ReviewComputational and structural biotechnology journal2015
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution.
Review in Computational and structural biotechnology journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Classification and prediction of protein-protein interaction interface using machine learning algorithm.Scientific reports · 2021Article
- Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy.Journal of chemical information and modeling · 2020Review
- Protein structure prediction using sparse NOE and RDC restraints with Rosetta in CASP13.Proteins · 2019Article
- Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.Current opinion in structural biology · 2019Review
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- Use of Computational Biochemistry for Elucidating Molecular Mechanisms of Nitric Oxide Synthase.Computational and structural biotechnology journal · 2019Review
- Article
- Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model.Bioscience reports · 2017Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM) and small angle X-ray scattering (SAXS) have opened up new avenues to define the structures of such assemblies. By systematically combining various sources of structural, biochemical and biophysical information, integrative modeling approaches aim to provide a unified structural description of such assemblies, starting from high-resolution structures of the individual components and integrating all available information from low-resolution experimental methods. In this review, we describe integrative modeling approaches, which use complementary data from either cryo-EM or SAXS. Specifically, we focus on the popular molecular dynamics flexible fitting (MDFF) method, which has been widely used for flexible fitting into cryo-EM maps. Second, we describe hybrid molecular dynamics, Rosetta Monte-Carlo and minimum ensemble search (MES) methods that can be used to incorporate SAXS into pseudoatomic structural models. We present concise descriptions of the two methods and their most popular alternatives, along with select illustrative applications to protein/nucleic acid assemblies involved in DNA replication and repair.
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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.