Current developments in  Coot  for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data

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Abstract

Coot is a tool widely used for model building, refinement, and validation of macromolecular structures. It has been extensively used for crystallography and, more recently, improvements have been introduced to aid in cryo‐EM model building and refinement, as cryo‐EM structures with resolution ranging 2.5–4 A are now routinely available. Model building into these maps can be time‐consuming and requires experience in both biochemistry and building into low‐resolution maps. To simplify and expedite the model building task, and minimize the needed expertise, new tools are being added in Coot. Some examples include morphing, Geman‐McClure restraints, full‐chain refinement, and Fourier‐model based residue‐type‐specific Ramachandran restraints. Here, we present the current state‐of‐the‐art in Coot usage.

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Most cited references 29

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Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Simon C. Lovell, Ian W. Davis, W Bryan Arendall … (2003)

Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage). Copyright 2003 Wiley-Liss, Inc.

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JSME: a free molecule editor in JavaScript

Bruno Bienfait, Peter Ertl (2013)

Background A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript. Summary The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. Conclusions A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/

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Model-based local density sharpening of cryo-EM maps

Arjen Jakobi, Matthias Wilmanns, Carsten Sachse (2017)

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement.

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Author and article information

Contributors

Paul Emsley:

ORCID: https://orcid.org/0000-0002-0138-5227

pemsley@mrc-lmb.cam.ac.uk

Journal

Journal ID (nlm-ta): Protein Sci

Journal ID (iso-abbrev): Protein Sci

Journal ID (doi): 10.1002/(ISSN)1469-896X

Journal ID (publisher-id): PRO

Title: Protein Science : A Publication of the Protein Society

Publisher: John Wiley & Sons, Inc. (Hoboken, USA )

ISSN (Print): 0961-8368

ISSN (Electronic): 1469-896X

Publication date (Electronic): 02 March 2020

Publication date (Print): April 2020

Publication date PMC-release: 02 March 2020

Volume: 29

Issue: 4 ( doiID: 10.1002/pro.v29.4 )

Pages: 1069-1078

Affiliations

[ ¹ ] MRC Laboratory of Molecular Biology Cambridge Biomedical Campus Cambridge UK

[ ² ] Division of Molecular Structural Biology, Department of Medical Biochemistry and Biophysics Karolinska Institutet Stockholm Sweden

Author notes

[*] [* ] Correspondence

Paul Emsley, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.

Email: pemsley@ 123456mrc-lmb.cam.ac.uk

Author information

Ana Casañal https://orcid.org/0000-0002-0334-0591

Bernhard Lohkamp https://orcid.org/0000-0002-5646-2090

Paul Emsley https://orcid.org/0000-0002-0138-5227

Article

Publisher ID: PRO3791

DOI: 10.1002/pro.3791

PMC ID: 7096722

PubMed ID: 31730249

SO-VID: 72692cd7-c153-48c3-bf86-4c872c01608d

License:

This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

History

Date received : 03 October 2019

Date revision received : 13 November 2019

Date accepted : 14 November 2019

Page count

Figures: 3, Tables: 0, Pages: 10, Words: 7019

Funding

Funded by: European Molecular Biology Organization , open-funder-registry 10.13039/100004410;

Award ID: ALTF66‐2015

Funded by: FP7 People: Marie‐Curie Actions , open-funder-registry 10.13039/100011264;

Award ID: ERC 725685

Award ID: GA‐2013‐609409

Funded by: Medical Research Council , open-funder-registry 10.13039/501100007155;

Award ID: MC_U105184330

Award ID: MC_U105192715

Award ID: MC_UP_A025_1012

Funded by: Röntgen‐Ångström Cluster , open-funder-registry 10.13039/501100011750;

Award ID: 349‐2013‐597

Funded by: Röntgen Ångström Cluster , open-funder-registry 10.13039/501100011750;

Funded by: UK Research and Innovation , open-funder-registry 10.13039/100014013;

Funded by: European Union's Horizon 2020 research and innovation programme

Funded by: European Commission , open-funder-registry 10.13039/501100000780;

Custom metadata

source-schema-version-number 2.0

cover-date April 2020

details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_JATSPMC version:5.7.8 mode:remove_FC converted:26.03.2020

ScienceOpen disciplines: Biochemistry

Keywords: ligands,macromolecular model building,molecular biophysics,real space refinement,rotamers,validation

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ScienceOpen disciplines: Biochemistry

Keywords: ligands, macromolecular model building, molecular biophysics, real space refinement, rotamers, validation

Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data

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Abstract

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Most cited references 29

Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

JSME: a free molecule editor in JavaScript

Model-based local density sharpening of cryo-EM maps

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