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View article: <i>Xtricorder</i> : a likelihood-enhanced self-rotation function and application to a machine learning-enhanced Matthews prediction of asymmetric unit copy number
<i>Xtricorder</i> : a likelihood-enhanced self-rotation function and application to a machine learning-enhanced Matthews prediction of asymmetric unit copy number Open
Analysis of crystallographic diffraction data after collection and integration but before phasing gives the crystallographer a `first-look' assessment of data quality and flags potential challenges in subsequent structure determination. We…
View article: Structure of Bovine Glycine <i>N</i>-Acyltransferase Clarifies Its Catalytic Mechanism
Structure of Bovine Glycine <i>N</i>-Acyltransferase Clarifies Its Catalytic Mechanism Open
Glycine N-acyltransferase (GLYAT; EC 2.3.1.13, Accession ID: AAI12537) is a key enzyme in mammalian homeostasis that has been linked to several pathologies in humans, including cancer. Here we report the first crystal structure of a…
View article: Model Quality Assessment for <scp>CASP16</scp>
Model Quality Assessment for <span>CASP16</span> Open
The CASP16 evaluation of model accuracy (EMA) experiment assessed the ability of predictors to estimate the accuracy of predicted models, with a particular emphasis on multimeric assemblies. Expanding on the CASP15 framework, CASP16 introd…
View article: Xtricorder: A likelihood-enhanced self-rotation function and application to a machine-learning enhanced Matthews prediction of asymmetric unit copy number
Xtricorder: A likelihood-enhanced self-rotation function and application to a machine-learning enhanced Matthews prediction of asymmetric unit copy number Open
Analysis of crystallographic diffraction data before phasing gives the crystallographer a ‘first look’ at the nature of the problem and the context in which the structure determination will be performed. We here report the development of X…
View article: The Molecular Pathology of Pre-Eclamptic Hypertension
The Molecular Pathology of Pre-Eclamptic Hypertension Open
The central role of angiotensinogen in the control of blood pressure is revealed by a series of crystallographic structures, including complexes with renin. Specifically, the structures provide an understanding of the sequential molecular …
View article: Model Quality Assessment for CASP16
Model Quality Assessment for CASP16 Open
View article: AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network
AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network Open
Advances in machine learning have transformed structural biology, enabling swift and accurate prediction of protein structure from sequence. However, challenges persist in capturing sidechain packing, condition-dependent conformational dyn…
View article: Welcoming two new Co-editors
Welcoming two new Co-editors Open
Two new Co-editors are welcomed to Acta Cryst. D - Structural Biology.
View article: Likelihood-based interactive local docking into cryo-EM maps in <i>ChimeraX</i>
Likelihood-based interactive local docking into cryo-EM maps in <i>ChimeraX</i> Open
The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map…
View article: CryoET of β-amyloid and tau within postmortem Alzheimer’s disease brain
CryoET of β-amyloid and tau within postmortem Alzheimer’s disease brain Open
A defining pathological feature of most neurodegenerative diseases is the assembly of proteins into amyloid that form disease-specific structures 1 . In Alzheimer’s disease, this is characterized by the deposition of β-amyloid and tau with…
View article: Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge Open
View article: Likelihood-based interactive local docking into cryo-EM maps in ChimeraX
Likelihood-based interactive local docking into cryo-EM maps in ChimeraX Open
The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map…
View article: Welcoming five new Co-editors
Welcoming five new Co-editors Open
Five new Co-editors are appointed to the Editorial Board of Acta Cryst. D - Structural Biology.
View article: phenix.mr_rosetta: a new tool for difficult molecular replacement problems
phenix.mr_rosetta: a new tool for difficult molecular replacement problems Open
The PHENIX development team is working with the Baker laboratory at the University of Washington to combine the power of Rosetta structure modeling with PHENIX automated molecular replacement (MR), model-building, density modification, and…
View article: Phenix - a comprehensive python-based system for macromolecular structure solution
Phenix - a comprehensive python-based system for macromolecular structure solution Open
Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need f…
View article: Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge Open
View article: AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination
AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination Open
View article: Michael James (1940–2023)
Michael James (1940–2023) Open
Michael James is remembered.
View article: Multimeric structure of a subfamily <scp>III</scp> haloalkane dehalogenase‐like enzyme solved by combination of <scp>cryo‐EM</scp> and x‐ray crystallography
Multimeric structure of a subfamily <span>III</span> haloalkane dehalogenase‐like enzyme solved by combination of <span>cryo‐EM</span> and x‐ray crystallography Open
Haloalkane dehalogenase (HLD) enzymes employ an S N 2 nucleophilic substitution mechanism to erase halogen substituents in diverse organohalogen compounds. Subfamily I and II HLDs are well‐characterized enzymes, but the mode and purpose of…
View article: <i>AlphaFold</i> and the future of structural biology
<i>AlphaFold</i> and the future of structural biology Open
This editorial acknowledges the transformative impact of new machine-learning methods, such as the use of AlphaFold, but also makes the case for the continuing need for experimental structural biology.
View article: <i>AlphaFold</i> and the future of structural biology
<i>AlphaFold</i> and the future of structural biology Open
This editorial acknowledges the transformative impact of new machine-learning methods, such as the use of AlphaFold, but also makes the case for the continuing need for experimental structural biology.
View article: <i>AlphaFold</i> and the future of structural biology
<i>AlphaFold</i> and the future of structural biology Open
This editorial acknowledges the transformative impact of new machine-learning methods, such as the use of AlphaFold, but also makes the case for the continuing need for experimental structural biology.
View article: The <i>CCP</i>4 suite: integrative software for macromolecular crystallography
The <i>CCP</i>4 suite: integrative software for macromolecular crystallography Open
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP 4 suite is a multiplatform collection of…
View article: Structures of apo Cas12a and its complex with crRNA and DNA reveal the dynamics of ternary complex formation and target DNA cleavage
Structures of apo Cas12a and its complex with crRNA and DNA reveal the dynamics of ternary complex formation and target DNA cleavage Open
Cas12a is a programmable nuclease for adaptive immunity against invading nucleic acids in CRISPR–Cas systems. Here, we report the crystal structures of apo Cas12a from Lachnospiraceae bacterium MA2020 (Lb2) and the Lb2 Cas12a+crRNA complex…
View article: Likelihood-based signal and noise analysis for docking of models into cryo-EM maps
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps Open
Fast, reliable docking of models into cryo-EM maps requires understanding of the errors in the maps and the models. Likelihood-based approaches to errors have proven to be powerful and adaptable in experimental structural biology, finding …
View article: Likelihood-based docking of models into cryo-EM maps
Likelihood-based docking of models into cryo-EM maps Open
Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function used in crys…
View article: Accelerating crystal structure determination with iterative <i>AlphaFold</i> prediction
Accelerating crystal structure determination with iterative <i>AlphaFold</i> prediction Open
Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold . Here, an automatic procedure requiring only sequence information and crystallographic data is …
View article: 30 years of <i>Acta D</i>
30 years of <i>Acta D</i> Open
This year we celebrate 30 years of Acta Crystallographica Section D, and so have a milestone at which to reflect on its history and future trajectory.A comprehensive and detailed account of the development of the IUCr Journals can be found…
View article: Likelihood-based signal and noise analysis for docking of models into cryo-EM maps
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps Open
Fast, reliable docking of models into cryo-EM maps requires understanding of the errors in the maps and the models. Likelihood-based approaches to errors have proven to be powerful and adaptable in experimental structural biology, finding …
View article: Likelihood-based docking of models into cryo-EM maps
Likelihood-based docking of models into cryo-EM maps Open
Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function used in crys…