Minimotif Miner 4: a million peptide minimotifs and counting

Nucleic Acids Res. 2018 Jan 4;46(D1):D465-D470. doi: 10.1093/nar/gkx1085.

Abstract

Minimotif Miner (MnM) is a database and web system for analyzing short functional peptide motifs, termed minimotifs. We present an update to MnM growing the database from ∼300 000 to >1 000 000 minimotif consensus sequences and instances. This growth comes largely from updating data from existing databases and annotation of articles with high-throughput approaches analyzing different types of post-translational modifications. Another update is mapping human proteins and their minimotifs to know human variants from the dbSNP, build 150. Now MnM 4 can be used to generate mechanistic hypotheses about how human genetic variation affect minimotifs and outcomes. One example of the utility of the combined minimotif/SNP tool identifies a loss of function missense SNP in a ubiquitylation minimotif encoded in the excision repair cross-complementing 2 (ERCC2) nucleotide excision repair gene. This SNP reaches genome wide significance for many types of cancer and the variant identified with MnM 4 reveals a more detailed mechanistic hypothesis concerning the role of ERCC2 in cancer. Other updates to the web system include a new architecture with migration of the web system and database to Docker containers for better performance and management. Weblinks:minimotifminer.org and mnm.engr.uconn.edu.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Consensus Sequence
  • Databases, Protein*
  • Gene Ontology
  • Genome, Human
  • Humans
  • Internet
  • Models, Molecular
  • Molecular Sequence Annotation
  • Neoplasms / genetics
  • Neoplasms / metabolism
  • Neoplasms / pathology
  • Peptides / chemistry*
  • Peptides / genetics
  • Peptides / metabolism
  • Polymorphism, Single Nucleotide
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Processing, Post-Translational*
  • Receptors, G-Protein-Coupled / chemistry*
  • Receptors, G-Protein-Coupled / genetics
  • Receptors, G-Protein-Coupled / metabolism
  • Sequence Alignment
  • Software*
  • Xeroderma Pigmentosum Group D Protein / chemistry*
  • Xeroderma Pigmentosum Group D Protein / genetics
  • Xeroderma Pigmentosum Group D Protein / metabolism

Substances

  • Peptides
  • Receptors, G-Protein-Coupled
  • Xeroderma Pigmentosum Group D Protein
  • ERCC2 protein, human