ArticleProteins2020
Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems.
Article in Proteins, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 40 citations in OpenAlex.
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning.Communications biology · 2023Article
- Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.Proteomics · 2023Article
- Structural predictions of protein-DNA binding: MELD-DNA.Nucleic acids research · 2023Article
- Identification of Relevant Protein Interactions with Partial Knowledge: A Complex Network and Deep Learning Approach.Biology · 2023Article
- Modeling the Dynamics of Protein-Protein Interfaces, How and Why?Molecules (Basel, Switzerland) · 2022Review
- Improved prediction of protein-protein interactions using AlphaFold2.Nature communications · 2022Article
- Searching for Low Probability Opening Events in a DNA Sliding Clamp.Life (Basel, Switzerland) · 2022Article
- Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.Frontiers in molecular biosciences · 2022Article
- Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction.Proteins · 2021Article
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Conformational selection of vasopressin upon VComputational and structural biotechnology journal · 2021Article
- Using yeast two-hybrid system and molecular dynamics simulation to detect venom protein-protein interactions.Current research in toxicology · 2021Article
- PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes.Journal of chemical information and modeling · 2020Article
- Challenges in protein docking.Current opinion in structural biology · 2020Review
- Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.Current opinion in structural biology · 2020Review
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.Current opinion in structural biology · 2020Review
- Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems.Proteins · 2020Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Incorporating the dynamic nature of biomolecules in the modeling of their complexes is a challenge, especially when the extent and direction of the conformational changes taking place upon binding is unknown. Estimating whether the binding of a biomolecule to its partner(s) occurs in a conformational state accessible to its unbound form ("conformational selection") and/or the binding process induces conformational changes ("induced-fit") is another challenge. We propose here a method combining conformational sampling using ClustENM-an elastic network-based modeling procedure-with docking using HADDOCK, in a framework that incorporates conformational selection and induced-fit effects upon binding. The extent of the applied deformation is estimated from its energetical costs, inspired from mechanical tensile testing on materials. We applied our pre- and post-docking sampling of conformational changes to the flexible multidomain protein-protein docking benchmark and a subset of the protein-DNA docking benchmark. Our ClustENM-HADDOCK approach produced acceptable to medium quality models in 7/11 and 5/6 cases for the protein-protein and protein-DNA complexes, respectively. The conformational selection (sampling prior to docking) has the highest impact on the quality of the docked models for the protein-protein complexes. The induced-fit stage of the pipeline (post-sampling), however, improved the quality of the final models for the protein-DNA complexes. Compared to previously described strategies to handle conformational changes, ClustENM-HADDOCK performs better than two-body docking in protein-protein cases but worse than a flexible multidomain docking approach. However, it does show a better or similar performance compared to previous protein-DNA docking approaches, which makes it a suitable alternative.
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