Elodie Drula, Marie-Line Garron, Suzan Dogan, Vincent Lombard, Bernard Henrissat, Nicolas Terrapon

Summary: The CAZy database, freely available for browsing and download, is deeply rooted in human curation and plays a crucial role in maintaining and updating family classification, classifying new sequences, and presenting functional information. Over the past 8 years, there has been an increase in novel families and extensive annotations conducted, highlighting the significant amount of work involved in analyzing and reporting biochemical data from the literature.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Search and sequence analysis tools services from EMBL-EBI in 2022

Fabio Madeira, Matt Pearce, Adrian R. N. Tivey, Prasad Basutkar, Joon Lee, Ossama Edbali, Nandana Madhusoodanan, Anton Kolesnikov, Rodrigo Lopez

Summary: The EMBL-EBI search and sequence analysis tools frameworks allow integrated access to data resources and core bioinformatics analytical tools. These tools can be interacted with through user-friendly web applications and APIs. Recent improvements have been made to accommodate the increasing data requirements during the COVID-19 pandemic.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes

Jan P. Meier-Kolthoff, Joaquim Sarda Carbasse, Rosa L. Peinado-Olarte, Markus Goeker

Summary: Microbial systematics is influenced by genome-based methods and faces challenges from the increasing number of taxon names and associated sequences. Accurate and reliable high-throughput platforms like LPSN and TYGS are essential for handling the data efficiently. The updates include new features and expanded database content to provide easy access to the data.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

Jaime A. Castro-Mondragon, Rafael Riudavets-Puig, Ieva Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolas Manosalva Perez, Oriol Fornes, Tiffany Y. Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris Lenhard, Klaas Vandepoele, Wyeth W. Wasserman, Francois Parcy, Anthony Mathelier

Summary: JASPAR is an open-access database containing manually curated, non-redundant transcription factor binding profiles across six taxonomic groups. The latest release introduces new profiles for plants, vertebrates, urochordates, and insects, as well as new tools for TFBS enrichment analysis and data access. The database can be accessed through various platforms, including the JASPAR website, RESTful API, R/Bioconductor data package, and a new Python package pyJASPAR.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies

Laura A. VanBlargan, John M. Errico, Peter J. Halfmann, Seth J. Zost, James E. Crowe, Lisa A. Purcell, Yoshihiro Kawaoka, Davide Corti, Daved H. Fremont, Michael S. Diamond

Summary: The emergence of the B.1.1.529 Omicron variant raises concerns about the efficacy of antibody countermeasures. This study shows that some of the antibodies currently in clinical use may lose their ability to neutralize the Omicron variant.

NATURE MEDICINE (2022)

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Article Biochemistry & Molecular Biology

HMDB 5.0: the Human Metabolome Database for 2022

David S. Wishart, AnChi Guo, Eponine Oler, Fei Wang, Afia Anjum, Harrison Peters, Raynard Dizon, Zinat Sayeeda, Siyang Tian, Brian L. Lee, Mark Berjanskii, Robert Mah, Mai Yamamoto, Juan Jovel, Claudia Torres-Calzada, Mickel Hiebert-Giesbrecht, Vicki W. Lui, Dorna Varshavi, Dorsa Varshavi, Dana Allen, David Arndt, Nitya Khetarpal, Aadhavya Sivakumaran, Karxena Harford, Selena Sanford, Kristen Yee, Xuan Cao, Zachary Budinski, Jaanus Liigand, Lun Zhang, Jiamin Zheng, Rupasri Mandal, Naama Karu, Maija Dambrova, Helgi B. Schioth, Russell Greiner, Vasuk Gautam

Summary: The Human Metabolome Database (HMDB) has been providing comprehensive information about human metabolites since 2007, and has undergone significant improvements and upgrades in its latest update, HMDB 5.0. These improvements include an increase in the number of metabolite entries, enhancements to metabolite descriptions, new visualization tools, and more accurately predicted spectral data sets. These upgrades are aimed at improving the usability and potential applications of the HMDB in various fields, including human metabolomics, exposomics, lipidomics, nutritional science, biochemistry, and clinical chemistry.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

SARS-CoV-2 vaccination induces immunological T cell memory able to cross-recognize variants from Alpha to Omicron

Alison Tarke, Camila H. Coelho, Zeli Zhang, Jennifer M. Dan, Esther Dawen Yu, Nils Methot, Nathaniel Bloom, Benjamin Goodwin, Elizabeth Phillips, Simon Mallal, John Sidney, Gilberto Filaci, Daniela Weiskopf, Ricardo da Silva Antunes, Shane Crotty, Alba Grifoni, Alessandro Sette

Summary: T cell responses induced by different vaccine platforms cross-recognize early SARS-CoV-2 variants, while memory B cells and neutralizing antibodies show significant decreases. The majority of memory T cell responses are preserved against variants, with lower recognition of Omicron by memory B cells.

CELL (2022)

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Article Biochemistry & Molecular Biology

The reactome pathway knowledgebase 2022

Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio

Summary: The Reactome Knowledgebase, a core resource of Elixir, provides manually curated molecular details of human biological processes, serving as a digital archive and tool for discovering functional relationships. Recent work has expanded annotations of signaling processes, drugs targeting them, infections by coronaviruses, and better analysis tools for high-throughput data and placement of unstudied proteins.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Database resources of the national center for biotechnology information

Eric W. Sayers, Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau, Ryan Connor, Kathryn Funk, Chris Kelly, Sunghwan Kim, Tom Madej, Aron Marchler-Bauer, Christopher Lanczycki, Stacy Lathrop, Zhiyong Lu, Francoise Thibaud-Nissen, Terence Murphy, Lon Phan, Yuri Skripchenko, Tony Tse, Jiyao Wang, Rebecca Williams, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry

Summary: The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including databases for nucleic acid sequences and life science journal citations. It provides search and retrieval operations for most of these data from 35 distinct databases, with E-utilities serving as the programming interface. Several resources received significant updates in the past year.

NUCLEIC ACIDS RESEARCH (2022)

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Review Biochemistry & Molecular Biology

Ferroptosis turns 10: Emerging mechanisms, physiological functions, and therapeutic applications

Brent R. Stockwell

Summary: This review describes the key regulators of ferroptosis and provides an overview of metabolism, ROS biology, and iron biology. Additionally, it highlights the important concepts and unanswered questions in the field of ferroptosis. The future holds promise for further breakthroughs in understanding the mechanisms of ferroptosis and utilizing it for therapeutic purposes.

CELL (2022)

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