ArticleBiophysical journal2002
Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition.
Article in Biophysical journal, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures.The journal of physical chemistry. B · 2021Article
- Limits in accuracy and a strategy of RNA structure prediction using experimental information.Nucleic acids research · 2019Article
- The Role of Data in Model Building and Prediction: A Survey Through Examples.Entropy (Basel, Switzerland) · 2018Article
- Topological transformations in proteins: effects of heating and proximity of an interface.Scientific reports · 2017Article
- Multidimensional persistence in biomolecular data.Journal of computational chemistry · 2015Article
- Knotted proteins: A tangled tale of Structural Biology.Computational and structural biotechnology journal · 2015Review
- The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations.Biomolecules · 2013Review
- Robotically assisted titration coupled to ion mobility-mass spectrometry reveals the interface structures and analysis parameters critical for multiprotein topology mapping.Analytical chemistry · 2013Article
- Is there an en route folding intermediate for Cold shock proteins?Protein science : a publication of the Protein Society · 2012Article
- Improvement of structure-based potentials for protein folding by native and nonnative hydrogen bonds.Biophysical journal · 2011Article
- Specificity of intramembrane protein-lipid interactions.Cold Spring Harbor perspectives in biology · 2011Review
- Continuum molecular simulation of large conformational changes during ion-channel gating.PloS one · 2011Article
- Nonnative interactions in coupled folding and binding processes of intrinsically disordered proteins.PloS one · 2010Article
- Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity.Physical chemistry chemical physics : PCCP · 2010Article
- Analysis of the free-energy surface of proteins from reversible folding simulations.PLoS computational biology · 2009Article
- Insights from coarse-grained Gō models for protein folding and dynamics.International journal of molecular sciences · 2009Review
- Selection of optimal variants of Gō-like models of proteins through studies of stretching.Biophysical journal · 2008Article
- Structural comparison of the two alternative transition states for folding of TI I27.Biophysical journal · 2006Article
- The effects of nonnative interactions on protein folding rates: theory and simulation.Protein science : a publication of the Protein Society · 2004Article
- Calculation of mutational free energy changes in transition states for protein folding.Biophysical journal · 2003Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Do Gō-type model potentials provide a valid approach for studying protein folding? They have been widely used for this purpose because of their simplicity and the speed of simulations based on their use. The essential assumption in such models is that only contact interactions existing in the native state determine the energy surface of a polypeptide chain, even for non-native configurations sampled along folding trajectories. Here we use an all-atom molecular mechanics energy function to investigate the adequacy of Gō-type potentials. We show that, although the contact approximation is accurate, non-native contributions to the energy can be significant. The assumed relation between residue-residue interaction energies and the number of contacts between them is found to be only approximate. By contrast, individual residue energies correlate very well with the number of contacts. The results demonstrate that models based on the latter should give meaningful results (e.g., as used to interpret phi values), whereas those that depend on the former are only qualitative, at best.
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