A 3D cellular context for the macromolecular world

We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

© 2015 The Authors. Published by OUP. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1093/nar/gkv1047The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data.The Wellcome Trust [88944, 104948]; UK Biotechnology and Biological Sciences Research Council [BB/J007471/1, BB/K016970/1, BB/M013146/1, BB/M011674/1]; National Institutes of Health [GM079429]; UK Medical Research Council [MR/L007835/1]; European Union [284209]; CCP4; European Molecular Biology Laboratory (EMBL). Funding for open access charge: The Wellcome Trust.Published versio

Computer-Assisted Organic Synthesis. Addition to Carbonyl Carbons and Aromatic Substitution

This thesis concerns the computer-assisted modelling of additions to ketones and aromatic substitution, and how this modelling can be used within an existing program for synthesis planning. I include a review of existing computer-assisted organic synthesis (CAOS) programs, and discuss how some of these programs deal with knowledge representation. The diastereoselectivities have been modelled for the addition to ketones. The steric requirements for two hypothetical transition states are calculated and the diastereoselectivity of the reaction is calculated in a very fast way (less than one second). For 399 reactions involving 223 substrates and eight reagents, diastereoselectivity data are taken from the literature and fitted to the model. The quotient between the calculated and the reported selectivity is taken as the minimization criterion. I found that steric interactions cannot alone explain the selectivity; it is necessary to include a correction term that includes the effects of torsional strain between the incoming reagent and the b-substituents of the substrate. A mean deviation of 2.17 between the literature and calculated selectivities is found, a fully satisfactory value for the purpose. For the aromatic substitution reactions, a fast calculational scheme is derived for calculating the regioselectivity. From the literature, 976 data points from 176 substrates with 22 reagents, representing approximately 400 different positions, were correlated within the model with a correlation factor, r = 0.905. Similar models have previously been correlated with much fewer data points, and have thus given somewhat higher correlation factors. The diverse types of substrates that can be treated in this method makes it well suited for the inclusion into an automated search procedure

Computer-Assisted Organic Synthesis. Addition to Carbonyl Carbons and Aromatic Substitution

This thesis concerns the computer-assisted modelling of additions to ketones and aromatic substitution, and how this modelling can be used within an existing program for synthesis planning. I include a review of existing computer-assisted organic synthesis (CAOS) programs, and discuss how some of these programs deal with knowledge representation. The diastereoselectivities have been modelled for the addition to ketones. The steric requirements for two hypothetical transition states are calculated and the diastereoselectivity of the reaction is calculated in a very fast way (less than one second). For 399 reactions involving 223 substrates and eight reagents, diastereoselectivity data are taken from the literature and fitted to the model. The quotient between the calculated and the reported selectivity is taken as the minimization criterion. I found that steric interactions cannot alone explain the selectivity; it is necessary to include a correction term that includes the effects of torsional strain between the incoming reagent and the b-substituents of the substrate. A mean deviation of 2.17 between the literature and calculated selectivities is found, a fully satisfactory value for the purpose. For the aromatic substitution reactions, a fast calculational scheme is derived for calculating the regioselectivity. From the literature, 976 data points from 176 substrates with 22 reagents, representing approximately 400 different positions, were correlated within the model with a correlation factor, r = 0.905. Similar models have previously been correlated with much fewer data points, and have thus given somewhat higher correlation factors. The diverse types of substrates that can be treated in this method makes it well suited for the inclusion into an automated search procedure

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB

The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed

Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps

Cryogenic electron microscopy (cryo-EM) is a powerful technique for determining structures of multiple conformational or compositional states of macromolecular assemblies involved in cellular processes. Recent technological developments have led to a leap in the resolution of many cryo-EM data sets, making atomic model building more common for data interpretation. We present a method for calculating differences between two cryo-EM maps or a map and a fitted atomic model. The proposed approach works by scaling the maps using amplitude matching in resolution shells. To account for variability in local resolution of cryo-EM data, we include a procedure for local amplitude scaling that enables appropriate scaling of local map contrast. The approach is implemented as a user-friendly tool in the CCP-EM software package. To obtain clean and interpretable differences, we propose a protocol involving steps to process the input maps and output differences. We demonstrate the utility of the method for identifying conformational and compositional differences including ligands. We also highlight the use of difference maps for evaluating atomic model fit in cryo-EM maps.BN/Arjen Jakobi La