Beyond rotamers: a generative, probabilistic model of side chains in proteins (Q30390027)

6 November 2017

Beyond rotamers: a generative, probabilistic model of side chains in proteins (English)

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6 November 2017

probabilistic modeling

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6 November 2017

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Jes Frellsen

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Kristoffer E Johansson

object named as

Kristoffer E Johansson

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Thomas Hamelryck

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Thomas Hamelryck

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author name string

Tim Harder

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PMCID

2902450

6 November 2017

Martin Paluszewski

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6 November 2017

5 June 2010

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6 November 2017

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6 November 2017

11

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6 November 2017

306

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https://scigraph.springernature.com/pub.10.1186/1471-2105-11-306

6 November 2017

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cites work

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20 June 2018

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Improved prediction of protein side-chain conformations with SCWRL4

20 June 2018

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A probabilistic model of RNA conformational space

20 June 2018

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20 June 2018

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Probabilistic models and machine learning in structural bioinformatics.

20 June 2018

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Minimizing and learning energy functions for side-chain prediction.

20 June 2018

1 reference

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Computational protein design with side-chain conformational entropy.

20 June 2018

1 reference

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A generative, probabilistic model of local protein structure

20 June 2018

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OPUS-Rota: a fast and accurate method for side-chain modeling

20 June 2018

1 reference

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Accurate structural correlations from maximum likelihood superpositions

20 June 2018

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A primer on learning in Bayesian networks for computational biology

20 June 2018

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IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models

20 June 2018

1 reference

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Sampling realistic protein conformations using local structural bias

20 June 2018

1 reference

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Configurational-bias sampling technique for predicting side-chain conformations in proteins

20 June 2018

1 reference

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Improved side-chain modeling for protein-protein docking

20 June 2018

1 reference

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

20 June 2018

1 reference

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PDB file parser and structure class implemented in Python

20 June 2018

1 reference

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Stereochemistry of polypeptide chain configurations

20 June 2018

1 reference

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A graph-theory algorithm for rapid protein side-chain prediction

20 June 2018

1 reference

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PISCES: a protein sequence culling server

20 June 2018

1 reference

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Rotamer libraries in the 21st century

20 June 2018

1 reference

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Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization.

20 June 2018

1 reference

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Side-chain modeling with an optimized scoring function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

Extending the accuracy limits of prediction for side-chain conformations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

The penultimate rotamer library

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

20 June 2018

The Protein Data Bank

1 reference

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Using information theory to discover side chain rotamer classes: analysis of the effects of local backbone structure.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

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

20 June 2018

1 reference

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An MML classification of protein structure that knows about angles and sequence.

20 June 2018

1 reference

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Bayesian statistical analysis of protein side-chain rotamer preferences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

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

20 June 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

20 June 2018

1 reference

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A new approach to the rapid determination of protein side chain conformations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

Free energy estimates of all-atom protein structures using generalized belief propagation.

20 June 2018

1 reference

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Computing van der Waals energies in the context of the rotamer approximation.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

The energetics of off-rotamer protein side-chain conformations

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2902450

HMM sampling and applications to gene finding and alternative splicing

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20525384

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20525384

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-11-306

1 reference

journals/bmcbi/HarderBPFJH10

6 November 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

6 November 2017

1 reference

PMCID

2902450