Chapter 1. Target selection in structural genomics projects to increase knowledge of protein structure and function space (Q30392866)

21 June 2017

title

Chapter 1. Target selection in structural genomics projects to increase knowledge of protein structure and function space (English)

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21 June 2017

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3

Christine Orengo

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author name string

Phil Carter

series ordinal

1

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21 June 2017

David Lee

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2

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21 June 2017

language of work or name

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1 January 2008

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Advances in protein chemistry and structural biology

21 June 2017

published in

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21 June 2017

volume

75

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21 June 2017

page(s)

1-52

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PDP: protein domain parser.

21 June 2017

cites work

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https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The Biomolecular Interaction Network Database and related tools 2005 update

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

PRINTS and its automatic supplement, prePRINTS.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Improved prediction of signal peptides: SignalP 3.0

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Improved membrane protein topology prediction by domain assignments

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Prolinks: a database of protein functional linkages derived from coevolution

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The ProDom database of protein domain families: more emphasis on 3D

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The impact of structural genomics: expectations and outcomes

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

MINT: the Molecular INTeraction database

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

TargetDB: a target registration database for structural genomics projects

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

A machine learning information retrieval approach to protein fold recognition.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Automated prediction of CASP-5 structures using the Robetta server.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Conservation of gene order: a fingerprint of proteins that physically interact

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Coupling of folding and binding for unstructured proteins

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https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Intrinsically unstructured proteins and their functions

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https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Profile hidden Markov models

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https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

COACH: profile-profile alignment of protein families using hidden Markov models

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Protein interaction maps for complete genomes based on gene fusion events

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

An efficient algorithm for large-scale detection of protein families

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

SPEPlip: the detection of signal peptide and lipoprotein cleavage sites

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Modeller: generation and refinement of homology-based protein structure models

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Clustering by passing messages between data points

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Automated annotation of microbial proteomes in SWISS-PROT.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Protein domain identification and improved sequence similarity searching using PSI-BLAST.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

SnapDRAGON: a method to delineate protein structural domains from sequence data

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Scooby-domain: prediction of globular domains in protein sequence

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

How representative are the known structures of the proteins in a complete genome? A comprehensive structural census

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Comparative analysis of coiled-coil prediction methods.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

ADDA: a domain database with global coverage of the protein universe

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

WoLF PSORT: protein localization predictor

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

FFAS03: a server for profile--profile sequence alignments

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Protein secondary structure prediction based on position-specific scoring matrices

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Improving the accuracy of transmembrane protein topology prediction using evolutionary information

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Reactome: a knowledgebase of biological pathways

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https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Basic charge clusters and predictions of membrane protein topology.

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https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

A combined transmembrane topology and signal peptide prediction method

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

ProtoNet 4.0: a hierarchical classification of one million protein sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

IntAct--open source resource for molecular interaction data

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Protein structure prediction and analysis using the Robetta server.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

A simple method for displaying the hydropathic character of a protein

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The state of the Protein Structure Initiative.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

SMART 5: domains in the context of genomes and networks

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

NORSp: Predictions of long regions without regular secondary structure

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

CHOP proteins into structural domain-like fragments

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Predicting coiled coils from protein sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Detecting protein function and protein-protein interactions from genome sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Rapid protein domain assignment from amino acid sequence using predicted secondary structure

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Bayesian search of functionally divergent protein subgroups and their function specific residues.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Improvement of the GenTHREADER method for genomic fold recognition

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Human protein reference database--2006 update

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Critical assessment of methods of protein structure prediction-Round VII

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

New developments in the InterPro database

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Automatic prediction of protein domains from sequence information using a hybrid learning system

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The use of gene clusters to infer functional coupling

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

A normalised scale for structural genomics target ranking: the OB-Score

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Improved tools for biological sequence comparison

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

EVEREST: a collection of evolutionary conserved protein domains

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Structural diversity of domain superfamilies in the CATH database

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The Database of Interacting Proteins: 2004 update

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Natively unstructured loops differ from other loops

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Structural biology. Structural genomics, round 2

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The challenge of protein structure determination--lessons from structural genomics.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

XtalPred: a web server for prediction of protein crystallizability

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Identification of common molecular subsequences

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Evaluation of domain prediction in CASP6.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The COG database: an updated version includes eukaryotes

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Protein structural domain identification

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

History of the enzyme nomenclature system

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Evolution of function in protein superfamilies, from a structural perspective.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Progress of structural genomics initiatives: an analysis of solved target structures.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Assessment of predictions submitted for the CASP7 domain prediction category.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Crystal structure of an inactive duck delta II crystallin mutant with bound argininosuccinate

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Structure, function and evolution of multidomain proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

STRING 7--recent developments in the integration and prediction of protein interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

The SUPERFAMILY database in 2007: families and functions

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

Non-globular domains in protein sequences: automated segmentation using complexity measures

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

PIRSF: family classification system at the Protein Information Resource

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2807%2975001-5

7 January 2021

10.1016/S0065-3233(07)75001-5

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DOI

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21 June 2017

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