pdb-profiling

A Python package that profiling Protein Structures from Protein Data Bank and integrate various resources.

version:

What is the representative set of my target proteins?

The demand for defining a non-redundant set of protein tertiary structures in Monomeric or Homomeric or Heteromeric state is long-standing. With the required information and the user-defined criteria, the greedy algorithm plus the metric used to measure the degree of similarity between sets can be implemented to achieve this goal.

Want to study in an interactional level?

The molecular details contained in the interaction are essential to the understanding of the biological process. And there exists a rich resource that can be dig in the different Assembly of the PDB entry.

Want to perform precise bidirectional mapping from or to PDBResidue?

There exists a logical correspondence from the trinucleotide codon to the amino acids in the polypeptide chain and then to the residues in the protein tertiary structure. This correspondence is based on the sequential property of nucleic acid sequences and the derived polypeptide chain.

Want to perform batch retrieval of metadata from PDBe RESTful API?

The Protein Data Bank is regarded as one of the most valuable resources in bioinformatics researches but requires huge storage to scan through a large amount of PDB entries. The RESTful services provided by EBI save users’ life by providing different API calls that focus on a different aspect of relevant information like data scheme, experimental details, and so on.

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Features

Provides a convenient solution for data collection and processing of PDB metadata. 🏄‍♂️

Collection

Implement various API to collect the well-organized metadata of PDB in real time.

Integration

Provide a unified call for API-interface and return-data-form as well as subsequent data processing.

Detection

Reorganize metadata to evaluate a PDB structure in Entry-Assembly/Model-Entity-Chain-Residue level and integrated with UniProt-KB.

Interaction

Include UniProt Isoform Interaction in Asymmetric unit plus Biological Assembly level.

Selection

Define the representative set of PDB structures in Monomeric|Homomeric|Heteromeric states.

Mapping

Provide interface for both entry-identifier/accession-level and residue-level bidirectional mapping.

Zefeng Zhu

Undergraduate Research Training

Minghui Lab

Biography

Currently, I am working on programming and have a thirst for the insight of mathematic modeling. My involvement in science lays in the study of the protein 3D structure.🌏

Interests

Pattern Recognition
Machine Learning
Stochastic Process
Graph Theory
Lie Group Theory

Education

Undergraduate Student Major in Bioinformatics, 2017-2021
School of Biology & Basic Medical Sciences, Soochow University (PRC)