Proteomic analysis software tools and databases

Proteomics applications

Proteomes are characterized by large protein-abundance differences, cell-type- and time-dependent expression patterns and post-translational modifications, all of which carry biological information that is not accessible by genomics or transcriptomics. Source text: Wilhelm et…

Proteomic analysis software tools and databases

Most Recent Tools

Desktop app
Uniprot DAT File… Uniprot DAT File Parser

Uniprot DAT File Parser

Can read a Uniprot .Dat file and parse out the information for each entry,…

Can read a Uniprot .Dat file and parse out the information for each entry, creating a series of tab delimited text files or creating a FASTA file. Uniprot DAT File Parser is a command-line (console)…

Desktop app
Protein Sequence… Protein Sequence Motif Extractor

Protein Sequence Motif Extractor

Reads a fasta file or tab delimited file containing protein sequences, then…

Reads a fasta file or tab delimited file containing protein sequences, then looks for the specified motif in each protein sequence. Protein Sequence Motif Extractor uses the /N switch to specify the…

Desktop app
Random Forest… Random Forest Protein-Protein Interaction

RF PPI Random Forest Protein-Protein Interaction

Captures the common properties of both homodimer and heterodimer interfaces. RF…

Captures the common properties of both homodimer and heterodimer interfaces. RF PPI contains the backbone flexibility score predicted by DynaMine which is the first direct predictor of dynamics from…

Web app
Desktop app
MMLigner MMLigner

MMLigner

Infers statistically significant structural alignments. MLigner can also…

Infers statistically significant structural alignments. MLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes.…

Most Popular Tools

footprintDB footprintDB

footprintDB

Predicts transcription factors which bind a specific DNA site or motif and DNA…

Predicts transcription factors which bind a specific DNA site or motif and DNA motifs or sites likely to be recognized by a specific DNA-binding protein.

Plant Transcription… Plant Transcription Factor Database

PlantTFDB Plant Transcription Factor Database

A database of functional and evolutionary study of plant transcription factors.…

A database of functional and evolutionary study of plant transcription factors. With the version 4.0, PlantTFDB offers 320 370 TFs from 165 species. Three types of annotation provide more directly…

PLACE PLACE

PLACE

A database of nucleotide sequence motifs found in plant cis-acting regulatory…

A database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements. Motifs were extracted from previously published reports on genes in vascular plants. In addition to the…

Web app
POLYVIEW-MM POLYVIEW-MM

POLYVIEW-MM

Integrates high-quality animation of molecular motion (MM) with structural and…

Integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules.

Curators for Proteomics

  • Stephen Osborne's avatar image
    Stephen Osborne
    Pastel BioScience Limited, The…
  • Yashwanth Subbannayya's avatar image Yashwanth Subbannayya's country flag
    Yashwanth Subbannayya
    YU-IOB Center for Systems Biology…
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