(Q40675058)

English

Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants.

scientific article published on August 2001

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants (English)

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

protein folding

0 references

Maria Arménia Carrondo

3

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

António M. Baptista

2

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

Cláudio M. Soares

4

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

author name string

J Mendes

1

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

language of work or name

1 reference

based on heuristic

inferred from title

publication date

1 August 2001

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

Journal of Computer - Aided Molecular Design

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

15

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

721-740

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

8

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

https://scigraph.springernature.com/pub.10.1023/a:1012279810260

0 references

The folding of an enzyme. V. H/2H exchange-nuclear magnetic resonance studies on the folding pathway of barnase: complementarity to and agreement with protein engineering studies

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Energy functions for protein design

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

WHAT IF: a molecular modeling and drug design program

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Rapid refinement of protein interfaces incorporating solvation: application to the docking problem

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Atomic solvation parameters applied to molecular dynamics of proteins in solution

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modeling side-chain conformation for homologous proteins using an energy-based rotamer search

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Selecting near-native conformations in homology modeling: the role of molecular mechanics and solvation terms

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Predicting protein mutant energetics by self-consistent ensemble optimization.

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Side-chain and backbone flexibility in protein core design

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The denatured state (the other half of the folding equation) and its role in protein stability.

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Repacking protein cores with backbone freedom: structure prediction for coiled coils

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Affinities of amino acid side chains for solvent water

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Dominant forces in protein folding

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Surface area included in energy refinement of proteins. A comparative study on atomic solvation parameters

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Homology modelling of annexin I: implicit solvation improves side-chain prediction and combination of evaluation criteria allows recognition of different types of conformational error

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The folding of an enzyme. III. Structure of the transition state for unfolding of barnase analysed by a protein engineering procedure

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Solvation energy in protein folding and binding

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Empirical correlation between hydrophobic free energy and aqueous cavity surface area

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The dead-end elimination theorem and its use in protein side-chain positioning

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Pairwise calculation of protein solvent-accessible surface areas

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Solvation: how to obtain microscopic energies from partitioning and solvation experiments

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Denatured states of proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Homology modeling by the ICM method

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The folding of an enzyme. VI. The folding pathway of barnase: comparison with theoretical models

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hydrophobic bonding and accessible surface area in proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction.

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Electrostatic screening in molecular dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The interpretation of protein structures: Estimation of static accessibility

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Optimal sequence selection in proteins of known structure by simulated evolution

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analysed by a protein engineering procedure

1 reference

https://pubmed.ncbi.nlm.nih.gov/11718477

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1023/A:1012279810260

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

DBLP publication ID

journals/jcamd/MendesBCS01

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11718477%20AND%20SRC:MED&resulttype=core&format=json

3 December 2019

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q40675058&oldid=1619247004"