ReviewBiochimica et biophysica acta2016
Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.
Review in Biochimica et biophysica acta, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
What it found
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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.
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Who cites it
60 citing papers in PubMed.
- Article
- Cancer Immunotherapy via Disruption of Integrin αvβ3 and CD47 Costabilization on Cancer Cell Surface.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Simulated Solute Tempering 2: An Efficient and Practical Approach to Protein Conformational Sampling and Binding Events.Journal of chemical theory and computation · 2025Article
- Molecular insights on the mechanism of α1-antitrypsin condensate formation and maturation.PLoS computational biology · 2025Article
- CHARMM-GUIJournal of chemical information and modeling · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- The analysis of neutron reflectivity from Langmuir monolayers of lipids using molecular dynamics simulations: the role of lipid area.Royal Society open science · 2025Article
- Atomistic Simulations and Analysis of Peripheral Membrane Proteins with Model Lipid Bilayers.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Efficiently determining membrane-bound conformations of peripheral membrane proteins using replica exchange with hybrid tempering: Orientation of PMP on lipid bilayer using replica exchange.The European physical journal. Special topics · 2024Article
- Hybrid neMD/MC lipid swapping algorithm to equilibrate membrane simulation with thermodynamic reservoir.The Journal of chemical physics · 2024Article
- SMARTINI3 parametrization of multi-scale membrane models via unsupervised learning methods.Scientific reports · 2024Article
- Discovery of Antibacterial Compounds with Potential Multi-Pharmacology against StaphylococcusMolecules (Basel, Switzerland) · 2024Article
- Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane.Journal of chemical theory and computation · 2024Article
- Simulation and Modeling of the Adhesion ofPathogens (Basel, Switzerland) · 2024Article
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.The journal of physical chemistry. B · 2024Article
- Molecular Dynamics as a Tool for Virtual Ligand Screening.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Neighbor List Artifacts in Molecular Dynamics Simulations.Journal of chemical theory and computation · 2023Article
- Physico-Chemical Approaches to Investigate Surface Hydroxyls as Determinants of Molecular Initiating Events in Oxide Particle Toxicity.International journal of molecular sciences · 2023Review
- Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry.Membranes · 2023Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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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.