Protein structure homology modeling using SWISS-MODEL workspace. (Q30374281)

21 June 2017

Protein structure homology modeling using SWISS-MODEL workspace. (English)

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21 June 2017

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Lorenza Bordoli

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Torsten Schwede

object named as

Torsten Schwede

6

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Konstantin Arnold

3

object named as

Konstantin Arnold

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21 June 2017

Lorenza Bordoli

1

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21 June 2017

Florian Kiefer

2

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21 June 2017

Pascal Benkert

4

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21 June 2017

James Battey

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21 June 2017

1 January 2009

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21 June 2017

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1-13

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1

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The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

21 June 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

The Universal Protein Resource (UniProt): an expanding universe of protein information

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

One thousand families for the molecular biologist

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

The relation between the divergence of sequence and structure in proteins

31 March 2020

2 references

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

31 March 2020

https://pubmed.ncbi.nlm.nih.gov/19131951

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Comparative protein modelling by satisfaction of spatial restraints

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Assessment of homology-based predictions in CASP5.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Assessment of predictions submitted for the CASP6 comparative modeling category

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Assessment of CASP7 structure predictions for template free targets

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Assessment of CASP7 predictions for template-based modeling targets

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Progress from CASP6 to CASP7.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Utility of homology models in the drug discovery process.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Automated protein structure homology modeling: a progress report.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Comparative protein structure modeling of genes and genomes

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

About the use of protein models

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Protein structure prediction and structural genomics

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Loop modeling: Sampling, filtering, and scoring

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Modeling structurally variable regions in homologous proteins with rosetta.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Modeling of loops in protein structures

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Twilight zone of protein sequence alignments

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Sequence comparison and protein structure prediction.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Improving the quality of protein structure models by selecting from alignment alternatives

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Predicting reliable regions in protein alignments from sequence profiles.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Near-optimal sequence alignment

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Assessing protein structures with a non-local atomic interaction energy.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Local quality assessment in homology models using statistical potentials and support vector machines

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Identification of correct regions in protein models using structural, alignment, and consensus information

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

PROCHECK: a program to check the stereochemical quality of protein structures

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Errors in protein structures

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Protein complexes: structure prediction challenges for the 21st century

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Determining the architectures of macromolecular assemblies

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

The plug domain of yeast Sec61p is important for efficient protein translocation, but is not essential for cell viability

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Automated server predictions in CASP7

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

EVA: Evaluation of protein structure prediction servers.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Tools for comparative protein structure modeling and analysis

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

M4T: a comparative protein structure modeling server.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Conducting research on the web: 2007 update for the bioinformatics links directory

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Protein structure computing in the genomic era.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

SWISS-MODEL: An automated protein homology-modeling server

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

SCOP database in 2004: refinements integrate structure and sequence family data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

The Pfam protein families database

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

InterProScan--an integration platform for the signature-recognition methods in InterPro

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

New developments in the InterPro database

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Protein secondary structure prediction based on position-specific scoring matrices

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Prediction of disordered regions in proteins from position specific score matrices

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

A model recognition approach to the prediction of all-helical membrane protein structure and topology

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Natively unfolded proteins

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Intrinsic disorder and functional proteomics

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Intrinsically unstructured proteins and their functions

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Database resources of the National Center for Biotechnology Information

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Protein homology detection by HMM-HMM comparison

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

The HHpred interactive server for protein homology detection and structure prediction

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

QMEAN: A comprehensive scoring function for model quality assessment.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

The Pfam protein families database

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

31 March 2020

The PROSITE database.

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

A mechanistic perspective on the chemistry of DNA repair glycosylases

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

The base excision repair pathway

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Topological characteristics of helical repeat proteins

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Membrane phospholipid degradation and protein kinase C for cell signalling

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

The extended protein kinase C superfamily

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Crystal structure of the cys2 activator-binding domain of protein kinase C delta in complex with phorbol ester

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

PQS: a protein quaternary structure file server.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

Inference of macromolecular assemblies from crystalline state

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.197

An assessment of COMPOSER: a rule-based approach to modelling protein structure

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19131951

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NPROT.2008.197

1 reference

Dimensions Publication ID

21 June 2017

0 references

1 reference