ArticleBMC structural biology2010
Tracing conformational changes in proteins.
Article in BMC structural biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- StrEAMM-Thioether: Efficient Structure Prediction for Thioether-Linked Cyclic Peptides.The journal of physical chemistry. B · 2026Article
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- The proliferation rates of HT-1080 human fibrosarcoma cells can be accelerated or inhibited by weak static and extremely low frequency magnetic fields.Frontiers in public health · 2025Article
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- An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid.Chemical science · 2021Article
- Force Field Parameters for FeMolecules (Basel, Switzerland) · 2021Article
- Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC.Molecules (Basel, Switzerland) · 2021Article
- ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths.Journal of computer-aided molecular design · 2019Article
- Article
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- Using Spectral Representation to Classify Proteins' Conformational States.International journal of molecular sciences · 2018Article
- Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Detecting intermediate protein conformations using algebraic topology.BMC bioinformatics · 2017Article
- Vulnerable atherosclerotic plaque detection by resonance Raman spectroscopy.Journal of biomedical optics · 2016Article
- USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques.Nucleic acids research · 2016Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- A user-friendly web portal for analyzing conformational changes in structures of Mycobacterium tuberculosis.Journal of molecular modeling · 2015Article
- Insights into mechanism kinematics for protein motion simulation.BMC bioinformatics · 2014Article
- Analysis of conformational motions and residue fluctuations for Escherichia coli ribose-binding protein revealed with elastic network models.International journal of molecular sciences · 2013Article
- Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.BMC structural biology · 2013Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundMany proteins undergo extensive conformational changes as part of their functionality. Tracing these changes is important for understanding the way these proteins function. Traditional biophysics-based conformational search methods require a large number of calculations and are hard to apply to large-scale conformational motions.
resultsIn this work we investigate the application of a robotics-inspired method, using backbone and limited side chain representation and a coarse grained energy function to trace large-scale conformational motions. We tested the algorithm on four well known medium to large proteins and we show that even with relatively little information we are able to trace low-energy conformational pathways efficiently. The conformational pathways produced by our methods can be further filtered and refined to produce more useful information on the way proteins function under physiological conditions.
conclusionsThe proposed method effectively captures large-scale conformational changes and produces pathways that are consistent with experimental data and other computational studies. The method represents an important first step towards a larger scale modeling of more complex biological systems.
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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.