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Biochemistry & Molecular Biology
Noemi del Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal, Colin Combe, Elisabet Barrera, Livia Perfetto, Karyn How, Prashansa Ratan, Gautam Shirodkar, Odilia Lu, Balint Meszaros, Xavier Watkins, Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria Jesus Martin, Simona Panni, Margaret Duesbury, Sylvain D. Vallet, Juri Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwinski, Sandra Orchard, Pablo Porras, Kalpana Panneerselvam, Henning Hermjakob
Summary: IntAct is a curated database of molecular interactions derived from scientific literature, containing over one million binary interactions curated by twelve global partners. The IMEx curation policy emphasizes fine-grained data and curation model to capture essential experimental details for interpretation of the molecular interaction data. Recently, IntAct has introduced a completely redeveloped website to present data in a more user-friendly and detailed way.
NUCLEIC ACIDS RESEARCH
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Biochemistry & Molecular Biology
Marcus Mendes, Jarjapu Mahita, Nina Blazeska, Jason Greenbaum, Brendan Ha, Kelly Wheeler, Jiyao Wang, Deborah Shackelford, Alessandro Sette, Bjoern Peters
Summary: The Immune Epitope Database (IEDB) is a database that catalogs T cell, B cell, and major histocompatibility complex ligand information in the context of infectious disease, allergy, autoimmunity, and transplantation. IEDB-3D is an important component of this database, which provides three-dimensional structural data on T cell receptors, antibodies, and pairwise residue interactions between immune receptors and antigens. With the release of IEDB-3D 2.0, a new 3D viewer experience and epitope mapping system have been implemented, allowing for better visualization of epitope data and highlighting immunogenic regions of antigens.
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Biochemistry & Molecular Biology
Artem Stetsenko, Pavlo Stehantsev, Natalia O. Dranenko, Mikhail S. Gelfand, Albert Guskov
Summary: The study reports the functional and structural analysis of a membrane protein CmaX from a pathogenic Pseudomonas aeruginosa bacterium, which has a signature motif deviating from the canonical one. Despite the difference in composition, CmaX shows no changes in substrate selectivity or transport, suggesting that deviations from the canonical motif can easily alter during evolution.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
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Dentistry, Oral Surgery & Medicine
W. W. Lau, M. Hardt, Y. H. Zhang, M. Freire, S. Ruhl
Summary: Saliva is now being used for on-site, remote, and real-time monitoring of oral and systemic health. The Human Salivary Proteome (HSP) Wiki is a public platform that integrates data from various sources to help researchers explore the protein composition of saliva.
JOURNAL OF DENTAL RESEARCH
(2021)
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Biochemistry & Molecular Biology
Hamidreza Ghafouri, Tamas Lazar, Alessio Del Conte, Luiggi G. Tenorio Ku, Silvio C. E. PED Consortium, Peter Tompa, Silvio C. E. Tosatto, Alexander Miguel Monzon
Summary: The Protein Ensemble Database is a primary resource for storing structural ensembles of intrinsically disordered proteins. The updated version reflects advancements in the field and includes new features to improve the accessibility and usability of the database.
NUCLEIC ACIDS RESEARCH
(2023)
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Biochemistry & Molecular Biology
Broto Chakrabarty, Nita Parekh
Summary: Recent research has focused on repeat proteins due to stable folds, high conservation, and diverse functions they offer. A database called DbStRiPs was developed for annotation and classification of tandem structural repeat proteins, integrating sequence and structure information to refine annotations and identify novel repeat families. Analysis revealed novel protein repeat families and clusters, enhancing understanding of repeat protein diversity and function.
