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The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

Nucleic acids research, 2016-07, Vol.44 (W1), p.W410-W415

2016

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Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale

Journal of proteome research, 2018-11, Vol.17 (11), p.3614-3627

2018

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Collisions or electrons? Protein sequence analysis in the 21st century

Analytical chemistry (Washington), 2009-05, Vol.81 (9), p.3208-3215

Coon, Joshua J

2009

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Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

Biochimica et biophysica acta, 2015-08, Vol.1854 (8), p.1019-1037

2015

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Sensitive sequencing: Instrumentation led to biological revolution

The Journal of biological chemistry, 2017-10, Vol.292 (43), p.17977-17978

Taylor, Alexandra A.

2017

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PyMOL and Inkscape Bridge the Data and the Data Visualization

Structure (London), 2016-12, Vol.24 (12), p.2041-2042

2016

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Paving the way to single-molecule protein sequencing

Nature nanotechnology, 2018-09, Vol.13 (9), p.786-796

2018

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Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence–Function Space and Genome Context to Discover Novel Functions

Biochemistry (Easton), 2017-08, Vol.56 (33), p.4293-4308

Gerlt, John A

2017

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TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

Nature methods, 2016-09, Vol.13 (9), p.777-783

2016

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Clustal W and Clustal X version 2.0

Bioinformatics, 2007-11, Vol.23 (21), p.2947-2948

2007

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FreeContact: fast and free software for protein contact prediction from residue co-evolution

BMC bioinformatics, 2014-03, Vol.15 (1), p.85-85, Article 85

2014

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Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics

BMC bioinformatics, 2007-11, Vol.8 (1), p.468-468, Article 468

2007

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Selection of relevant features from amino acids enables development of robust classifiers

Amino acids, 2014-05, Vol.46 (5), p.1343-1351

2014

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Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification?

Briefings in bioinformatics, 2018-09, Vol.19 (5), p.954-970

2018

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A novel alignment-free method to classify protein folding types by combining spectral graph clustering with Chou's pseudo amino acid composition

Journal of theoretical biology, 2017-07, Vol.424, p.49-54

2017

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Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation

Journal of proteome research, 2017-07, Vol.16 (7), p.2653-2659

2017

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The abc's (and xyz's) of peptide sequencing

Nature reviews. Molecular cell biology, 2004-09, Vol.5 (9), p.699-711

2004

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Prediction of Protein Structures, Functions, and Interactions

Bujnicki, Janusz M

1. Aufl., 2009

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Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou’s pseudo amino acid composition

Journal of theoretical biology, 2013-02, Vol.318, p.1-12

2013

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Peptide and Protein Sequence Analysis by Electron Transfer Dissociation Mass Spectrometry

Proceedings of the National Academy of Sciences - PNAS, 2004-06, Vol.101 (26), p.9528-9533

2004

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Boosting phosphorylation site prediction with sequence feature‐based machine learning

Proteins, structure, function, and bioinformatics, 2020-02, Vol.88 (2), p.284-291

2020

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Identification of differentially expressed peptides in high-throughput proteomics data

Briefings in bioinformatics, 2018-09, Vol.19 (5), p.971-981

2018

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A Generative Angular Model of Protein Structure Evolution

Molecular biology and evolution, 2017-08, Vol.34 (8), p.2085-2100

2017

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pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra

Journal of proteome research, 2013-02, Vol.12 (2), p.615-625

2013

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The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale

Collisions or electrons? Protein sequence analysis in the 21st century

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

Sensitive sequencing: Instrumentation led to biological revolution

PyMOL and Inkscape Bridge the Data and the Data Visualization

Paving the way to single-molecule protein sequencing

Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence–Function Space and Genome Context to Discover Novel Functions

Validation of Structures in the Protein Data Bank

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

Clustal W and Clustal X version 2.0

FreeContact: fast and free software for protein contact prediction from residue co-evolution

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics

Selection of relevant features from amino acids enables development of robust classifiers

Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification?

A novel alignment-free method to classify protein folding types by combining spectral graph clustering with Chou's pseudo amino acid composition

Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation

The abc's (and xyz's) of peptide sequencing

Prediction of Protein Structures, Functions, and Interactions

Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou’s pseudo amino acid composition

Peptide and Protein Sequence Analysis by Electron Transfer Dissociation Mass Spectrometry

Boosting phosphorylation site prediction with sequence feature‐based machine learning

Identification of differentially expressed peptides in high-throughput proteomics data

A Generative Angular Model of Protein Structure Evolution

pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra

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