ArticleProteins2014
An effective coarse-grained model for biological simulations: recent refinements and validations.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 57 citations in OpenAlex.
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- Exploring the activation mechanism of metabotropic glutamate receptor 2.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Energetic and structural insights behind calcium induced conformational transition in calmodulin.Proteins · 2024Article
- Predicting Mutational Effects on CaJournal of the American Chemical Society · 2024Article
- Exploring the Phospholipid Transport Mechanism of ATP8A1-CDC50.Biomedicines · 2023Article
- Physical pictures of rotation mechanisms of FFrontiers in molecular biosciences · 2023Article
- The Nature of Functional Features of Different Classes of G-Protein-Coupled Receptors.Biology · 2022Article
- Application of Computational Biology and Artificial Intelligence in Drug Design.International journal of molecular sciences · 2022Review
- Mechanism Study of Proteins under Membrane Environment.Membranes · 2022Article
- Automated Protein Secondary Structure Assignment from CBiomolecules · 2022Article
- Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines.Entropy (Basel, Switzerland) · 2022Article
- A systematic study on the binding affinity of SARS-CoV-2 spike protein to antibodies.AIMS microbiology · 2022Article
- Predicting Mutational Effects on Receptor Binding of the Spike Protein of SARS-CoV-2 Variants.Journal of the American Chemical Society · 2021Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Exploring the free energy landscape of proteins and modeling the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of various simplified coarse grained (CG) models offers an effective way of sampling the landscape, but most current models are not expected to give a reliable description of protein stability and functional aspects. The main problem is associated with insufficient focus on the electrostatic features of the model. In this respect, our recent CG model offers significant advantage as it has been refined while focusing on its electrostatic free energy. Here we review the current state of our model, describing recent refinements, extensions, and validation studies while focusing on demonstrating key applications. These include studies of protein stability, extending the model to include membranes, electrolytes and electrodes, as well as studies of voltage-activated proteins, protein insertion through the translocon, the action of molecular motors, and even the coupling of the stalled ribosome and the translocon. The examples discussed here illustrate the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins and large macromolecular complexes.
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Registered trials
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.