(Q34247986)

31 July 2017

Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii (English)

1 reference

31 July 2017

Alessandra Corazza

2

0 references

Federico Fogolari

object named as

Federico Fogolari

1

0 references

Paolo Viglino

5

object named as

Paolo Viglino

1 reference

31 July 2017

Vijaylakshmi Yarra

3

1 reference

PubMed ID

22536964

31 July 2017

Anusha Jalaru

4

1 reference

PubMed ID

22536964

31 July 2017

Gennaro Esposito

6

1 reference

31 July 2017

28 March 2012

1 reference

31 July 2017

1 reference

31 July 2017

13 Suppl 4

1 reference

31 July 2017

S18

1 reference

Creative Commons Attribution 2.0 Generic

31 July 2017

start time

28 March 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1186/1471-2105-13-s4-s18

0 references

cites work

COSMO-RS: an alternative to simulation for calculating thermodynamic properties of liquid mixtures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

A fast and accurate computational approach to protein ionization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Very fast prediction and rationalization of pKa values for protein-ligand complexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Recent advances in implicit solvent-based methods for biomolecular simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Electrostatics calculations: latest methodological advances

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Very fast empirical prediction and rationalization of protein pKa values

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

H++: a server for estimating pKas and adding missing hydrogens to macromolecules

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Improving implicit solvent simulations: a Poisson-centric view

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Recent advances in the development and application of implicit solvent models in biomolecule simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Exploring protein native states and large-scale conformational changes with a modified generalized born model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Protein electrostatics: a review of the equations and methods used to model electrostatic equations in biomolecules--applications in biotechnology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Effective Born radii in the generalized Born approximation: the importance of being perfect

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Electrostatics of nanosystems: application to microtubules and the ribosome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

What are the dielectric "constants" of proteins and how to validate electrostatic models?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Generalized born models of macromolecular solvation effects

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Reduced surface: an efficient way to compute molecular surfaces

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

VMD: visual molecular dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Prediction of pH-dependent properties of proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

A new method for computing the macromolecular electric potential.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis

6 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

Analytical electrostatics for biomolecules: beyond the generalized Born approximation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

Incorporating variable dielectric environments into the generalized Born model

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

Interpreting the Coulomb-field approximation for generalized-Born electrostatics using boundary-integral equation theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

Numerical solution of boundary-integral equations for molecular electrostatics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

GBr6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

Analysis of integral expressions for effective Born radii.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

A fast and accurate method for predicting pKa of residues in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

A parameterized, continuum electrostatic model for predicting protein pKa values.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

Constant pH molecular dynamics in generalized Born implicit solvent

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

An empirical model for electrostatic interactions in proteins incorporating multiple geometry‐dependent dielectric constants

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S18

Benchmarking pKa Prediction Methods for Residues in Proteins.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

GBr(6): a parameterization-free, accurate, analytical generalized born method.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

Generalized born model with a simple smoothing function.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434445

A statistical approach to the prediction of pK(a) values in proteins

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22536964

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-13-S4-S18

1 reference

journals/bmcbi/FogolariCYJVE12

31 July 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

31 July 2017

1 reference

PubMed ID

22536964