(Q39434682)

11 September 2017

Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future (English)

1 reference

11 September 2017

1 reference

Sebastian Kelm

1

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Anna Vangone

Anna Vangone

2

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Yoonjoo Choi

Yoonjoo Choi

3

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Jiye Shi

Jiye Shi

5

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Charlotte Deane

Charlotte M Deane

6

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author name string

Jean-Paul Ebejer

4

1 reference

PubMed ID

23589399

11 September 2017

language of work or name

English

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publication date

17 October 2013

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11 September 2017

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11 September 2017

82

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11 September 2017

2

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11 September 2017

175-186

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The membrane protein universe: what's out there and why bother?

11 September 2017

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Cyclic coordinate descent: A robotics algorithm for protein loop closure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Protein loop modeling by using fragment assembly and analytical loop closure

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

A hierarchical approach to all-atom protein loop prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Long loop prediction using the protein local optimization program.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Modeling of loops in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Progress in super long loop prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Loops In Proteins (LIP)--a comprehensive loop database for homology modelling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

A supersecondary structure library and search algorithm for modeling loops in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Modeling protein loops with knowledge-based prediction of sequence-structure alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

CODA: a combined algorithm for predicting the structurally variable regions of protein models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

SCOP: a structural classification of proteins database for the investigation of sequences and structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Saturating representation of loop conformational fragments in structure databanks

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

21 January 2018

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Predicting antibody complementarity determining region structures without classification.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

OPM: orientations of proteins in membranes database

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

PISCES: a protein sequence culling server

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

iMembrane: homology-based membrane-insertion of proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

JOY: protein sequence-structure representation and analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

MEDELLER: homology-based coordinate generation for membrane proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Constant time clash detection in protein folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Environment specific substitution tables improve membrane protein alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

TM-align: a protein structure alignment algorithm based on the TM-score

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Loop prediction for a GPCR homology model: algorithms and results.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

MP-T: improving membrane protein alignment for structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24299

21 January 2018

Identifiers

DOI

10.1002/PROT.24299

1 reference

11 September 2017

1 reference

PubMed ID

23589399