lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
TLDR
The lDDT is a superposition-free score that evaluates local distance differences of all atoms in a model, including validation of stereochemical plausibility, which makes it a robust tool for the automated assessment of structure prediction servers without manual intervention.Abstract:
The assessment of protein structure prediction techniques requires objective criteria to measure the similarity between a computational model and the experimentally determined reference structure. Conventional similarity measures based on a global superposition of Cα atoms are strongly influenced by domain motions and do not assess the accuracy of local atomic details in the model.; The local Distance Difference Test (lDDT) is a superposition-free score which evaluates local distance differences of all atoms in a model, including validation of stereo-chemical plausibility. The reference can be a single structure, or an ensemble of equivalent structures. We demonstrate that lDDT is well suited to assess local model quality, even in presence of domain movements, while maintaining good correlation to global measures. These properties make lDDT a robust tool for the automated assessment of structure prediction servers without manual intervention.Availability and Implementation: Source code, binaries for Linux and MacOSX, and an interactive web server are available at http://swissmodel.expasy.org/lddt CONTACT: torsten.schwede@unibas.ch.read more
Citations
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Journal ArticleDOI
Highly accurate protein structure prediction with AlphaFold
John M. Jumper,Richard O. Evans,Alexander Pritzel,Tim Green,Michael Figurnov,Olaf Ronneberger,Kathryn Tunyasuvunakool,Russell Bates,Augustin Žídek,Anna Potapenko,Alex Bridgland,Clemens Meyer,Simon A. A. Kohl,Andrew J. Ballard,Andrew Cowie,Bernardino Romera-Paredes,Stanislav Nikolov,R. D. Jain,Jonas Adler,Trevor Back,Stig Petersen,David Reiman,Ellen Clancy,Michal Zielinski,Martin Steinegger,Michalina Pacholska,Tamas Berghammer,Sebastian Bodenstein,David L. Silver,Oriol Vinyals,Andrew W. Senior,Koray Kavukcuoglu,Pushmeet Kohli,Demis Hassabis +33 more
TL;DR: For example, AlphaFold as mentioned in this paper predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture. But the accuracy is limited by the fact that no homologous structure is available.
Journal ArticleDOI
SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse,Andrew Waterhouse,Martino Bertoni,Martino Bertoni,Stefan Bienert,Stefan Bienert,Gabriel Studer,Gabriel Studer,Gerardo Tauriello,Gerardo Tauriello,Rafal Gumienny,Rafal Gumienny,Florian T Heer,Florian T Heer,Tjaart A. P. de Beer,Tjaart A. P. de Beer,Christine Rempfer,Christine Rempfer,Lorenza Bordoli,Lorenza Bordoli,Rosalba Lepore,Rosalba Lepore,Torsten Schwede,Torsten Schwede +23 more
TL;DR: An update to the SWISS-MODEL server is presented, which includes the implementation of a new modelling engine, ProMod3, and the introduction a new local model quality estimation method, QMEANDisCo.
Journal ArticleDOI
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
Marco Biasini,Stefan Bienert,Andrew Waterhouse,Konstantin Arnold,Gabriel Studer,Tobias Schmidt,Florian Kiefer,Tiziano Gallo Cassarino,Martino Bertoni,Lorenza Bordoli,Torsten Schwede,Torsten Schwede +11 more
TL;DR: The latest version of the SWISS-MODEL expert system for protein structure modelling is described, which makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models.
Journal ArticleDOI
Improved protein structure prediction using potentials from deep learning
Andrew W. Senior,Richard Evans,John M. Jumper,James Kirkpatrick,Laurent Sifre,Tim Green,Chongli Qin,Augustin Žídek,Alexander Nelson,Alex Bridgland,Hugo Penedones,Stig Petersen,Karen Simonyan,Steve Crossan,Pushmeet Kohli,David T. Jones,David T. Jones,David Silver,Koray Kavukcuoglu,Demis Hassabis +19 more
TL;DR: It is shown that a neural network can be trained to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions, and the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures.
Journal ArticleDOI
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.
Mihaly Varadi,Stephen Anyango,Mandar Deshpande,Sreenath Nair,Cindy Natassia,Galabina Yordanova,David Yu Yuan,Oana Stroe,Gemma Wood,Agata Laydon,Augustin Žídek,Tim Green,Kathryn Tunyasuvunakool,Stig Petersen,John M. Jumper,Ellen Clancy,Richard E. Green,Ankur Vora,Mira Lutfi,Michael Figurnov,Andrew Cowie,Nicole Hobbs,Pushmeet Kohli,Gerard J. Kleywegt,Ewan Birney,Demis Hassabis,Sameer Velankar +26 more
TL;DR: The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions.
References
More filters
Journal ArticleDOI
MolProbity: all-atom structure validation for macromolecular crystallography
Vincent B. Chen,W. Bryan Arendall,Jeffrey J. Headd,Daniel A. Keedy,R.M. Immormino,Gary J. Kapral,Laura Weston Murray,Jane S. Richardson,David S. Richardson +8 more
TL;DR: MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction.
Journal ArticleDOI
The Cambridge Structural Database: a quarter of a million crystal structures and rising
TL;DR: The Cambridge Structural Database now contains data for more than a quarter of a million small-molecule crystal structures, and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.
Journal ArticleDOI
Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement
Richard A. Engh,Robert Huber +1 more
TL;DR: In this article, a statistical survey of X-ray structures of small compounds from the Cambridge Structural Database is used for the refinement of protein structures determined by X-Ray crystallography.
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