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Beatriz Seoane, Alessandra Carbone
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PLOS COMPUTATIONAL BIOLOGY
(2021)
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Mavrik Zavarin, Elliot Chang, Haruko Wainwright, Nicholas Parham, Rahul Kaukuntla, Jadallah Zouabe, Amanda Deinhart, Victoria Genetti, Sam Shipman, Frank Bok, Vinzenz Brendler
Summary: This paper presents a comprehensive data-to-model workflow, including the development of a FAIR sorption database and a data fitting workflow. The workflow efficiently optimizes surface complexation reaction constants and is used for parameterizing reactive transport models.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
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Ecology
Irena Beidler, Craig S. Robb, Silvia Vidal-Melgosa, Marie-Katherin Zuhlke, Daniel Bartosik, Vipul Solanki, Stephanie Markert, Dorte Becher, Thomas Schweder, Jan-Hendrik Hehemann
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Multidisciplinary Sciences
Shigeharu Moriya
Summary: Many microbes in the natural environment are difficult to cultivate, making culture-independent analysis crucial for understanding their ecological functions. Total RNA sequencing offers advantages for analyzing entire microbial communities, but biases may arise in quantitative analysis. This study developed a mapping-based total RNA-seq analysis, which showed superior outcomes compared to other strategies, providing quantitative information on microbial community structure.
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Biochemistry & Molecular Biology
Michael Loukeris, Zahra Assur Sanghai, Jeremie Vendome, Wayne A. Hendrickson, Brian Kloss, Filippo Mancia
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JOURNAL OF MOLECULAR BIOLOGY
(2021)
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Biochemical Research Methods
Kristen D. Curry, Qi Wang, Michael G. Nute, Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, Tor Savidge, Sonia Villapol, Alexander Dilthey, Todd J. Treangen
Summary: 16S ribosomal RNA-based analysis is the standard method for studying microbial community composition. Full-length 16S rRNA gene sequences have the potential to provide species-level accuracy. Emu is an approach that can generate taxonomic abundance profiles from full-length 16S rRNA reads, accurately estimating microbial abundance.
Review
Biochemistry & Molecular Biology
Karolina Michalska, Andrzej Joachimiak
Summary: Structural Genomics emerged over the last three decades to bridge the gap between microbial genomic, functional, and structural data. The field has developed structure-determination pipelines and applied them to uncharacterized proteins, leading to rapid progress in molecular and structural biology. The Protein Data Bank played a central role in coordinating efforts and maintaining high quality of structural data.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
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Ecology
Robert M. Bowers, Stephen Nayfach, Frederik Schulz, Sean P. Jungbluth, Ilona A. Ruhl, Andriy Sheremet, Janey Lee, Danielle Goudeau, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Rex R. Malmstrom, Nikos C. Kyrpides, Peter F. Dunfield, Tanja Woyke
Summary: Advancements in single-cell genomics have enabled rapid and affordable sequencing of microbial communities, providing a comprehensive snapshot of community composition and function. This approach also allows for the direct linkage of mobile elements to hosts and analysis of population heterogeneity among dominant community members.
Review
Biochemistry & Molecular Biology
Rachel Evans, Sravani Ramisetty, Prakash Kulkarni, Keith Weninger
Summary: Intense study of intrinsically disordered proteins (IDPs) began in the late 1990s and revealed their important functions. Over the past two decades, it has become clear that IDPs play critical roles in various biological phenomena. The application of integrative structural biology has emerged as an essential approach to understanding IDP phenomena.
