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AlphaFold Protein Structure Database: A Must-Have Tool for Biomedical Research

The function of a protein is often determined by how it folds into a 3D structure. Therefore, knowledge of a protein’s structure is essential for a deeper understanding of its role in various cellular processes. However, for most proteins known to mankind, our experimental knowledge lacks their determined structure. For instance, the universal protein database Uniprot archives 229 million unique protein sequences, while the Protein Data Bank, the single worldwide archive for experimentally resolved protein structures, holds 206,000 proteins. X-ray crystallography, or cryo-electron microscopy, the traditional protein-structure-determination method that fires X-rays or electron beams at proteins to create a picture of their shape, is very time-consuming and technologically challenging. It thus contributes to the massive (more than a 1,000-fold) gap between known protein sequences and experimental protein structures.

This gap could be closed by predicting proteins’ 3D configurations straight from their linear amino acid sequence, a solution that AlphaFold may offer. AlphaFold is a program powered by artificial intelligence (AI), developed by DeepMind, part of Alphabet Inc., Google’s parent company. AlphaFold transforms a protein’s sequence into its structure with high accuracy. EMBL-European Bioinformatics Institute (EMBL-EBI), partnering with DeepMind, made the predicted structures of over 200 million cataloged proteins available to science through the AlphaFold Protein Structure Database (AlphaFold DB). This freely available resource offers programmatic access to its data and interactive visualization of predicted structures. Continue reading →

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The EBM Resource Pyramid: Helping to Find and Use the Strongest Evidence

The EBM Resource Pyramid guide from HSLS enables health sciences readers to tour the hierarchy and levels of evidence-based medicine (EBM) and practice in a self-paced manner. Evidence-based resources beyond medicine are included, such as nursing and physiotherapy. The graphical display of the pyramid breaks down the categories into seven levels. Those levels are matched with links to HSLS resources, each described in detail. Incorporated into the pyramid structure are the distinctions between filtered and unfiltered resources. Via this guide, you can quickly link to groups of filtered and unfiltered resources.

Not all evidence is created equal. The pyramid’s structure facilitates recognition and grading of the evidence. The evidence at the top (systematic reviews) ranks higher than that at lower levels (e.g., cohort studies). For instance, a guideline formulated by a Delphi survey of experts’ opinions rates weaker than one based on systematic reviews of guideline recommendations. Hints for searching for evidence in the various database descriptions help guide strategies to find the strongest levels of evidence. Continue reading →

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Featured Workshop on Risk of Bias: What Is It? How Do I Assess For It? What Do I Use To Assess?

Join us for a new workshop on Risk of Bias:

Thursday, November 10, from noon to 1 p.m., online

Register for Risk of Bias: What is it? How do I assess for it? What do I use to assess?*

Assessing for Risk of Bias (RoB) is one of the expected steps when conducting a systematic review, but it can also be used to self-assess study conduct as practiced or as written in your proposal or protocol. Risk of bias assessments are important in research to determine flaws in the design, conduct, or analysis of randomized trials and other types of studies that could lead to an overestimation or underestimation of the true effect of the intervention or exposure. Continue reading →

Treasures from the Rare Book Room: A Complete Treatise on Childbirth Well-Valued in 18th-Century France

Guillaume Mauquest de la Motte was a surgeon-accoucheur. Accoucheurs were male surgeons specializing in childbirth, which became fashionable in 17th-century France as an alternative to the tradition of women as birth attendants. In the early 18th century, accoucheurs were at the center of a polemic by physician Philippe Hecquet, who wrote on the indecency of male birthing attendants. Guillaume Mauquest de la Motte, who responded with a defense of accoucheurs, argued that the skills and expertise that accoucheurs have are necessary to save both mother and child. This midwifery debate was more about whether physicians or surgeons are the best medical providers, rather than justifying or challenging the role of midwives. Change was coming. Only seven years later, the first school for surgeons opened in Paris in 1725, and from then on, surgeons’ training began to resemble the training of physicians.

Guillaume Mauquest de la Motte is also the author of one of the best treatises on childbirth (Traité complet des accouchements, 1721), which was also very popular and had multiple editions. Mauquest de La Motte (1655-1737) studied at the Hôtel-Dieu. After obtaining his degree, he returned to his native region of France and established a practice in Valognes in 1701. He became well known and sought after, because he gained a reputation among women for delivering babies safely. He attended to three or four deliveries daily, and he practiced surgery and obstetrics for more than fifty years. The books he published helped solidify his reputation, because his writing was grounded in his extensive experience. Continue reading →

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HSLS Staff News

The HSLS Staff News section includes recent HSLS presentations, publications, staff changes, staff promotions, degrees earned, and more.

News

Two new instructional designers have joined HSLS to support the Network of the National Library of Medicine (NNLM) All of Us Program Center (NAPC):

Neda Hashmi, NAPC Instructional Designer, comes to HSLS from AppFolio, where she designed and developed employee training and Help Center content for a cloud-based property management firm, and Rumie, where she designed learning experiences for open online courses reaching broad audiences. Hashmi also has more than ten years of experience in freelance content and technical writing, teaching, and other experiences that involve creative storytelling, visual arts, and digital media that complement her skills in training development and design. For NAPC, Hashmi will support the design and development of learning experiences and programs for National Program Training, which focuses on public-serving NNLM audiences like public libraries and community-based organizations and the communities that they serve.

Patrick Norman, NAPC Instructional Designer, comes to HSLS from Erlanger Health System in Chattanooga, TN, where he designed and delivered employee training at the multi-hospital academic medical center. He holds a Master of Education, and his professional experiences also include leadership development support at Teach For America, curriculum design and digital content production for a NASA education grant, and service in the U. S. Marine Corps Reserve. For NAPC, Norman will support the design and development of trainings and learning experiences for healthcare provider organizations, community engagement partners, and NIH program staff who work within the All of Us Research Program. Continue reading →