ArticleBMC bioinformatics2015
ProteinVolume: calculating molecular van der Waals and void volumes in proteins.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 129 citations in OpenAlex.
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- Directed Evolution of T7 RNA Polymerase Minimizes dsRNA By-product and Enables High-Fidelity mRNA Synthesis for Demanding Therapeutic Applications.Research (Washington, D.C.) · 2026Article
- Binding of Tetrapentylammonium to a c-MYC G-quadruplex Depicted through NMR and Volumetric Assessment.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Use of High Pressure NMR Spectroscopy to Rapidly Identify Proteins with Internal Ligand-Binding Voids.bioRxiv : the preprint server for biology · 2025Article
- Theoretical Methods for Assessing the Density of Protein Nanodroplets.International journal of molecular sciences · 2025Article
- Role of vinculin in the structural dynamics of cadherin-catenin complexes and its implications for F-actin binding.Protein science : a publication of the Protein Society · 2025Article
- Prediction of Small-Molecule Partitioning into Biomolecular Condensates from Simulation.JACS Au · 2025Article
- AMPEC4:Molecules (Basel, Switzerland) · 2025Article
- Prediction of small-molecule partitioning into biomolecular condensates from simulation.bioRxiv : the preprint server for biology · 2025Article
- Characteristics of kidney stone-modulatory proteins decoded from proteins identified in stone matrix and urine of stone formers and non-stone subjects.Computational and structural biotechnology journal · 2025Article
- Comparative evaluation of methods for the prediction of protein-ligand binding sites.Journal of cheminformatics · 2024Article
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- Single Molecule Thermodynamic Penalties Applied to Enzymes by Whispering Gallery Mode Biosensors.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- CageCavityCalc (Journal of chemical information and modeling · 2024Article
- Article
6 more citing papers are in PubMed but not listed here.
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 at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundVoids and cavities in the native protein structure determine the pressure unfolding of proteins. In addition, the volume changes due to the interaction of newly exposed atoms with solvent upon protein unfolding also contribute to the pressure unfolding of proteins. Quantitative understanding of these effects is important for predicting and designing proteins with predefined response to changes in hydrostatic pressure using computational approaches. The molecular surface volume is a useful metric that describes contribution of geometrical volume, which includes van der Waals volume and volume of the voids, to the total volume of a protein in solution, thus isolating the effects of hydration for separate calculations.
resultsWe developed ProteinVolume, a highly robust and easy-to-use tool to compute geometric volumes of proteins. ProteinVolume generates the molecular surface of a protein and uses an innovative flood-fill algorithm to calculate the individual components of the molecular surface volume, van der Waals and intramolecular void volumes. ProteinVolume is user friendly and is available as a web-server or a platform-independent command-line version.
conclusionsProteinVolume is a highly accurate and fast application to interrogate geometric volumes of proteins. ProteinVolume is a free web server available on http://gmlab.bio.rpi.edu . Free-standing platform-independent Java-based ProteinVolume executable is also freely available at this web site.
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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.