(Q51547005)

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TSAR, a new graph-theoretical approach to computational modeling of protein side-chain flexibility: modeling of ionization properties of proteins.

scientific article published on 18 July 2011

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scholarly article

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Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

TSAR, a new graph-theoretical approach to computational modeling of protein side-chain flexibility: modeling of ionization properties of proteins. (English)

1 reference

Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

computational biology

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author name string

Oleg V Stroganov

1

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Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

Fedor N Novikov

2

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Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

Alexey A Zeifman

3

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Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

Viktor S Stroylov

4

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Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

Ghermes G Chilov

5

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Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

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publication date

18 July 2011

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Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

1 reference

Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

79

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Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

9

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Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

2693-2710

1 reference

Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

Modeling electrostatic effects in proteins

1 reference

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21 January 2018

Calculations of electrostatic interactions in biological systems and in solutions

1 reference

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21 January 2018

Energetics of charge-charge interactions in proteins.

1 reference

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pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

1 reference

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21 January 2018

Prediction of pH-dependent properties of proteins

1 reference

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Generalized born models of macromolecular solvation effects

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

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Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin

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Constant pH molecular dynamics in generalized Born implicit solvent

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Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models

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Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility

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Optimizing pKa computation in proteins with pH adapted conformations.

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21 January 2018

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

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21 January 2018

Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy

1 reference

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21 January 2018

Accurate, conformation-dependent predictions of solvent effects on protein ionization constants

1 reference

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Lead finder: an approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening.

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21 January 2018

Complexity of Finding Embeddings in a k-Tree

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21 January 2018

The fuzzy-end elimination theorem: correctly implementing the side chain placement algorithm based on the dead-end elimination theorem

1 reference

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21 January 2018

Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains

1 reference

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21 January 2018

Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23099

21 January 2018

Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23099

21 January 2018

Electrostatic effects in proteins: comparison of dielectric and charge models

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23099

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23099

21 January 2018

PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values

1 reference

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21 January 2018

Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23099

21 January 2018

Very fast empirical prediction and rationalization of protein pKa values

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23099

21 January 2018

Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23099

21 January 2018

Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by two-dimensional 1H NMR.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23099

21 January 2018

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

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21 January 2018

Automated sampling assessment for molecular simulations using the effective sample size

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23099

21 January 2018

Identifiers

10.1002/PROT.23099

1 reference

Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

6 April 2018

http://europepmc.org/abstract/MED/21769942

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