ArticleBiophysical journal2012
Exploring the energy landscapes of protein folding simulations with Bayesian computation.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- In Silico Analysis of CMolecules (Basel, Switzerland) · 2025Article
- From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA.NAR genomics and bioinformatics · 2024Article
- Predicting and Interpreting Protein Developability Via Transfer of Convolutional Sequence Representation.ACS synthetic biology · 2023Article
- Intrinsically Disordered Proteins: Critical Components of the Wetware.Chemical reviews · 2022Review
- Likelihood-free nested sampling for parameter inference of biochemical reaction networks.PLoS computational biology · 2020Article
- Targeting Tumors Using Peptides.Molecules (Basel, Switzerland) · 2020Review
- Mean Shift Cluster Recognition Method Implementation in the Nested Sampling Algorithm.Entropy (Basel, Switzerland) · 2020Article
- A Benchmark for Homomeric Enzyme Active Site Structure Prediction Highlights the Importance of Accurate Modeling of Protein Symmetry.ACS omega · 2019Article
- AutoDock CrankPep: combining folding and docking to predict protein-peptide complexes.Bioinformatics (Oxford, England) · 2019Article
- Docking Flexible Cyclic Peptides withJournal of chemical theory and computation · 2019Article
- Article
- An in-silico glimpse into the pH dependent structural changes of T7 RNA polymerase: a protein with simplicity.Scientific reports · 2017Article
- A computational assessment of pH-dependent differential interaction of T7 lysozyme with T7 RNA polymerase.BMC structural biology · 2017Article
- Incorporating prior knowledge improves detection of differences in bacterial growth rate.BMC systems biology · 2015Article
- SYSBIONS: nested sampling for systems biology.Bioinformatics (Oxford, England) · 2015Article
- Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.PloS one · 2015Article
- Bayesian model comparison and parameter inference in systems biology using nested sampling.PloS one · 2014Article
- Efficient Parameter Estimation of Generalizable Coarse-Grained Protein Force Fields Using Contrastive Divergence: A Maximum Likelihood Approach.Journal of chemical theory and computation · 2013Article
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4 authors.
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Abstract
Nested sampling is a Bayesian sampling technique developed to explore probability distributions localized in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence (marginal likelihood) of the model. The nested sampling algorithm also provides an efficient way to calculate free energies and the expectation value of thermodynamic observables at any temperature, through a simple post processing of the output. Previous applications of the algorithm have yielded large efficiency gains over other sampling techniques, including parallel tempering. In this article, we describe a parallel implementation of the nested sampling algorithm and its application to the problem of protein folding in a Gō-like force field of empirical potentials that were designed to stabilize secondary structure elements in room-temperature simulations. We demonstrate the method by conducting folding simulations on a number of small proteins that are commonly used for testing protein-folding procedures. A topological analysis of the posterior samples is performed to produce energy landscape charts, which give a high-level description of the potential energy surface for the protein folding simulations. These charts provide qualitative insights into both the folding process and the nature of the model and force field used.
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