ArticleJournal of chemical theory and computation2019
Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 47 citations in OpenAlex.
- Structural insights into the substrate binding mechanism of the class I dehydratase MadB.Communications biology · 2025Article
- Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction.Nature communications · 2024Article
- The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.Nature protocols · 2024Review
- Breaking the 'don't eat me' signal: in silico design of CD47-directed peptides for cancer immunotherapy.Molecular diversity · 2024Article
- Article
- Host Cell Membrane Capture by the SARS-CoV-2 Spike Protein Fusion Intermediate.ACS central science · 2023Article
- Machine learned coarse-grained protein force-fields: Are we there yet?Current opinion in structural biology · 2023Review
- Review
- Molecular determinants associated with temporal succession of SARS-CoV-2 variants in Uttar Pradesh, India.Frontiers in microbiology · 2023Article
- An in-frame deletion mutation in the degron tail of auxin coreceptorProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Towards design of drugs and delivery systems with the Martini coarse-grained model.QRB discovery · 2022Review
- Unified Nanotechnology Format: One Way to Store Them All.Molecules (Basel, Switzerland) · 2021Article
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations.Frontiers in molecular biosciences · 2021Article
- Integrative modeling of membrane-associated protein assemblies.Nature communications · 2020Article
- 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
- Protein-ligand binding with the coarse-grained Martini model.Nature communications · 2020Article
- Coarse-grained (hybrid) integrative modeling of biomolecular interactions.Computational and structural biotechnology journal · 2020Review
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Predicting the 3D structure of protein interactions remains a challenge in the field of computational structural biology. This is in part due to difficulties in sampling the complex energy landscape of multiple interacting flexible polypeptide chains. Coarse-graining approaches, which reduce the number of degrees of freedom of the system, help address this limitation by smoothing the energy landscape, allowing an easier identification of the global energy minimum. They also accelerate the calculations, allowing for modeling larger assemblies. Here, we present the implementation of the MARTINI coarse-grained force field for proteins into HADDOCK, our integrative modeling platform. Docking and refinement are performed at the coarse-grained level, and the resulting models are then converted back to atomistic resolution through a distance restraints-guided morphing procedure. Our protocol, tested on the largest complexes of the protein docking benchmark 5, shows an overall ∼7-fold speed increase compared to standard all-atom calculations, while maintaining a similar accuracy and yielding substantially more near-native solutions. To showcase the potential of our method, we performed simultaneous 7 body docking to model the 1:6 KaiC-KaiB complex, integrating mutagenesis and hydrogen/deuterium exchange data from mass spectrometry with symmetry restraints, and validated the resulting models against a recently published cryo-EM structure.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.