ArticleBiophysical journal2003
Configurational temperature density of states simulations of proteins.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed.
- Folding a protein with equal probability of being helix or hairpin.Biophysical journal · 2012Article
- Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.Current protein & peptide science · 2009Review
- Novel procedure for thermal equilibration in molecular dynamics simulation.Molecular simulation · 2009Article
- A mesoscale model of DNA and its renaturation.Biophysical journal · 2009Article
- Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways.Journal of physics. Condensed matter : an Institute of Physics journal · 2009Article
- An entropic perspective of protein stability on surfaces.Biophysical journal · 2008Article
- Conformational study of Met-enkephalin based on the ECEPP force fields.Biophysical journal · 2006Article
- Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations.Biophysical journal · 2006Article
- A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA).Protein science : a publication of the Protein Society · 2005Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
A novel method has been implemented to compute the density of states of proteins. A united atom representation and the CHARMM (Brooks et al., 1983) force-field parameters have been adopted for all the simulations. In this approach, an intrinsic temperature is computed based on configurational information about the protein. A random walk is performed in potential energy space and the configurational temperature is collected as a function of potential energy of the system. The density of states is then calculated by integrating the reciprocal of temperature. Unlike previously available methods, this approach does not involve calculations based on histograms of stochastic visits to distinct energy states. It is found that the proposed method is more efficient than earlier, related schemes for simulation of protein folding. Furthermore, it directly provides thermodynamic information, including free energies. The usefulness of the method is discussed by presenting results of simulations of the 16-residue beta-hairpin taken from the C-terminal fragment (41-56) of protein G.
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.