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Protein modeling: what happened to the "protein structure gap"?
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scholarly article
1 reference
stated in
Europe PubMed Central
PMCID
3816506
retrieved
19 August 2017
title
Protein modeling: what happened to the "protein structure gap"?
(English)
1 reference
stated in
Europe PubMed Central
PMCID
3816506
retrieved
19 August 2017
main subject
protein structure
0 references
author
Torsten Schwede
object named as
Torsten Schwede
series ordinal
1
0 references
publication date
1 September 2013
1 reference
stated in
Europe PubMed Central
PMCID
3816506
retrieved
19 August 2017
published in
Structure
1 reference
stated in
Europe PubMed Central
PMCID
3816506
retrieved
19 August 2017
volume
21
1 reference
stated in
Europe PubMed Central
PMCID
3816506
retrieved
19 August 2017
page(s)
1531-1540
1 reference
stated in
Europe PubMed Central
PMCID
3816506
retrieved
19 August 2017
issue
9
1 reference
stated in
Europe PubMed Central
PMCID
3816506
retrieved
19 August 2017
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RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction
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Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies
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3 June 2018
Assessment of template based protein structure predictions in CASP9.
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3 June 2018
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3 June 2018
Critical assessment of methods of protein structure prediction (CASP)--round IX
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CASP9 assessment of free modeling target predictions
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3 June 2018
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Crystal structure of a monomeric retroviral protease solved by protein folding game players
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Cryo-electron tomography: gaining insight into cellular processes by structural approaches
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Dynamic allostery: linkers are not merely flexible
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3 June 2018
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Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation
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3 June 2018
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3 June 2018
Improved molecular replacement by density- and energy-guided protein structure optimization
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3 June 2018
Challenges for the prediction of macromolecular interactions
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3 June 2018
The three-dimensional molecular structure of the desmosomal plaque
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3 June 2018
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction
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3 June 2018
Interactome networks and human disease
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3 June 2018
Three-dimensional modeling of protein interactions and complexes is going 'omics
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3 June 2018
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3 June 2018
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
An inventory of the bacterial macromolecular components and their spatial organization.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Quo vadis, virtual screening? A comprehensive survey of prospective applications
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Macromolecular docking restrained by a small angle X-ray scattering profile
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Protein-protein docking tested in blind predictions: the CAPRI experiment
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
MolProbity: all-atom structure validation for macromolecular crystallography
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Disentangling direct from indirect co-evolution of residues in protein alignments
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Three-dimensional structural view of the central metabolic network of Thermotoga maritima
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Structure prediction for CASP8 with all-atom refinement using Rosetta.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Fast and accurate automatic structure prediction with HHpred.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Nature of the protein universe
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Protein structure prediction on the Web: a case study using the Phyre server
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Outcome of a workshop on applications of protein models in biomedical research
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
The Protein Model Portal
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
De novo protein structure generation from incomplete chemical shift assignments.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
The SWISS-MODEL Repository and associated resources
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Macromolecular modeling with rosetta
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Integrating diverse data for structure determination of macromolecular assemblies
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
New G-protein-coupled receptor crystal structures: insights and limitations
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
The molecular sociology of the cell
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
The molecular architecture of the nuclear pore complex
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Determining the architectures of macromolecular assemblies
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Structural systems biology: modelling protein interactions.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Screening drug-like compounds by docking to homology models: a systematic study.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Principles of selective ion transport in channels and pumps
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
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3 June 2018
EVA: Evaluation of protein structure prediction servers.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
3D-Jury: a simple approach to improve protein structure predictions
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
A vision for the future of genomics research
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Protein structure prediction and structural genomics
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
Errors in protein structures
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
The relation between the divergence of sequence and structure in proteins
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
3 June 2018
The genome folding mechanism in yeast
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
A toolkit and benchmark study for FRET-restrained high-precision structural modeling.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Efficient a priori identification of drug resistant mutations using Dead-End Elimination and MM-PBSA.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Macromolecular assembly structures by comparative modeling and electron microscopy
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
RNA tertiary structure prediction with ModeRNA.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Modeling of proteins and their assemblies with the integrative modeling platform
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Using a homology model of cytochrome P450 2D6 to predict substrate site of metabolism
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Outcome of a workshop on archiving structural models of biological macromolecules.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Inferential structure determination.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Performance of 3D-database molecular docking studies into homology models
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3816506
retrieved
26 November 2018
Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures
1 reference
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PubMed
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https://pubmed.ncbi.nlm.nih.gov/24010712
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Proceedings of the Third Annual Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) Challenge and Workshop. June 2009. Montreal, Canada
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24010712
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1016/J.STR.2013.08.007
1 reference
stated in
Europe PubMed Central
PMCID
3816506
retrieved
19 August 2017
PMCID
3816506
1 reference
stated in
Europe PubMed Central
PMCID
3816506
retrieved
19 August 2017
PubMed ID
24010712
1 reference
stated in
Europe PubMed Central
PMCID
3816506
retrieved
19 August 2017
ResearchGate publication ID
256466583
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