Binding Affinity Estimation from Restrained Umbrella Sampling Simulations Article Swipe
Vivek Govind Kumar
,
Shilpi Agrawal
,
Thallapuranam Krishnaswamy Suresh Kumar
,
Mahmoud Moradi
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-1443106/v1
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-1443106/v1
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. Our proposed method generalizes and simplifies previously suggested stratification strategies that use umbrella sampling (US) or other enhanced sampling simulations with additional collective-variable based restraints. The novel approach presented here uses a flexible 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 ligand plays the most crucial role in reaching a reasonable estimate for binding affinity. The general framework presented here provides a general scheme for designing practical binding free energy estimation methods for flexible ligands and proteins.
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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.21203/rs.3.rs-1443106/v1
- https://www.researchsquare.com/article/rs-1443106/latest.pdf
- OA Status
- gold
- Cited By
- 4
- References
- 98
- Related Works
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- OpenAlex ID
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https://doi.org/10.21203/rs.3.rs-1443106/v1Digital Object Identifier
- Title
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Binding Affinity Estimation from Restrained Umbrella Sampling SimulationsWork title
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-
preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
-
2022-08-01Full 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/10.21203/rs.3.rs-1443106/v1Publisher landing page
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https://www.researchsquare.com/article/rs-1443106/latest.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://www.researchsquare.com/article/rs-1443106/latest.pdfDirect OA link when available
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Sampling (signal processing), Estimation, Umbrella sampling, Computer science, Chemistry, Economics, Computational chemistry, Molecular dynamics, Telecommunications, Detector, ManagementTop concepts (fields/topics) attached by OpenAlex
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4Total citation count in OpenAlex
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2024: 4Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.(hFGF1) | 110 |
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| abstract_inverted_index.<title>Abstract</title> | 0 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 97 |
| corresponding_author_ids | https://openalex.org/A5071912456 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 4 |
| corresponding_institution_ids | https://openalex.org/I78715868 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/7 |
| sustainable_development_goals[0].score | 0.7099999785423279 |
| sustainable_development_goals[0].display_name | Affordable and clean energy |
| citation_normalized_percentile.value | 0.58064882 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |