26 papers · ranked by Valyu relevance
Oliviero Carugo, Kristina Djinović-Carugo
In the past 2 decades, structural biology has transformed from a single technique used on single proteins to a multimodal integrative approach. Recently, protein structure prediction algorithms have opened new avenues to address challenging biological questions.
Gerard J. Kleywegt, Sameer Velankar, Ardan Patwardhan
For almost 50 years, structural biology has endeavoured to conserve and share its experimental data and their interpretations (usually, atomistic models) through global public archives such as the Protein Data Bank, Electron Microscopy Data Bank and Biological Magnetic Resonance Data Bank (BMRB). These archives are…
George N. Phillips Jr., Eaton Edward Lattman
About 100 years ago, the field of structural biology was born, led by James B. Sumner who recognized that enzymes were molecules with specific functions. In its contemporary form structural biology is used to interpret and understand molecular and cellular function, to design drugs, and to advance biotechnology in…
Stephen Curry
When the first atomic structures of salt crystals were determined by the Braggs in 1912-1913, the analytical power of X-ray crystallography was immediately evident. Within a few decades the technique was being applied to the more complex molecules of chemistry and biology and is rightly regarded as the foundation stone…
Gnanaprakash Jeyaraj, Anith Kumar Rajendran, Kuppusamy Sathishkumar, Bader O. Almutairi + 4 more
The structural elucidation of proteins is fundamental to understanding their biological functions and advancing drug discovery. Recent breakthroughs in cryo-electron microscopy (cryo-EM) and artificial intelligence (AI)-based structure prediction have revolutionized protein modeling by enabling near-atomic resolution…
Authors not listed
The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins these models. By systematically collecting, validating, and indexing these models, the PDB has accelerated structural…
Samuel Hoff, Maximilian Zinke, Nadia Izadi‐Pruneyre, Massimiliano Bonomi
'Massimiliano Bonomi'] Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method comprehensively reveals the behavior of biological systems…
Dinakar M. Salunke
Structure determination utilizing X-ray crystallography involves collection of diffraction data, determination of initial phases followed by iterative rounds of model building and crystallographic refinement to improve the phases and minimize the differences between calculated and observed structure factors. At each of…
Jessica I. Kelz, Gemma R. Takahashi, Fatemeh Safizadeh, Vesta Farahmand + 9 more
A major challenge for science educators is teaching foundational concepts while introducing their students to current research. Here we describe an active learning module developed to teach protein structure fundamentals while supporting ongoing research in enzyme discovery. It can be readily implemented in both…
Nathan Mih, Elizabeth Brunk, Ke Chen, Edward Catoiu + 5 more
Working with protein structures at the genome-scale has been challenging in a variety of ways. Here, we present ssbio, a Python package that provides a framework to easily work with structural information in the context of genome-scale network reconstructions, which can contain thousands of individual proteins. The…
Michael J. Stam, Diego A. Oyarzún, Nadanai Laohakunakorn, Christopher W. Wood
Rapid advancements in protein structure prediction methods have ushered in a new era of abundant and accurate structural data, providing opportunities to analyse proteins at a scale that has not been possible before. Here we show that features derived solely from predicted structures can be used to understand in vivo…
Irène Barbarin-Bocahu, Marc Graille
The determination of three dimensional structures of macromolecules is one of the actual challenge in biology with the ultimate objective of understanding their function. So far, X-ray crystallography is the most popular method to solve structure, but this technique relies on the generation of diffracting crystals.…
Jose Gavaldá-García, Bas Stringer, Olga Ivanova, Sanne Abeln + 2 more
'K. Anton Feenstra' 'Halima Mouhib'] | 4 | Data Resources for Structural Bioinformatics | 1 | | --- | --- | --- | | | Jose Gavald´a-Garc´ıa Bas Stringer Olga Ivanova | | | Sanne Abeln | K. Anton Feenstra and Halima Mouhib* | | | | 1 Experimental protein structures | 4 | | | 1.1 The Protein DataBank | 4 | | | The PDB…
Mike Sleutel, Brajabandhu Pradhan, Han Remaut
Two decades have passed since the initial proposition that amyloids are not only (toxic) byproducts of an unintended aggregation cascade, but that they can also be produced by an organism to serve a defined biological function. That revolutionary idea was borne out of the realization that a large fraction of the…
Maarten L. Hekkelman, Daniel Álvarez Salmoral, Anastassis Perrakis, Robbie P. Joosten
Protein secondary structure annotation is essential for understanding protein architecture, serving as a cornerstone for structural classification, alignment, visualisation, and machine learning applications. The Define Secondary Structure of Proteins (DSSP) algorithm has long been the standard for assigning secondary…
K. Anton Feenstra, Sanne Abeln
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the…
Babu A. Manjasetty, Konrad Büssow, Santosh Panjikar, Andrew P. Turnbull
'Andrew P. Turnbull'] A broad working definition of structural proteomics (SP) is that it is the process of the high-throughput characterization of the three-dimensional structures of biological macromolecules. Recently, the process for protein structure determination has become highly automated and SP platforms have…
Annika Jacobsen, Erik van Dijk, Halima Mouhib, Bas Stringer + 5 more
Annika Jacobsen Erik van Dijk Halima Mouhib Bas Stringer Olga Ivanova Jose Gavald´a-Garc´ıa Laura Hoekstra K. Anton Feenstra Sanne Abeln* * editorial responsability Within the living cell, protein molecules perform specific functions, typically by interacting with other proteins, DNA, RNA or small molecules. They take…
Stephanie Wankowicz, James Fraser
In their folded state, biomolecules exchange between multiple conformational states, crucial for their function. However, most structural models derived from experiments and computational predictions only encode a single state. To represent biomolecules more accurately, we must move towards modeling and predicting…
Mahmood A. Rashid, Firas Khatib, Abdul Sattar
—Protein structure prediction is a challenging and unsolved problem in computer science. Proteins are the sequence of amino acids connected together by single peptide bond. The combinations of the twenty primary amino acids are the constituents of all proteins. In-vitro laboratory methods used in this problem are very…
Madeline Harper, Uma Nudurupati, Riley Workman, Taras Lakoba + 2 more
Using amylin(2029) as a model system, we demonstrate that experimental constraints measured by Raman spectroscopy can be used to determine the molecular structure of amyloid fibrils. We employ both polarized and non-polarized Raman spectroscopy measurements to determine the distributions of peptide backbone amide C=O…
Authors not listed
Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical tool that can be used to determine the structures of both small organic molecules and large biomacromolecules. Many undergraduate students are exposed to NMR spectral analysis during organic chemistry courses, but few students have the opportunity…
Tatjana Škrbić, Trinh Xuan Hoang, Achille Giacometti, Amos Maritan + 1 more
'Jayanth R. Banavar'] Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow from their native state structures and therefore…
Peter B. Moore
This essay, which was written to commemorate the 50th anniversary of the Protein Data Bank, opens with some comments about the intentions of the scientists who pressed for its establishment and the nature of services it provides. It includes a brief account of the events that resulted in the determination of the…
Theodore L. Fobe, Christopher C. Walker, Garrett A. Meek, Michael R. Shirts
Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a nontrivial process, often involving many iterations of trial synthesis and characterization until folded structures are…
Louis Y.P. Luk, Yi Jin, Alexander J. Lander
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in D-enantiomers facilitating mirror-image…