(Q33581606)

28 July 2017

title

Protein thermostability calculations using alchemical free energy simulations (English)

1 reference

28 July 2017

Daniel Seeliger

1

1 reference

28 July 2017

Bert L de Groot

series ordinal

2

1 reference

28 July 2017

language of work or name

English

0 references

publication date

1 May 2010

1 reference

28 July 2017

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28 July 2017

volume

98

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28 July 2017

issue

10

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28 July 2017

page(s)

2309-2316

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

28 July 2017

cites work

1 reference

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Design of therapeutic proteins with enhanced stability.

21 June 2018

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λ-Dynamics free energy simulation methods

21 June 2018

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Computational structure-based redesign of enzyme activity

21 June 2018

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Kemp elimination catalysts by computational enzyme design

21 June 2018

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De novo computational design of retro-aldol enzymes

21 June 2018

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Minimalist active-site redesign: teaching old enzymes new tricks

21 June 2018

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Canonical sampling through velocity rescaling

21 June 2018

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Statistical potential for assessment and prediction of protein structures

21 June 2018

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

21 June 2018

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Dramatic performance enhancements for the FASTER optimization algorithm

21 June 2018

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Potent antibody therapeutics by design

21 June 2018

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ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions

21 June 2018

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The FoldX web server: an online force field

21 June 2018

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I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure

21 June 2018

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Computational thermostabilization of an enzyme

21 June 2018

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Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity.

21 June 2018

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De novo design of catalytic proteins

21 June 2018

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Protein structure prediction using Rosetta

21 June 2018

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The folding pathway of barnase: the rate-limiting transition state and a hidden intermediate under native conditions

21 June 2018

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The many roles of computation in drug discovery

21 June 2018

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Rational design and engineering of therapeutic proteins

21 June 2018

1 reference

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Industrial biocatalysis today and tomorrow

21 June 2018

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Combinatorial and computational challenges for biocatalyst design

21 June 2018

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Improving enzymes by using them in organic solvents

21 June 2018

1 reference

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Enzymes for chemical synthesis

21 June 2018

1 reference

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Enabling the chemistry of life

21 June 2018

1 reference

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Backbone-dependent rotamer library for proteins. Application to side-chain prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Extrapolation to water of kinetic and equilibrium data for the unfolding of barnase in urea solutions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

pKA values of carboxyl groups in the native and denatured states of barnase: the pKA values of the denatured state are on average 0.4 units lower than those of model compounds

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

21 June 2018

1 reference

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Capping and alpha-helix stability

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Mapping the transition state and pathway of protein folding by protein engineering

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Effect of the substitution Ala----Gly at each of five residue positions in the C-peptide helix

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Free energy via molecular simulation: applications to chemical and biomolecular systems

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

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

21 June 2018

1 reference

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Alpha-helix stability in proteins. II. Factors that influence stability at an internal position

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Specific interactions for ab initio folding of protein terminal regions with secondary structures.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Geometry-based sampling of conformational transitions in proteins.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Bioinformatics-driven, rational engineering of protein thermostability

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Proteins in organic solvents

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Factors enhancing protein thermostability

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

New approach to the study of transient protein conformations: the formation of a semiburied salt link in the folding pathway of barnase.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872215

Histidine-aromatic interactions in barnase. Elevation of histidine pKa and contribution to protein stability

31 October 2018

1 reference

12 December 2020

Alpha-helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at solvent-exposed surfaces

1 reference

12 December 2020

Contribution of hydrophobic interactions to protein stability

1 reference

12 December 2020

Predicting free energy changes using structural ensembles

1 reference

12 December 2020

Histidine residues at the N- and C-termini of alpha-helices: perturbed pKas and protein stability

1 reference

12 December 2020

10.1016/J.BPJ.2010.01.051

Identifiers

DOI

1 reference

28 July 2017

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28 July 2017

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