Meeting Abstract
Biochemistry & Molecular Biology
Jared Sagendorf, Helen M. Berman, Remo Rohs
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2015)
Letter
Biochemistry & Molecular Biology
Aleksandras Gutmanas, Paul D. Adams, Benjamin Bardiaux, Helen M. Berman, David A. Case, Rasmus H. Fogh, Peter Guentert, Pieter M. S. Hendrickx, Torsten Herrmann, Gerard J. Kleywegt, Naohiro Kobayashi, Oliver F. Lange, John L. Markley, Gaetano T. Montelione, Michael Nilges, Timothy J. Ragan, Charles D. Schwieters, Roberto Tejero, Eldon L. Ulrich, Sameer Velankar, Wim F. Vranken-, Jonathan R. Wedell, John Westbrook, David S. Wishart, Geerten W. Vuister
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NUCLEIC ACIDS RESEARCH
(2016)
News Item
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Andrej Sali, Helen M. Berman, Torsten Schwede, Jill Trewhella, Gerard Kleywegt, Stephen K. Burley, John Markley, Haruki Nakamura, Paul Adams, Alexandre M. J. J. Bonvin, Wah Chiu, Matteo Dal Peraro, Frank Di Maio, Thomas E. Ferrin, Kay Gruenewald, Aleksandras Gutmanas, Richard Henderson, Gerhard Hummer, Kenji Iwasaki, Graham Johnson, Catherine L. Lawson, Jens Meiler, Marc A. Marti-Renom, Gaetano T. Montelione, Michael Nilges, Ruth Nussinov, Ardan Patwardhan, Juri Rappsilber, Randy J. Read, Helen Saibil, Gunnar F. Schroeder, Charles D. Schwieters, Claus A. M. Seidel, Dmitri Svergun, Maya Topf, Eldon L. Ulrich, Sameer Velankar, John D. Westbrook
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Helen M. Berman, Stephen K. Burley, Gerard J. Kleywegt, John L. Markley, Haruki Nakamura, Sameer Velankar
CURRENT OPINION IN STRUCTURAL BIOLOGY
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Biochemistry & Molecular Biology
Peter W. Rose, Andreas Prlic, Ali Altunkaya, Chunxiao Bi, Anthony R. Bradley, Cole H. Christie, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Rachel Kramer Green, David S. Goodsell, Brian Hudson, Tara Kalro, Robert Lowe, Ezra Peisach, Christopher Randle, Alexander S. Rose, Chenghua Shao, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John D. Westbrook, Jesse Woo, Huangwang Yang, Jasmine Y. Young, Christine Zardecki, Helen M. Berman, Stephen K. Burley
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Paul D. Adams, Kathleen Aertgeerts, Cary Bauer, Jeffrey A. Bell, Helen M. Berman, Talapady N. Bhat, Jeff M. Blaney, Evan Bolton, Gerard Bricogne, David Brown, Stephen K. Burley, David A. Case, Kirk L. Clark, Tom Darden, Paul Emsley, Victoria A. Feher, Zukang Feng, Colin R. Groom, Seth F. Harris, Jorg Hendle, Thomas Holder, Andrzej Joachimiak, Gerard J. Kleywegt, Tobias Krojer, Joseph Marcotrigiano, Alan E. Mark, John L. Markley, Matthew Miller, Wladek Minor, Gaetano T. Montelione, Garib Murshudov, Atsushi Nakagawa, Haruki Nakamura, Anthony Nicholls, Marc Nicklaus, Robert T. Nolte, Anil K. Padyana, Catherine E. Peishoff, Susan Pieniazek, Randy J. Read, Chenghua Shao, Steven Sheriff, Oliver Smart, Stephen Soisson, John Spurlino, Terry Stouch, Radka Svobodova, Wolfram Tempel, Thomas C. Terwilliger, Dale Tronrud, Sameer Velankar, Suzanna C. Ward, Gregory L. Warren, John D. Westbrook, Pamela Williams, Huanwang Yang, Jasmine Young
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NUCLEIC ACIDS RESEARCH
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Stephen K. Burley, Genji Kurisu, John L. Markley, Haruki Nakamura, Sameer Velankar, Helen M. Berman, Andrej Sali, Torsten Schwede, Jill Trewhella
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Brinda Vallat, Benjamin Webb, John D. Westbrook, Andrej Sali, Helen M. Berman
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Stephen K. Burley, Helen M. Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S. Goodsell, Rachel K. Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Tara Kalro, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Periskova, Andreas Prlic, Chris Randle, Alexander Rose, Peter Rose, Raul Sala, Monica Sekharan, Chenghua Shao, Lihua Tan, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young, Marina Zhuravleva, Christine Zardecki
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(2019)
Meeting Abstract
Chemistry, Multidisciplinary
Catherine L. Lawson, Margaret J. Gabanyi, John Westbrook, Jasmine Young, Shuchismita Dutta, Ezra Peisach, Brian P. Hudson, Peter Rose, Jose Duarte, Amy Sarjeant, Stephen K. Burley, Helen M. Berman
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