NaProLink
Analysis of Interactions between Nucleic Acids and Proteins
NaProGraph
RNA and DNA interactions with proteins play a primary role in intracellular processes. Investigating the relationships between these macromolecules is essential for understanding mechanisms of living organisms, disorders diagnoses, aptamer drug design, and other applications. This study proposes an online and user-friendly network provider tool for interactions between Nucleic Acids (NA) and proteins. The processed and produced dataset consists of almost all interacting macromolecules in the RCSB Protein Data Bank (PDB). Researchers can use this online tool to focus on a preferred portion of PDB and related relationships, visualize, and extract information. This tool provides the frequency of atoms and residues between proteins and NAs, and the similarity of the macromolecules` primary structures. Also, the functional similarity of proteins can be employed using protein families and clans from Pfam.
NaProBase
All files are available for download.
  • Sequences (RNA, DNA, and protein) involved in complexes
  • Protein Families
  • Protein Clans
  • Interactions
  • General information
  • Similarities
  • Graph (pickle file of Networkx)
NaProPred
Predicting Affinity and Interaction based on computational approaches.
Complexes
Explore
Unique Sequences
Graph Elements
PFAM
  • Protein Families: 1545
  • Protein Clans: 450
Graph Elements
Title Type Count Neighbor Nodes Embedded data
RNA Node 2605 RNA, Protein UID, PDB ID, PDB description, Sequence
Protein Node 12445 Protein, RNA, DNA, Protein Family UID, PDB ID, PDB description, Sequence
Clan Node 656 Protein Family Clan Accession, Clan name
Protein Family Node 19632 Clan, Protein Pfam Accession, Pfam name, description
PDB-Pfam Map Edge 127445 Protein Family, Protein Start and end residues (PDB and Uniprot)
RNA similarity Edge 42268 RNA Score, Coverage, Identical similarity, Alignment
DNA similarity Edge 134297 DNA Score, Coverage, Identical similarity, Alignment
Protein similarity Edge 32332 Protein Score, Coverage, Identical similarity, Alignment
RNA-protein interaction Edge 109190 RNA, Protein Residue and atoms frequencies in distances
DNA-protein interaction Edge 27142 DNA, Protein Residue and atoms frequencies in distances
Cite:
nematzadeh.sajjad@gmail.com