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YPD specifications


Unique identifier OMICS_15726
Name YPD
Alternative name Yeast Protein Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

Publication for Yeast Protein Database

YPD citations


Comparative Genomics of Sibling Species of Fonsecaea Associated with Human Chromoblastomycosis

Front Microbiol
PMCID: 5640708
PMID: 29062304
DOI: 10.3389/fmicb.2017.01924

[…] Protein-coding genes were predicted with GeneMark-ES v4.39 (Besemer, ). The automatic annotation was done by RAFTS3 (Vialle et al., ) best hits comparison with self-score cutoff of 0.5 using a black yeast protein database available on (www.broadinstitute.org/annotation/genome/Black_Yeasts/). Protein domain families and functional annotation was accessed using InterProScan5 (Quevillon et al., ). T […]


In depth method assessments of differentially expressed protein detection for shotgun proteomics data with missing values

Sci Rep
PMCID: 5469784
PMID: 28611393
DOI: 10.1038/s41598-017-03650-8

[…] ortal.georgetown.edu/cptac/public?scope=Phase+I. MaxQuant (version was used for protein identification and label-free quantification. Using default settings, we searched against the UniProt yeast protein database (version 2013–11) combined with the 48 UPS1 protein sequences. A peptide and protein FDR of 0.01 was applied for quality control in identification and quantification. Finally, 1 […]


Binding interface change and cryptic variation in the evolution of protein protein interactions

BMC Evol Biol
PMCID: 4758157
PMID: 26892785
DOI: 10.1186/s12862-016-0608-1
call_split See protocol

[…] ify any PISA complexes containing orthologues to known yeast genes. Here, individual protein chains were extracted from the PISA structures and those with ≥80 % sequence identity to a BLAST-formatted yeast protein database were considered orthologous. On average the largest aligned region for these BLAST hits covered >70 % of the yeast protein sequence indicating high global alignment identity of […]


The Presence of Pretreated Lignocellulosic Solids from Birch during Saccharomyces cerevisiae Fermentations Leads to Increased Tolerance to Inhibitors – A Proteomic Study of the Effects

PLoS One
PMCID: 4743953
PMID: 26849651
DOI: 10.1371/journal.pone.0148635
call_split See protocol

[…] e Discoverer version 1.3 (Thermo Fisher Scientific, Waltham, MA, USA). A database search for each set was performed with the Mascot search engine (Matrix Science Ltd., London, UK) using a custom-made yeast protein database (protein sequence file of CEN.PK113-7D from Saccharomyces genome database) with MS peptide tolerance of 10 ppm and MS/MS tolerance of 100 millimass units (mmu). The Mascot signi […]


Environmental Interactions and Epistasis Are Revealed in the Proteomic Responses to Complex Stimuli

PLoS One
PMCID: 4527715
PMID: 26247773
DOI: 10.1371/journal.pone.0134099

[…] lysis: RAW files generated by the MudPIT experiments were searched using the Sequest HT database search engine running under Proteome Discoverer v1.4 (Thermo Scientific) against a forward and reverse yeast protein database (S.cererevisiae_orf_trans_all_SGD.fasta.6718) with appended common contaminant sequences [,]. Beta-methylthiolation and iTRAQ modifications were included as constant modificatio […]


Rapid, Optimized Interactomic Screening

Nat Methods
PMCID: 4449307
PMID: 25938370
DOI: 10.1038/nmeth.3395

[…] seconds was used. The RAW files were converted to MZXML format with the MM File Conversion tool (http://www.massmatrix.net/mm-cgi/downloads.py) or MGF format by ProteoWizard and searched against the yeast protein database with X! Tandem.For the analysis of whole affinity captured fractions in and , the protein samples were run ~4–6mm into an SDS-polyacrylamide gel (gel plug), and gels were Cooma […]


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YPD institution(s)
Proteome, Inc., Beverly, MA, USA
YPD funding source(s)
This work was supported by a Small Business Innovation Research grant, Phase II, (2 R44 GM54110-02) from the National Institute of General Medical Sciences.

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