An advocate for Africa.

With rigorous science and good-humored braggadocio, Tulio de Oliveira champions coronavirus research from the Global South.

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

The evolution of the antimicrobial peptide database over 18 years: Milestones and new features.

The antimicrobial peptide database (APD) has served the antimicrobial peptide field for 18 years. Because it is widely used in research and education, this article documents database milestones and key events that have transformed it into the current form. A comparison is made for the APD peptide statistics between 2010 and 2020, validating the major database findings to date. We also describe new additions ranging from peptide entries to search functions. Of note, the APD also contains antimicrobial peptides from host microbiota, which are important in shaping immune systems and could be linked to a variety of human diseases. Finally, the database has been re-programmed to the web branding and latest security compliance of the University of Nebraska Medical Center. The reprogrammed APD can be accessed at https://aps.unmc.edu.

Structural genomics and the Protein Data Bank.

The field of Structural Genomics arose over the last 3 decades to address a large and rapidly growing divergence between microbial genomic, functional, and structural data. Several international programs took advantage of the vast genomic sequence information and evaluated the feasibility of structure determination for expanded and newly discovered protein families. As a consequence, structural genomics has developed structure-determination pipelines and applied them to a wide range of novel, uncharacterized proteins, often from "microbial dark matter," and later to proteins from human pathogens. Advances were especially needed in protein production and rapid de novo structure solution. The experimental three-dimensional models were promptly made public, facilitating structure determination of other members of the family and helping to understand their molecular and biochemical functions. Improvements in experimental methods and databases resulted in fast progress in molecular and structural biology. The Protein Data Bank structure repository played a central role in the coordination of structural genomics efforts and the structural biology community as a whole. It facilitated development of standards and validation tools essential for maintaining high quality of deposited structural data.

In conversation with Janet Thornton.

Professor Dame Janet Thornton is a pioneer in structural bioinformatics who has developed an extensive computational toolkit for the analysis of protein structure and inference of function and evolution. She began her career in science as a physicist, following an undergraduate degree in physics from the University of Nottingham with a Master's and PhD in biophysics in London. After undertaking a postdoctoral position in the group of Sir David Phillips at the University of Oxford, Janet returned to London where she eventually held professorial appointments at both University College London and Birkbeck College. During this period, she formed a number of long-standing and fruitful collaborations that, amongst other advances, led to the development of a software that revolutionised protein structure validation - PROCHECK - as well as a unique classification system for protein structures, CATH. Janet was Director of the European Bioinformatics Institute EMBL-EBI between 2001 until 2015 and played a pivotal role in launching ELIXIR, a pan-European infrastructure for biological data. She remains at EMBL-EBI as a senior scientist, and her group primarily focuses on understanding protein structure and function and how these contribute to our understanding of diseases and ageing. Her contributions to the life sciences have been distinguished through numerous awards and honours, and in 2012, she was appointed a Dame Commander of the Order of the British Empire for services to bioinformatics.

The Future of Protein Secondary Structure Prediction Was Invented by Oleg Ptitsyn.

When Oleg Ptitsyn and his group published the first secondary structure prediction for a protein sequence, they started a research field that is still active today. Oleg Ptitsyn combined fundamental rules of physics with human understanding of protein structures. Most followers in this field, however, use machine learning methods and aim at the highest (average) percentage correctly predicted residues in a set of proteins that were not used to train the prediction method. We show that one single method is unlikely to predict the secondary structure of all protein sequences, with the exception, perhaps, of future deep learning methods based on very large neural networks, and we suggest that some concepts pioneered by Oleg Ptitsyn and his group in the 70s of the previous century likely are today's best way forward in the protein secondary structure prediction field.

SciPy 1.0: fundamental algorithms for scientific computing in Python.

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

Half a century of computer methods and programs in biomedicine: A bibliometric analysis from 1970 to 2017.

