(Q34142889)

31 July 2017

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title

Energy estimation in protein design (English)

1 reference

31 July 2017

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Joaquim Mendes

1

1 reference

PubMed ID

12163065

31 July 2017

Raphael Guerois

series ordinal

2

1 reference

PubMed ID

12163065

31 July 2017

Luis Serrano

series ordinal

3

1 reference

31 July 2017

1 August 2002

1 reference

Current Opinion in Structural Biology

31 July 2017

1 reference

31 July 2017

12

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31 July 2017

441-446

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31 July 2017

4

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Effective energy functions for protein structure prediction.

31 July 2017

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Statistical potentials extracted from protein structures: how accurate are they?

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Knowledge-based potential defined for a rotamer library to design protein sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

A self-consistent knowledge-based approach to protein design

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

De novo protein design. I. In search of stability and specificity.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Prediction of amino acid sequence from structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

The design of a hyperstable mutant of the Abp1p SH3 domain by sequence alignment analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Stabilization of GroEL minichaperones by core and surface mutations

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Prediction of local structure in proteins using a library of sequence-structure motifs

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

A polar, solvent-exposed residue can be essential for native protein structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Improving the refolding yield of interleukin-4 through the optimization of local interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Stabilisation of α-helices by site-directed mutagenesis reveals the importance of secondary structure in the transition state for acylphosphatase folding

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins?

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

The SH3-fold family: experimental evidence and prediction of variations in the folding pathways

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Local water bridges and protein conformational stability

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Long-range order in the src SH3 folding transition state

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Electrostatics significantly affect the stability of designed homeodomain variants

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C' position of the C-capping box of alpha-helices

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Probing the structural determinants of type II' beta-turn formation in peptides and proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Energy functions for protein design

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Computational protein design

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Review: protein design--where we were, where we are, where we're going.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Configurational entropy of native proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

A new approach to the design of uniquely folded thermally stable proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Conformational strain in the hydrophobic core and its implications for protein folding and design

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Protein design automation

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

De novo design of the hydrophobic core of ubiquitin

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

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/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Computer-aided design of beta-sheet peptides

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Computer-aided design of a PDZ domain to recognize new target sequences.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Side-chain and backbone flexibility in protein core design

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Rotamer strain energy in protein helices - quantification of a major force opposing protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Increasing protein stability by altering long-range coulombic interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Rational Modification of Protein Stability by the Mutation of Charged Surface Residues†

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

To charge or not to charge?

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Designing protein beta-sheet surfaces by Z-score optimization.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Stabilization of proteins by rational design of alpha-helix stability using helix/coil transition theory.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Automatic protein design with all atom force-fields by exact and heuristic optimization

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Pairwise calculation of protein solvent-accessible surface areas

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

A Strategy for the Incorporation of Water Molecules Present in a Ligand Binding Site into a Three-Dimensional Quantitative Structure−Activity Relationship Analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Computationally accessible method for estimating free energy changes resulting from site-specific mutations of biomolecules: systematic model building and structural/hydropathic analysis of deoxy and oxy hemoglobins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

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://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Statistical mechanics of simple models of protein folding and design

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Native protein sequences are close to optimal for their structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Persistence of native-like topology in a denatured protein in 8 M urea

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Composites of local structure propensities: evidence for local encoding of long-range structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

NMR characterization of residual structure in the denatured state of protein L

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

The beta-beta-alpha fold: explorations in sequence space

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Contribution of surface salt bridges to protein stability

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Evaluation of the energetic contribution of an ionic network to beta-sheet stability

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Achieving stability and conformational specificity in designed proteins via binary patterning

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

Accurate computer-based design of a new backbone conformation in the second turn of protein L

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2802%2900345-7

7 January 2021

10.1016/S0959-440X(02)00345-7

Identifiers

DOI

1 reference

31 July 2017

1 reference

PubMed ID

12163065