ArticleProteins2010
Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Understanding hypertrophic cardiomyopathy and its regulation by myosin drugs.Protein science : a publication of the Protein Society · 2025Article
- Exploring the Activation Process of the Glycine Receptor.Journal of the American Chemical Society · 2024Article
- 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
- Exploring the Phospholipid Transport Mechanism of ATP8A1-CDC50.Biomedicines · 2023Article
- Mechanism Study of Proteins under Membrane Environment.Membranes · 2022Article
- Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines.Entropy (Basel, Switzerland) · 2022Article
- Simulating the directional translocation of a substrate by the AAA+ motor in the 26S proteasome.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- "Dividing and Conquering" and "Caching" in Molecular Modeling.International journal of molecular sciences · 2021Review
- A Review on Applications of Computational Methods in Drug Screening and Design.Molecules (Basel, Switzerland) · 2020Review
- The FPhotosynthesis research · 2017Review
- Simulating the dynamics of the mechanochemical cycle of myosin-V.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA.Nature communications · 2016Article
- Analyzing the electrogenicity of cytochrome c oxidase.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Article
- Torque, chemistry and efficiency in molecular motors: a study of the rotary-chemical coupling in F1-ATPase.Quarterly reviews of biophysics · 2015Review
- Modeling gating charge and voltage changes in response to charge separation in membrane proteins.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.Proteins · 2014Article
- An effective coarse-grained model for biological simulations: recent refinements and validations.Proteins · 2014Article
- Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Evaluating the free-energy landscape of proteins and 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 simplified coarse-grained (CG) folding models offers an effective way of sampling the landscape but such a treatment, however, may not give the correct description of the effect of the actual protein residues. A general way around this problem that has been put forward in our early work (Fan et al., Theor Chem Acc 1999;103:77-80) uses the CG model as a reference potential for free-energy calculations of different properties of the explicit model. This method is refined and extended here, focusing on improving the electrostatic treatment and on demonstrating key applications. These applications include: evaluation of changes of folding energy upon mutations, calculations of transition-states binding free energies (which are crucial for rational enzyme design), evaluations of catalytic landscape, and evaluations of the time-dependent responses to pH changes. Furthermore, the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins is discussed.
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Registered trials
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