ArticlePloS one2010
APBSmem: a graphical interface for electrostatic calculations at the membrane.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Extending MMPBSA for membrane proteins: Addressing P2YBiophysical journal · 2026Article
- Conformational changes upon pore blocker removal reveal conductive states of TMEM16A.bioRxiv : the preprint server for biology · 2026Article
- Computational Evidence for Digenic Contribution ofInternational journal of molecular sciences · 2025Article
- Ion-conducting and gating molecular mechanisms of channelrhodopsin revealed by true-atomic-resolution structures of open and closed states.Nature structural & molecular biology · 2025Article
- Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces.Journal of chemical information and modeling · 2025Article
- Cholesterol Concentration in Cell Membranes and its Impact on Receptor-Ligand Interaction: A Computational Study of ATP-Sensitive Potassium Channels and ATP Binding.The Journal of membrane biology · 2025Article
- Isoleucine gate blocks KeLife · 2024Article
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- Computational Methods to Target Protein-Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Membrane potential accelerates sugar uptake by stabilizing the outward facing conformation of the Na/glucose symporter vSGLT.Nature communications · 2023Article
- Studying the Effect of Amino Acid Substitutions in the M2 Ion Channel of the Influenza Virus on the Antiviral Activity of the Aminoadamantane DerivativeAdvanced pharmaceutical bulletin · 2021Article
- Constructing ion channels from water-soluble α-helical barrels.Nature chemistry · 2021Article
- Ste24: An Integral Membrane Protein Zinc Metalloprotease with Provocative Structure and Emergent Biology.Journal of molecular biology · 2020Review
- Single-channel properties of skeletal muscle ryanodine receptor pore ΔCell calcium · 2020Article
- A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology.The Journal of general physiology · 2020Article
- A size-modified poisson-boltzmann ion channel model in a solvent of multiple ionic species: Application to voltage-dependent anion channel.Journal of computational chemistry · 2020Article
- Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules.Journal of the American Chemical Society · 2019Article
- Article
- Predicting Humoral Alloimmunity from Differences in Donor and Recipient HLA Surface Electrostatic Potential.Journal of immunology (Baltimore, Md. : 1950) · 2018Article
- Molecular Signature for Receptor Engagement in the Metabolic Peptide Hormone Amylin.ACS pharmacology & translational science · 2018Article
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Authors and funding
6 authors.
Funding
Abstract
Electrostatic forces are one of the primary determinants of molecular interactions. They help guide the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular method for computing the electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation, and there are several easy-to-use software packages available that solve the PB equation for soluble proteins. Here we present a freely available program, called APBSmem, for carrying out these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS) is used as a back-end for solving the PB equation, and a Java-based graphical user interface (GUI) coordinates a set of routines that introduce the influence of the membrane, determine its placement relative to the protein, and set the membrane potential. The software Jmol is embedded in the GUI to visualize the protein inserted in the membrane before the calculation and the electrostatic potential after completing the computation. We expect that the ease with which the GUI allows one to carry out these calculations will make this software a useful resource for experimenters and computational researchers alike. Three examples of membrane protein electrostatic calculations are carried out to illustrate how to use APBSmem and to highlight the different quantities of interest that can be calculated.
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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.