Use PDBsum1 Online

PDBsum1: Standalone Protein Structure Analysis with LIGPLOT, PROCHECK and ProMotif

PDBsum1 is a standalone set of programs that performs the same structural analyses as the PDBsum web server, generating schematic diagrams, interaction plots and structure-quality reports for Protein Data Bank (PDB) entries. It was developed by Roman A. Laskowski at the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) and published in Protein Science in 2022. It runs on Linux, Windows and macOS and is freely available for academic use.

PDBsum began at University College London in 1995 and moved to EMBL-EBI in 2002. It provides pages for every PDB entry, presented mainly as schematic diagrams of the protein, ligands, DNA and the interactions between them. The server is updated weekly and cross-referenced to related servers, and it has recently added analyses of SARS-CoV-2 protein structures and AlphaFold2 models of human proteins.

The web server can also process user-uploaded structures, but results are returned as a password-protected set of pages kept for around 3 months, with turnaround from a few minutes to several hours depending on the queue. It receives an average of 140 structures per day, over 4,000 per month. Some users also worry about placing data on a public server. PDBsum1 was created for in-house processing and indefinite retention of results.

Why PDBsum Analyses of Protein Structures Matter

A PDB file on its own is hard to read. PDBsum-style reports turn coordinates into pictures and tables: which residues bind a ligand, how two chains meet at an interface, how well the geometry conforms to expectations, and where clefts lie on the surface. Because PDBsum1 pre-generates every data file and image rather than creating them on the fly, results are easy to access, and an index page tracks all structures processed.

How PDBsum1 Works: Component Analyses and Outputs

• HBPLUS: calculates hydrogen bonds and non-bonded contacts, as used by LIGPLOT and NUCPLOT.

• LIGPLOT: draws schematic diagrams of protein-ligand and protein-metal interactions.

• NUCPLOT: draws protein-DNA interaction diagrams.

• PROCHECK: assesses stereochemical quality, including Ramachandran plots, chi1 and chi2 torsion angle plots and distorted-geometry diagrams.

• ProMotif: reports secondary structure motifs such as beta turns, beta hairpins, beta bulges, beta-alpha-beta units, psi-loops and helix-helix interactions.

• SURFNET: finds cavities and surface clefts using the speedfill algorithm.

What the Result Pages Contain

For the example entry 18gs, the main page shows an interactive 3D thumbnail, the protein, ligand and metal content, header information and Pfam domains. Further pages show interface interactions between chains (salt bridges, hydrogen bonds and non-bonded contacts), a secondary structure diagram with active site residues, a LIGPLOT diagram of the bound ligand, and coloured surface clefts. Images can be opened in RasMol or PyMOL, and LIGPLOT diagrams can be edited in LigPlot+ if installed.

What is Tamarind Bio?

Tamarind Bio is a no-code bioinformatics platform built to give life scientists and researchers access to powerful computational tools. Many cutting-edge machine learning models are hard to deploy and use. Tamarind provides an intuitive, web-based environment that removes the complexity of high-performance computing, software dependencies and command-line interfaces.

The platform is designed for biologists, chemists and other researchers who may not have a background in programming or cloud infrastructure but want to run models on their own data. Key features include:

• A user-friendly graphical interface for setting up and launching experiments

• A robust API for integration into existing research pipelines

• An automated system for managing and scaling computational resources

Tamarind treats information and data security as a top priority, as detailed in its Trust Center and Terms of Service.

Accelerating Discovery with PDBsum1 on Tamarind Bio

• Ligand binding sites: inspect which residues contact a bound ligand or metal.

• Interface analysis: review salt bridges, hydrogen bonds and contacts between chains.

• Model quality checks: use PROCHECK plots to spot residues with distorted geometry or disallowed torsion angles.

• Pocket finding: view surface clefts ranked by volume.

How to Use PDBsum1 on Tamarind Bio

1. Log in: sign in at tamarind.bio and open the PDBsum1 tool.

2. Provide a structure: upload a PDB file or enter a PDB code, if exposed.

3. Set options: adjust any options the form exposes.

4. Run the job: submit it and wait for the analyses to finish.

5. Download outputs: retrieve the HTML pages, images and PyMOL or RasMol scripts.

6. Interpret results: open the index page, then the interface, ligand, secondary structure and quality pages.

7. Use downstream: use the findings to guide mutagenesis, docking or model refinement.

Things to Keep in Mind

• The software is described as freely available for academic use, so check licensing terms for other uses.

• The programs include code dating back to the early 1990s, and some third-party tools (PyMOL, ImageMagick, wget, ps2pdf) are needed locally.

• Analyses describe the supplied structure and do not replace experimental validation.

Source: Laskowski RA. PDBsum1: A standalone program for generating PDBsum analyses. Protein Science 2022;31:e4473. DOI 10.1002/pro.4473. Software: https://www.ebi.ac.uk/thornton-srv/software/PDBsum1