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Peer-reviewedCC BYFrontiers in bioengineering and biotechnology

RCSB PDB web portal RCSB.org for biotechnology research: exploration and visualization of plastic-degrading enzymes at the atomic level in 3D.

  • Alison Biester1,2
  • Christine Zardecki1,2
  • Yana Rose3
  • Joan Segura3
  • Jose M Duarte3
  • Stephen K Burley1,2,3,4,5,6
6 affiliations
  1. 1Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.
  2. 2Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.
  3. 3Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA, United States.
  4. 4Rutgers Cancer Institute, The State University of New Jersey, New Brunswick, NJ, United States.
  5. 5Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.
  6. 6Rutgers Artificial Intelligence and Data Science (RAD) Collaboratory, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.
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Abstract

Introduction

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops resources for biomolecular structure exploration and analysis that are used by an interdisciplinary community of bio scientists, researchers, and students numbering in the many millions worldwide. The RCSB.org website and suite of APIs provide access to more than 250,000 experimentally determined structures archived in the PDB, making it an invaluable tool for biotechnology, such as research on plastic-degrading enzymes. Engineering plastic-degrading enzymes represents a promising strategy for mitigating environmental accumulation of polyethylene terephthalate (PET).Methods

In recent years, RCSB.org has provided access to more than 1 million Computed Structure Models (CSMs) alongside experimentally determined structures and introduced new tools for 3D Motif Search, Visualizing Sequence Annotations in 3D, and Pairwise Structure Alignment.Results and discussion

To identify site-directed mutagenesis targets for improving PET-degrading enzyme efficiency, biotechnology researchers utilize 3D structure data freely available from the PDB. This article describes how RCSB PDB tools for Advanced Search, Visualizing Sequence Annotations in 3D, and Pairwise Structure Alignment can be used to study plastic-degrading enzyme structure and function.

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Cite

BibTeXRIS
BibTeX
@article{biester2026rcsb,
  title = {{RCSB PDB web portal RCSB.org for biotechnology research: exploration and visualization of plastic-degrading enzymes at the atomic level in 3D.}},
  author = {Alison Biester and Christine Zardecki and Yana Rose and Joan Segura and Jose M Duarte and Stephen K Burley},
  journal = {Frontiers in bioengineering and biotechnology},
  year = {2026},
  month = oct,
  doi = {10.3389/fbioe.2026.1947029},
  url = {https://europepmc.org/article/MED/42898362},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - RCSB PDB web portal RCSB.org for biotechnology research: exploration and visualization of plastic-degrading enzymes at the atomic level in 3D.
AU  - Alison Biester
AU  - Christine Zardecki
AU  - Yana Rose
AU  - Joan Segura
AU  - Jose M Duarte
AU  - Stephen K Burley
PY  - 2026
DA  - 2026/10/05
JO  - Frontiers in bioengineering and biotechnology
DO  - 10.3389/fbioe.2026.1947029
UR  - https://europepmc.org/article/MED/42898362
AB  - Introduction  The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops resources for biomolecular structure exploration and analysis that are used by an interdisciplinary community of bio scientists, researchers, and students numbering in the many millions worldwide. The RCSB.org website and suite of APIs provide access to more than 250,000 experimentally determined structures archived in the PDB, making it an invaluable tool for biotechnology, such as research on plastic-degrading enzymes. Engineering plastic-degrading enzymes represents a promising strategy for mitigating environmental accumulation of polyethylene terephthalate (PET).Methods  In recent years, RCSB.org has provided access to more than 1 million Computed Structure Models (CSMs) alongside experimentally determined structures and introduced new tools for 3D Motif Search, Visualizing Sequence Annotations in 3D, and Pairwise Structure Alignment.Results and discussion  To identify site-directed mutagenesis targets for improving PET-degrading enzyme efficiency, biotechnology researchers utilize 3D structure data freely available from the PDB. This article describes how RCSB PDB tools for Advanced Search, Visualizing Sequence Annotations in 3D, and Pairwise Structure Alignment can be used to study plastic-degrading enzyme structure and function.
SN  - 2296-4185
ER  -