ArticleBiophysical journal2008
Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens.Journal of chemical theory and computation · 2023Article
- Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.Journal of chemical theory and computation · 2019Article
- Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.PLoS computational biology · 2015Article
- Aligning experimental and theoretical anisotropic B-factors: water models, normal-mode analysis methods, and metrics.The journal of physical chemistry. B · 2014Article
- PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.Journal of molecular biology · 2013Article
- Progress in developing Poisson-Boltzmann equation solvers.Molecular based mathematical biology · 2013Article
- Normal-mode-analysis-guided investigation of crucial intersubunit contacts in the cAMP-dependent gating in HCN channels.Biophysical journal · 2012Article
- Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models.Archives of biochemistry and biophysics · 2011Article
- Water evaporation and conformational changes from partially solvated ubiquitin.Biochemistry research international · 2010Article
- Comparative modeling of DNA and RNA polymerases from Moniliophthora perniciosa mitochondrial plasmid.Theoretical biology & medical modelling · 2009Article
- Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach.The Journal of chemical physics · 2009Article
- Article
- A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Normal mode analysis (NMA) has received much attention as a direct approach to extract the collective motions of macromolecules. However, the stringent requirement of computational resources by classical all-atom NMA limits the size of the macromolecules to which the method is normally applied. We implemented a novel coarse-grained normal mode approach based on partitioning the all-atom Hessian matrix into relevant and nonrelevant parts. It is interesting to note that, using classical all-atom NMA results as a reference, we found that this method generates more accurate results than do other coarse-grained approaches, including elastic network model and block normal mode approaches. Moreover, this new method is effective in incorporating the energetic contributions from the nonrelevant atoms, including surface water molecules, into the coarse-grained protein motions. The importance of such improvements is demonstrated by the effect of surface water to shift vibrational modes to higher frequencies and by an increase in overlap of the coarse-grained eigenvector space (the motion directions) with that obtained from molecular dynamics simulations of solvated protein in a water box. These results not only confirm the quality of our method but also point out the importance of incorporating surface structural water in studying protein dynamics.
Indexed as
Identifiers
What OpenQuestion holds
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.