How to use PLIP Interaction Profiler Online

Use PLIP online to profile noncovalent interactions in bound molecular complexes.

PLIP identifies chemically and geometrically defined interactions in existing structures. Upload bound PDB, CIF, or mmCIF complexes and choose Small Molecules, Peptide / Interchain, or Intrachain analysis. Ligands must already be placed in their binding pose; PLIP does not dock molecules or predict binding affinity.

How PLIP Interaction Profiler Works

Small Molecules mode automatically identifies ligands from the structure and applies PLIP's standard ligand filtering and composite-ligand grouping. Binding Sites optionally restricts reports using RESNAME:CHAIN:NUMBER identifiers. Peptide / Interchain mode requires Ligand Chains; Intrachain requires Analysis Chain. Each selected chain must exist in every uploaded complex.

Waters and heteroatoms are retained. Structures are converted to PDB before profiling, and analysis uses one model. Add Polar Hydrogens uses OpenBabel; Use Input Hydrogens retains your preparation and is useful for repeatable analysis. Automatic protonation, ligand chemistry, coordinate quality, and geometric thresholds affect which contacts are detected.

summary.csv contains one row per binding site, including zero-contact sites, and a zero-count row for structures with no detected sites. interactions.csv contains detailed interaction records, with separate distance and angle fields for each interaction family; blank fields do not apply to that record. Atom identifiers and coordinate fields refer to PLIP's processed PDB representation. The downloadable XML reports preserve native PLIP annotations. Output complex PDBs retain PLIP's fixed atom numbering used in the reports. Separate protonated PDBs are provided when generated; OpenBabel may renumber atoms in those files. Interaction counts are structural annotations, not affinity scores or experimental evidence of binding.

What is Neurosnap?

Neurosnap is the leading platform for bioinformatics and computational science focused on expanding access to powerful modeling and simulation tools. Because many state-of-the-art machine learning systems remain complex to install, configure, and scale, Neurosnap offers a clean, browser-based workspace that removes the burden of infrastructure management, dependency conflicts, and command-line tooling.

Built for biologists, chemists, and cross-disciplinary scientists, the platform enables advanced computational workflows without requiring expertise in software engineering or cloud architecture. Researchers can launch analyses through an intuitive interface, connect programmatically through a comprehensive API, and rely on automated resource management to scale workloads efficiently. By taking care of the underlying compute and operational complexity, Neurosnap allows teams to devote their energy to scientific progress and faster iteration. Security and data protection remain foundational principles, with clear safeguards outlined in our Terms of Use and Privacy Policy to ensure your work stays protected.

Advancing Discovery with PLIP Interaction Profiler on Neurosnap

Using PLIP Interaction Profiler on Neurosnap could drastically accelerate binding-site and molecular-interface interpretation with automated PLIP interaction profiling.

Detailed site reports: Inspect eight interaction classes without writing analysis scripts.
Multiple workflows: Analyze bound small molecules, chain interfaces, and intrachain contacts.
Reusable results: Review structures and export CSV tables and native XML annotations.

How to Use PLIP Interaction Profiler on Neurosnap

To harness the capabilities of PLIP Interaction Profiler, researchers can follow this streamlined workflow within Neurosnap:

Access Neurosnap: Start by logging in to the Neurosnap website.
Select Tool: From the list of available tools, choose PLIP Interaction Profiler.
Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
Run Tool: Submit the PLIP Interaction Profiler job and Neurosnap will execute it in the cloud, automatically notifying you as soon as your results are ready.
Review Output: Explore your results through rich visualizations, including figures, plots, and interactive views designed to help you analyze findings with clarity and confidence.

Citations

Please cite the original work when using PLIP Interaction Profiler in publications or research outputs.

Schake P, Bolz SN, et al. PLIP 2025: introducing protein-protein interactions to the protein-ligand interaction profiler. Nucleic Acids Research. 2025. doi:10.1093/nar/gkaf361.

Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/

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