ArticleBMC bioinformatics2012
Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 67 citations in OpenAlex.
- Bluues2: An enhanced web server for fast and accurate electrostatic analysis of proteins and protein complexes.Protein science : a publication of the Protein Society · 2026Article
- Bluues_cplx: Electrostatics at Protein-Protein and Protein-Ligand Interfaces.Molecules (Basel, Switzerland) · 2025Article
- Structural basis for human OGG1 processing 8-oxodGuo within nucleosome core particles.Nature communications · 2024Article
- Chemical Synthesis and Structure-Activity Relationship Studies of the Coagulation Factor Xa Inhibitor Tick Anticoagulant Peptide from the Hematophagous ParasiteBiomimetics (Basel, Switzerland) · 2024Article
- MAHOMES II: A webserver for predicting if a metal binding site is enzymatic.Protein science : a publication of the Protein Society · 2023Article
- MAHOMES II: A webserver for predicting if a metal binding site is enzymatic.bioRxiv : the preprint server for biology · 2023Article
- Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 ofComputational and structural biotechnology journal · 2023Article
- BiallelicNeurology. Genetics · 2022Article
- Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol.Frontiers in immunology · 2022Article
- Pathogenic D76N Variant of βBiology · 2021Article
- Machine learning differentiates enzymatic and non-enzymatic metals in proteins.Nature communications · 2021Article
- Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders.Frontiers in molecular biosciences · 2021Article
- Quantitative Description of Surface Complementarity of Antibody-Antigen Interfaces.Frontiers in molecular biosciences · 2021Article
- Insights into the Interaction Mechanism of DTP3 with MKK7 by Using STD-NMR and Computational Approaches.Biomedicines · 2020Article
- Molecular Dynamics Simulations Reveal Canonical Conformations in Different pMHC/TCR Interactions.Cells · 2020Article
- A novel strategy for molecular interfaces optimization: The case of Ferritin-Transferrin receptor interaction.Computational and structural biotechnology journal · 2020Article
- Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design.Computational and structural biotechnology journal · 2020Review
- Structure of Turnip mosaic virus and its viral-like particles.Scientific reports · 2019Article
- Novel PathogenicFrontiers in genetics · 2019Article
- Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations.BioMed research international · 2018Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Poisson-Boltzmann (PB) equation and its linear approximation have been widely used to describe biomolecular electrostatics. Generalized Born (GB) models offer a convenient computational approximation for the more fundamental approach based on the Poisson-Boltzmann equation, and allows estimation of pairwise contributions to electrostatic effects in the molecular context.
resultsWe have implemented in a single program most common analyses of the electrostatic properties of proteins. The program first computes generalized Born radii, via a surface integral and then it uses generalized Born radii (using a finite radius test particle) to perform electrostaic analyses. In particular the ouput of the program entails, depending on user's requirement: 1) the generalized Born radius of each atom; 2) the electrostatic solvation free energy; 3) the electrostatic forces on each atom (currently in a developmental stage); 4) the pH-dependent properties (total charge and pH-dependent free energy of folding in the pH range -2 to 18; 5) the pKa of all ionizable groups; 6) the electrostatic potential at the surface of the molecule; 7) the electrostatic potential in a volume surrounding the molecule;
conclusionsAlthough at the expense of limited flexibility the program provides most common analyses with requirement of a single input file in PQR format. The results obtained are comparable to those obtained using state-of-the-art Poisson-Boltzmann solvers. A Linux executable with example input and output files is provided as supplementary material.
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