BACKGROUND AND OBJECTIVE: Computer Methods and Programs in Biomedicine (CMPB) is a leading international journal that presents developments about computing methods and their application in biomedical research. The journal published its first issue in 1970. In 2020, the journal celebrates the 50th anniversary. Motivated by this event, this article presents a bibliometric analysis of the publications of the journal during this period (1970-2017). METHODS: The objective is to identify the leading trends occurring in the journal by analysing the most cited papers, keywords, authors, institutions and countries. For doing so, the study uses the Web of Science Core Collection database. Additionally, the work presents a graphical mapping of the bibliographic information by using the visualization of similarities (VOS) viewer software. This is done to analyze bibliographic coupling, co-citation and co-occurrence of keywords. RESULTS: CMPB is identified as a leading and core journal for biomedical researchers. The journal is strongly connected to IEEE Transactions on Biomedical Engineering and IEEE Transactions on Medical Imaging. Paper from Wang, Jacques, Zheng (published in 1995) is its most cited document. The top author in this journal is James Geoffrey Chase and the top contributing institution is Uppsala U (Sweden). Most of the papers in CMPB are from the USA followed by the UK and Italy. China and Taiwan are the only Asian countries to appear in the top 10 publishing in CMPB. A keyword co-occurrences analysis revealed strong co-occurrences for classification, picture archiving and communication system (PACS), heart rate variability, survival analysis and simulation. Keywords analysis for the last decade revealed that machine learning for a variety of healthcare problems (including image processing and analysis) dominated other research fields in CMPB. CONCLUSIONS: It can be concluded that CMPB is a world-renowned publication outlet for biomedical researchers which has been growing in a number of publications since 1970. The analysis also conclude that the journal is very international with publications from all over the world although today European countries are the most productive ones.

Heineken, Tsuchiya and Aris on the mathematical status of the pseudo-steady state hypothesis: A classic from volume 1 of Mathematical Biosciences.

Volume 1, Issue 1 of Mathematical Biosciences was the venue for a now-classic paper on the application of singular perturbation theory in enzyme kinetics, "On the mathematical status of the pseudo-steady state hypothesis of biochemical kinetics" by F. G. Heineken, H. M. Tsuchiya and R. Aris. More than 50 years have passed, and yet this paper continues to be studied and mined for insights. This perspective discusses both the strengths and weaknesses of the work presented in this paper. For many, the justification of the pseudo-steady-state approximation using singular perturbation theory is the main achievement of this paper. However, there is so much more material here, which laid the foundation for a great deal of research in mathematical biochemistry in the intervening decades. The parameterization of the equations, construction of the first-order uniform singular-perturbation solution, and an attempt to apply similar principles to the pseudo-equilibrium approximation are discussed in particular detail.

Out with the old, in with the new: Virtual versus physical crossmatching in the modern era.

The virtual crossmatch (VXM) is gaining acceptance as an alternative approach to assess donor:recipient compatibility prior to transplantation. In contrast to a physical crossmatch, the virtual crossmatch does not require viable donor cells but rather relies on complete HLA typing of the donor and current antibody assessment of the recipient. Thus, the VXM can be performed in minutes which allows for faster transplant decisions thereby increasing the likelihood that organs can be shipped across significant distances yet safely transplanted. Here, we present a brief review of the past 50 years of histocompatibility testing; from the original complement-dependent cytotoxicity crossmatch in 1969 to the new era of molecular HLA typing, solid-phase antibody testing and virtual crossmatching. These advancements have shaped a paradigm shift in our approach to transplantation. That is, foregoing a prospective physical crossmatch in favor of a VXM. In this review, we undertake an in-depth analysis of the pros- and cons- of physical and virtual crossmatching.Finally, we provide objective data on the selected use of the VXM which demonstrate the value of a VXM in lieu of the traditional physical crossmatch for safe and efficient organ transplantation.

The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development.

For more than one decade, CELLmicrocosmos tools are being developed. Here, we discus some of the technical and administrative hurdles to keep a software suite running so many years. The tools were being developed during a number of student projects and theses, whereas main developers refactored and maintained the code over the years. The focus of this publication is laid on two Java-based Open Source Software frameworks. Firstly, the CellExplorer with the PathwayIntegration combines the mesoscopic and the functional level by mapping biological networks onto cell components using database integration. Secondly, the MembraneEditor enables users to generate membranes of different lipid and protein compositions using the PDB format. Technicalities will be discussed as well as the historical development of these tools with a special focus on group-based development. In this way, university-associated developers of Integrative Bioinformatics applications should be inspired to go similar ways. All tools discussed in this publication can be downloaded and installed from https://www.CELLmicrocosmos.org.

Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient.

The International Society for Computational Biology (ISCB) honors a leader in the fields of computational biology and bioinformatics each year with the Accomplishments by a Senior Scientist Award. This award is the highest honor conferred by ISCB to a scientist who is recognized for significant research, education, and service contributions. Bonnie Berger, Simons Professor of Mathematics and Professor of Electrical Engineering and Computer Science at the Massachusetts Institute of Technology (MIT) is the 2019 recipient of the Accomplishments by a Senior Scientist Award. She is receiving her award and presenting a keynote address at the 2019 Joint International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology in Basel, Switzerland on July 21-25, 2019.