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 for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallo­graphic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

/pdf/phenix-a-comprehensive-python-based-system-for-1gmhvrnie4.pdf

PHENIX: a comprehensive Python-based system for macromolecular structure solution

MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallo­graphy easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

/pdf/molprobity-all-atom-structure-validation-for-macromolecular-55t3n3noll.pdf

MolProbity: all-atom structure validation for macromolecular crystallography

J. Appl. Cryst.の発刊に際して

https://www.biorxiv.org/content/biorxiv/early/2020/02/20/2020.02.19.956581.full.pdf

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.

The iterative threading assembly refinement (I-TASSER) server is an integrated platform for automated protein structure and function prediction based on the sequence-to-structure-to-function paradigm. Starting from an amino acid sequence, I-TASSER first generates three-dimensional (3D) atomic models from multiple threading alignments and iterative structural assembly simulations. The function of the protein is then inferred by structurally matching the 3D models with other known proteins. The output from a typical server run contains full-length secondary and tertiary structure predictions, and functional annotations on ligand-binding sites, Enzyme Commission numbers and Gene Ontology terms. An estimate of accuracy of the predictions is provided based on the confidence score of the modeling. This protocol provides new insights and guidelines for designing of online server systems for the state-of-the-art protein structure and function predictions. The server is available at http://zhanglab.ccmb.med.umich.edu/I-TASSER.

/pdf/i-tasser-a-unified-platform-for-automated-protein-structure-1ek4kamd4l.pdf

I-TASSER: a unified platform for automated protein structure and function prediction

Multiconformer synchrotron model of CypA at 100 K

Multiconformer synchrotron model of CypA at 260 K

Hen Egg White Lysozyme at 278K, Data set 10

With the advent of AlphaFold, protein structure prediction has attained remarkable accuracy. These achievements resulted from a focus on single static structures. The next frontier in this field involves enhancing our ability to model conformational ensembles, not just the ground states of proteins. Notably, deposited structures result from interpretation of density maps, which are derived from either X-ray crystallography or cryogenic electron microscopy (cryo-EM). These maps represent ensemble averages, reflecting molecules in multiple conformations. Here, we present the latest developments in qFit, an automated computational approach to model protein conformational heterogeneity into density maps. We present algorithmic advancements to qFit, validated by improved Rfree and geometry metrics across a broad and diverse set of proteins. Automated multiconformer modeling holds significant promise for interpreting experimental structural biology data and for generating novel hypotheses linking macromolecular conformational dynamics to function.

/pdf/uncovering-protein-ensembles-automated-multiconformer-model-1wk7i2m4.pdf

Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM

The first serial synchrotron crystallographic structure of apo PTP1B is reported and the conformational heterogeneity at several allosteric sites is compared with that seen in prior structures.

Daniel A. Keedy

Papers

Multiconformer synchrotron model of CypA at 100 K

Multiconformer synchrotron model of CypA at 260 K

Hen Egg White Lysozyme at 278K, Data set 10

Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM

Room-temperature serial synchrotron crystallography of the human phosphatase PTP1B