(Q33198535)

23 July 2017

title

Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library (English)

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23 July 2017

1 reference

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2

P Leslie Dutton

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23 July 2017

3

A Joshua Wand

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23 July 2017

Ronald W Peterson

1

1 reference

23 July 2017

publication date

1 March 2004

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23 July 2017

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23 July 2017

volume

13

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23 July 2017

issue

3

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23 July 2017

page(s)

735-751

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Side-chain modeling with an optimized scoring function

23 July 2017

cites work

1 reference

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28 July 2018

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Extending the accuracy limits of prediction for side-chain conformations

28 July 2018

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Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure.

28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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Side-chain and backbone flexibility in protein core design

28 July 2018

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

28 July 2018

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Accuracy of side-chain prediction upon near-native protein backbones generated by Ab initio folding methods

28 July 2018

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Torsion angle dynamics for NMR structure calculation with the new program DYANA

28 July 2018

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28 July 2018

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Bayesian statistical analysis of protein side-chain rotamer preferences

28 July 2018

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Prediction of protein side chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space.

28 July 2018

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Prediction of protein side-chain conformations by principal component analysis for fixed main-chain atoms.

28 July 2018

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All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination

28 July 2018

1 reference

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Hydrogen bonding stabilizes globular proteins

28 July 2018

1 reference

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

28 July 2018

1 reference

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De novo design of the hydrophobic cores of proteins

28 July 2018

1 reference

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286725

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286725

The interpretation of protein structures: Estimation of static accessibility

28 July 2018

1 reference

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Characterization of a helical protein designed from first principles

28 July 2018

1 reference

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Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

28 July 2018

1 reference

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Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors.

28 July 2018

1 reference

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Computational method for the design of enzymes with altered substrate specificity

28 July 2018

1 reference

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The nature of the accessible and buried surfaces in proteins

28 July 2018

1 reference

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Areas, volumes, packing and protein structure

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286725

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286725

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

31 October 2018

1 reference

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FLEXS: a method for fast flexible ligand superposition.

31 October 2018

1 reference

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LINUS: a hierarchic procedure to predict the fold of a protein.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286725

Side-chain prediction by neural networks and simulated annealing optimization.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286725

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

31 October 2018

1 reference

12 December 2020

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

1 reference

12 December 2020

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

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12 December 2020

Design and synthesis of multi-haem proteins

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12 December 2020

A method to configure protein side-chains from the main-chain trace in homology modelling

1 reference

12 December 2020

Protein sidechain conformer prediction: a test of the energy function

1 reference

12 December 2020

Identifiers

DOI

10.1110/PS.03250104

1 reference

23 July 2017

1 reference

23 July 2017

1 reference