Enhanced sampling techniques in molecular dynamics simulations of biological systems
Open accessAbstract
Background Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion.Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied.Major conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes.General significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Traditional molecular modeling methods usually provide reliable simulation results but require heavy computational resources, limiting their applicability.
“The methods in the first category, such as coarse-grained molecular dynamics simulations [9, 10], usually provide reliable simulation results but require heavy computational resources, which limits their applicability [11].”
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- Authors
- Bernardi, R. C., Melo, M. C. R., & Schulten, K.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- Corresponding author
- Schulten, Klaus
- Venue
- Biochimica et Biophysica Acta (BBA) - General Subjects
- Publisher
- Elsevier BV
- Published
- 2015-05
- Volume
- 1850
- Issue
- 5
- Pages
- 872-877
- ISSN
- 0304-4165 (ISSN-L)
- PMC
- PMC4339458
- OpenAlex
- W2036108598
- Cited by
- 757
- References
- 93
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- 3.04
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- journal article
- Language
- en
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- bronze
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- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (am, 265 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Biochimica et Biophysica Acta (BBA) - General Subjects (acceptedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Energy Biosciences Institute (231 UCB BP 2014OO4J01)
- National Science Foundation (MCB-1157615)
- National Institutes of Health (9P41GM104601)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- enhanced sampling, replica exchange molecular dynamics, metadynamics, simulated annealing, generalized simulated annealing, energy landscape, biomolecular dynamics, macromolecular complexes, protein flexibility
- MeSH terms
- Algorithms, Carbohydrate Conformation, Carbohydrates, Lipids, Nucleic Acid Conformation, Nucleic Acids, Protein Conformation, Proteins, Stochastic Processes, Structure-Activity Relationship, Surface Properties, Reproducibility of Results, Molecular Structure, Cellulosomes, Molecular Dynamics Simulation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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