ArticleJournal of chemical theory and computation2013
Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Free energy of collagen-mimetic peptide dimerization and implications for fibrillization.Biophysical journal · 2026Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces.The journal of physical chemistry. A · 2023Article
- Local Ion Densities can Influence Transition Paths of Molecular Binding.Frontiers in molecular biosciences · 2022Article
- Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding.The journal of physical chemistry. B · 2020Article
- Effect of Membrane Composition on Receptor Association: Implications of Cancer Lipidomics on ErbB Receptors.The Journal of membrane biology · 2018Review
- Dimer Interface of the Human Serotonin Transporter and Effect of the Membrane Composition.Scientific reports · 2018Article
- Conformational Heterogeneity of the HIV Envelope Glycan Shield.Scientific reports · 2017Article
- Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices.Journal of computational chemistry · 2017Article
- Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association.The journal of physical chemistry. B · 2017Article
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.Biochimica et biophysica acta · 2016Review
- Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.Journal of computational chemistry · 2016Article
- Computational Studies of Molecular Permeation through Connexin26 Channels.Biophysical journal · 2016Article
- Mechanism-Based Mathematical Model for Gating of Ionotropic Glutamate Receptors.The journal of physical chemistry. B · 2015Article
- Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.Journal of chemical theory and computation · 2015Article
- Density-biased sampling: a robust computational method for studying pore formation in membranes.Journal of chemical theory and computation · 2015Article
- Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.Journal of chemical theory and computation · 2014Article
- Theory of Adaptive Optimization for Umbrella Sampling.Journal of chemical theory and computation · 2014Article
- Cholesterol modulates the dimer interface of the β₂-adrenergic receptor via cholesterol occupancy sites.Biophysical journal · 2014Article
- Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers.Journal of computational chemistry · 2014Article
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
The method of window exchange umbrella sampling molecular dynamics (WEUSMD) with a pre-optimized parameter set was recently used to obtain the most probable conformations and the energetics of transmembrane (TM) helix assembly of a generic TM sequence. When applied to glycophorin A TM domain (GpA-TM) using the restraint potentials along the helix-helix distance, however, tight interfacial packing of GpA-TM resulted in insufficient conformational sampling at short helix-helix separation. This sampling issue is addressed by extending the WEUSMD into two dimensions with the restraint potentials along the helix-helix distance and crossing angle. The two-dimensional WEUSMD results demonstrate that the incomplete sampling in the one-dimensional WEUSMD arises from high barriers along the crossing angle between the GpA-TM helices. Together with the faster convergence in both the assembled conformations and the potential of mean force, the 2D-WEUSMD can be a general and efficient approach in computational studies of TM helix assembly.
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.