ArticleJournal of structural biology2010
Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.
Article in Journal of structural biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.Science (New York, N.Y.) · 2017Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- γ-TEMPy: Simultaneous Fitting of Components in 3D-EM Maps of Their Assembly Using a Genetic Algorithm.Structure (London, England : 1993) · 2015Article
- Numerical geometry of map and model assessment.Journal of structural biology · 2015Article
- Framework for 3D histologic reconstruction and fusion with in vivo MRI: Preliminary results of characterizing pulmonary inflammation in a mouse model.Medical physics · 2015Article
- Conformational States of macromolecular assemblies explored by integrative structure calculation.Structure (London, England : 1993) · 2013Article
- Modeling, docking, and fitting of atomic structures to 3D maps from cryo-electron microscopy.Methods in molecular biology (Clifton, N.J.) · 2013Article
- Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs.Journal of structural biology · 2012Article
- Conventions and workflows for using Situs.Acta crystallographica. Section D, Biological crystallography · 2012Article
- Evolutionary bidirectional expansion for the tracing of alpha helices in cryo-electron microscopy reconstructions.Journal of structural biology · 2012Article
- Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes.Journal of structural biology · 2011Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
A structural characterization of multi-component cellular assemblies is essential to explain the mechanisms governing biological function. Macromolecular architectures may be revealed by integrating information collected from various biophysical sources - for instance, by interpreting low-resolution electron cryomicroscopy reconstructions in relation to the crystal structures of the constituent fragments. A simultaneous registration of multiple components is beneficial when building atomic models as it introduces additional spatial constraints to facilitate the native placement inside the map. The high-dimensional nature of such a search problem prevents the exhaustive exploration of all possible solutions. Here we introduce a novel method based on genetic algorithms, for the efficient exploration of the multi-body registration search space. The classic scheme of a genetic algorithm was enhanced with new genetic operations, tabu search and parallel computing strategies and validated on a benchmark of synthetic and experimental cryo-EM datasets. Even at a low level of detail, for example 35-40 A, the technique successfully registered multiple component biomolecules, measuring accuracies within one order of magnitude of the nominal resolutions of the maps. The algorithm was implemented using the Sculptor molecular modeling framework, which also provides a user-friendly graphical interface and enables an instantaneous, visual exploration of intermediate solutions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.