How to use PLACER Online

Generate confidence-ranked protein–ligand conformational ensembles with PLACER online.

PLACER (Protein-Ligand Atomistic Conformational Ensemble Resolver) uses an atom-level graph neural network to recover molecular coordinates from partially corrupted structures. Stochastic sampling generates alternative ligand poses and nearby protein side-chain conformations, supporting binding-pocket analysis and structural hypotheses for drug discovery and protein engineering.

How PLACER Works

PLACER conditions local coordinate denoising on molecular connectivity and the protein environment. Each sample contains a local atom crop, not a reconstructed full-length protein. Ligand Ensemble mode scores the corrupted ligand atoms; Apo Side-Chain Ensemble mode evaluates the local crop. Predicted RMSD estimates positional uncertainty; predicted lDDT and its pairwise counterpart estimate structural confidence. Reference lDDT, ligand RMSD, aligned ligand RMSD, and FAPE compare predictions against the submitted coordinates. They do not establish experimental accuracy when the input pose is unknown, and none of these scores measures binding affinity.

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 PLACER on Neurosnap

Using PLACER on Neurosnap could drastically accelerate local protein–ligand ensemble analysis and binding-pocket engineering.

Ensemble sampling: Explore alternative pocket conformations rather than relying on one pose.
Cofactor controls: Select which ligands move and which remain fixed.
Confidence ranking: Review positional uncertainty and lDDT scores alongside structures.
Apo analysis: Sample protein side chains around a chosen residue without a ligand.

How to Use PLACER on Neurosnap

To harness the capabilities of PLACER, 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 PLACER.
Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
Run Tool: Submit the PLACER 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 PLACER in publications or research outputs.

PLACER: Protein-Ligand Atomistic Conformational Ensemble Resolver. https://doi.org/10.1101/2024.09.25.614868

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

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