Concepts

ProteinIQ is organized around a few stable concepts: workspaces, tools, inputs, jobs, results, files, collections, credits, and workflows. Understanding how they relate helps you choose the right tool, submit work confidently, and find results later.

Basic concepts

Workspace

A workspace is the container for shared work in ProteinIQ. Credits, jobs, files, workflows, members, invitations, and billing all belong to a workspace.

You can belong to more than one workspace and switch between them from the workspace switcher. The active workspace determines which jobs you see, which files and collections appear in the Files library, which credits are used, and which billing settings apply.

When you create a new account, ProteinIQ creates a personal workspace named My Workspace and grants 100 promotional credits.

Members and roles

Workspace access is controlled by membership. Each member has a role that determines what they can do inside that workspace.

• Owner: Owns the workspace and has full control over workspace settings, members, jobs, workflows, files, and billing
• Admin: Can manage workspace settings, members, billing, jobs, workflows, and files, with restrictions around the owner and other admins
• Member: Can view workspace data, run jobs, delete their own jobs and files, and work with workflows
• Viewer: Can view workspace data but cannot run jobs, delete jobs, change workflows, manage members, or manage billing

Roles are scoped to one workspace. Being an admin in one workspace does not grant access in another.

Tools

A tool is a single analysis entry point. Each tool defines its accepted inputs, settings, processing mode, credit cost, and result format.

Tools are grouped by scientific workflow area:

• Folding: Predict 3D protein structures from sequences
• Design: Design and engineer proteins, antibodies, and molecules
• Docking: Predict how molecules bind to proteins
• Simulation: Run molecular dynamics and related simulations
• Alignment: Align, search, and compare sequences and structures
• Screening: Filter compounds and predict molecular properties
• Analysis: Calculate properties, validate structures, and generate embeddings
• Utilities: Convert formats, clean files, and generate sequences

Open /app/tools to browse every tool, or use the category pages in the app sidebar when you already know the type of analysis you need.

Inputs

Inputs are the biological or chemical data you provide to a tool. Depending on the tool, inputs can include protein sequences, DNA sequences, RNA sequences, structures, small molecules, or supporting files.

ProteinIQ supports three common input methods:

• Text: Paste FASTA, SMILES, PDB, mmCIF, SDF, CSV, or another accepted text format
• File: Upload supported files such as .fasta, .pdb, .cif, .sdf, .mol2, or .csv
• External fetch: Retrieve data from supported sources such as RCSB PDB, PubChem, or UniProt

The tool page determines which input methods are available and validates the submitted data before a run starts.

Jobs

A job is a tracked execution of a server-side tool. Jobs store the tool, input summary, settings, status, submitter, credit usage, timestamps, and result references.

Jobs move through statuses such as Pending, Processing, Completed, Failed, and Timeout. Some jobs can also appear as Queued, Cancelled, or Retry depending on execution state.

Browser-side tools can return results immediately without creating a server-side compute job. Server-side tools create jobs so you can reopen past work from /app/jobs or from the tool page history.

Results

Results are the outputs returned by a tool. The result view depends on the tool and can include tables, structure viewers, plots, text output, downloadable files, logs, or archives.

Results stay connected to the job that produced them. When you reopen a job, ProteinIQ restores the input, settings, status, credits used, and available outputs for that run.

Files

Files are intentionally saved workspace assets. The Files library at /app/files lets you upload files, save important outputs from jobs, preview supported formats, download saved files, and send compatible files into tools.

Not every job input or output appears in the Files library. Job results stay attached to their jobs until you explicitly save selected outputs to the library.

Collections

Collections are named sets of saved files. They behave like libraries, not folders, so the same file can belong to multiple collections without being duplicated.

Deleting a collection removes the collection membership records, not the files themselves. Deleting a file removes it from the workspace library and from every collection that contains it.

Credits

Credits are the workspace compute balance used by paid jobs. The credit badge on a tool shows the estimated cost before submission, and paid jobs require enough workspace credits before they start.

Credits are deducted when the job is created. If a paid job ends in Failed or Timeout, ProteinIQ refunds eligible credits automatically.

Organizing analysis

Job history

Job history is the main record of completed and in-progress analyses. Use the global history at /app/jobs when you want to search across tools, or use a tool page's History view when you only need runs from that tool.

Good job names make history easier to scan. Use names that include the target, molecule, tool, or run purpose, such as 1ABC docking aspirin or BRCA1 AlphaFold2 test.

File library

The Files library is the saved asset view of your workspace. Use it when you know the file you need, want to reuse an output across tools, or want to organize uploaded files into collections.

Files can be searched, sorted, previewed inline, downloaded, deleted, sent to compatible tools, or organized into collections when you have permission.

Favorites

Favorites are personal shortcuts for tools and jobs. Favorite tools help you keep common analyses close at hand, while favorite jobs help you return to important results without searching history.

Favorites belong to your account, but the underlying tool or job still follows workspace access rules.

Workflows

Workflows combine multiple analysis steps into a reusable graph. A workflow definition contains input nodes, tool nodes, merge nodes, connections between nodes, annotations, layout, and workflow settings.

Workflow input nodes support scientific input types such as protein sequences, DNA sequences, RNA sequences, structures, and small molecules. Tool nodes run compatible ProteinIQ tools. Merge nodes combine previous-step outputs using modes such as union, intersection, concatenation, or left join.

When you run a workflow, ProteinIQ saves a workflow run with a snapshot of the workflow definition, input data, node states, estimated credits, actual credits when available, and associated jobs.

Taking actions

Actions are changes you make to workspace data, such as submitting a job, renaming a job, deleting a file, downloading outputs, changing workflow settings, or inviting a member.

ProteinIQ keeps most actions close to the object they affect:

• Tool actions: Submit a job, reset input, open configuration, preview input, or inspect history from the tool page
• Job actions: Rename, delete, retry, duplicate, share, export, copy a link, or open a job in a new tab from job menus
• File actions: Upload, save job outputs, preview, download, delete, send files to compatible tools, or organize files into collections
• Workflow actions: Add input nodes, add tool nodes, connect nodes, update settings, run the workflow, and download results from the workflow editor
• Workspace actions: Switch workspaces, invite members, change roles, manage billing, and review usage from settings

Use the sidebar for major areas: Home, History, Tools, Workflows, PDB Viewer, Storage, and app categories. Use menus and buttons inside each area for actions on the selected object.