Binding Affinity Estimation From Restrained Umbrella Sampling Simulations Article Swipe
Vivek Govind Kumar
,
Shilpi Agrawal
,
Thallapuranam Krishnaswamy Suresh Kumar
,
Mahmoud Moradi
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/2021.10.28.466324
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/2021.10.28.466324
The protein-ligand binding affinity quantifies the binding strength between a protein and its ligand. Computer modeling and simulations can be used to estimate the binding affinity or binding free energy using data- or physics-driven methods or a combination thereof. Here, we discuss a purely physics-based sampling approach based on biased molecular dynamics (MD) simulations, which in spirit is similar to the stratification strategy suggested previously by Woo and Roux. The proposed methodology uses umbrella sampling (US) simulations with additional restraints based on collective variables such as the orientation of the ligand. The novel extension of this strategy presented here uses a simplified and more general scheme that can be easily tailored for any system of interest. We estimate the binding affinity of human fibroblast growth factor 1 (hFGF1) to heparin hexasaccharide based on the available crystal structure of the complex as the initial model and four different variations of the proposed method to compare against the experimentally determined binding affinity obtained from isothermal calorimetry (ITC) experiments. Our results indicate that enhanced sampling methods that sample along the ligand-protein distance without restraining other degrees of freedom do not perform as well as those with additional restraint. In particular, restraining the orientation of the ligands plays a crucial role in reaching a reasonable estimate for binding affinity. The general framework presented here provides a flexible scheme for designing practical binding free energy estimation methods.
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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2021.10.28.466324
- https://www.biorxiv.org/content/biorxiv/early/2021/10/28/2021.10.28.466324.full.pdf
- OA Status
- green
- Cited By
- 2
- References
- 100
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4200005780
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- OpenAlex ID
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https://openalex.org/W4200005780Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2021.10.28.466324Digital Object Identifier
- Title
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Binding Affinity Estimation From Restrained Umbrella Sampling SimulationsWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2021Year of publication
- Publication date
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2021-10-28Full publication date if available
- Authors
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Vivek Govind Kumar, Shilpi Agrawal, Thallapuranam Krishnaswamy Suresh Kumar, Mahmoud MoradiList of authors in order
- Landing page
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https://doi.org/10.1101/2021.10.28.466324Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2021/10/28/2021.10.28.466324.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2021/10/28/2021.10.28.466324.full.pdfDirect OA link when available
- Concepts
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Umbrella sampling, Molecular dynamics, Isothermal titration calorimetry, Sampling (signal processing), Ligand (biochemistry), Binding site, Chemistry, Biological system, Computer science, Computational chemistry, Biology, Physical chemistry, Biochemistry, Receptor, Computer vision, Filter (signal processing)Top concepts (fields/topics) attached by OpenAlex
- Cited by
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2Total citation count in OpenAlex
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2025: 1, 2022: 1Per-year citation counts (last 5 years)
- References (count)
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100Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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