Navigate to the Portal
Click on 'Single Analysis' in the application header or navigate directly to `/single`.
Input API SMILES Structure
Type or copy/paste the SMILES string representing your Active Pharmaceutical Ingredient (API) in the first input block. The system supports up to 2,000 characters (e.g., `CC(=O)Oc1ccccc1C(=O)O` for Aspirin).
Input Excipient SMILES Structure
Type or paste the SMILES representation of the target excipient in the second input block.
Verify CAPTCHA & Inputs
Complete the Cloudflare Turnstile security checkbox and click 'Verify Input' to validate structure syntax and render the 2D SVG molecular drawings.
Execute Prediction Run
Complete the CAPTCHA once more and click 'Analyze Compatibility'. The 3-Tier ML pipeline computes descriptors and completes prediction in milliseconds.
Review Verdict, Charts & Exports
Inspect the compatibility verdict, conformal confidence score, feature contribution plots (SHAP), and physicochemical property radar charts. Non-guest users can click 'Export PDF' or 'Export CSV' to download complete reports.
Open the SHAP Section
Once a Single Analysis prediction completes successfully, scroll down past the core metrics card to the 'Explainable AI — Feature Contributions' panel.
Analyze Red Contribution Bars
Red bars representing positive values indicate chemical descriptors or features that increased the model's confidence toward a Compatible verdict.
Analyze Blue Contribution Bars
Blue bars representing negative values indicate features that decreased the prediction score (contributing toward an Incompatible verdict).
Inspect Details & Impact
Hover over the feature labels (such as LogP, TPSA, Ring Count, or H-Bond Donors) to read detailed descriptor definitions and assess how molecular variance drove the verdict.
Locate the Error Indicator
If a SMILES string is invalid, a red warning text block will appear directly below the input field detailing the validation failure.
Verify Syntactical Correctness
Ensure that rings (indicated by matching numbers like `c1ccccc1`) and bonds (double bonds `=`, triple bonds `#`) are correctly opened and closed. All brackets must match.
Utilize Real-Time Rendering
Look at the inline molecular structure card. If the structure is correct, our RDKit verification engine will automatically render the 2D SVG molecular drawing.
Check Valency Restrictions
Verify that atoms do not violate standard valency limits (e.g., carbon with 5 bonds). Explicitly define charges or hydrogen atoms if using hypervalent elements.
Verify Length Boundaries
Ensure your SMILES string does not exceed the system-wide maximum buffer size of 2,000 characters.
Go to the Batch Dashboard
Click on 'Batch Discovery' in the header navigation or go to `/batch`.
Define the API SMILES
Paste your primary drug candidate's SMILES string in the API input field.
Add Target Excipients
Build your candidate list: enter excipient SMILES strings one at a time and click 'Add' or press Enter (enforces a minimum of 2 and maximum of 20 excipients).
Submit Calculations
Solve the Turnstile CAPTCHA and click 'Analyze Compatibility' to calculate predictions for all candidate excipients in parallel.
Sort and Paginate Leaderboard
Once calculated, sort the ranked leaderboard by rank, compatibility score, or conformal confidence. Navigate results pages easily.
Export Batch Results
Non-guest users can click 'Export PDF' to download the full summary report, 'Export CSV' to download the Excel-friendly spreadsheet, or click the PDF icon on any expanded candidate row to download individual reports.
Open the Deep Scan Panel
Select 'Deep Scan' in the navigation bar or access `/deep-scan` directly.
Enter API Structure
Input your target molecule's SMILES string into the scan field and verify it.
Launch Global Telemetry
Choose your display threshold (Top 10, 30, 50, or 100), solve CAPTCHA, and click 'Run Deep Scan'. A secure Server-Sent Events stream displays real-time progress. Do not close the window.
Analyze Results Workstation
Once complete, results are organized into separate Machine Learning and Rule-Based tabs. Expand any row to inspect 2D structures, conformal confidence intervals, SHAP feature influence charts, and properties.
Download Reports
Registered users can download full batch PDF summaries, structured CSV spreadsheets of the results, or individual candidate PDF reports from the leaderboard list.
Access the Portal
Click 'Sign Up' in the header navigation or navigate to `/signup`.
Submit Registration Credentials
Fill in your full name, academic/institutional email, and a secure password. Or, click 'Sign Up with ORCID' to automatically sync your researcher record.
Submit Verification Code
Check your inbox for a verification email. Copy the 6-digit activation code, enter it on the verification page, and activate your account.
Log In to Your Workspace
Go to `/login`, supply your verified credentials, and authenticate. You will be redirected to the main dashboard.
Open Your Profile Panel
Ensure you are logged in, click your user avatar or name in the header, and select 'Profile' (or visit `/profile`).
Locate Security Settings
Scroll down to the 'Security Settings' or 'Change Password' form cards.
Provide Credentials
Enter your current account password, then input your strong new password in both the 'New Password' and 'Confirm New Password' boxes.
Confirm Update
Click the 'Update Password' button. A success notification will confirm that your security credentials have been updated.
Trigger Reset Flow
From the Log In screen (`/login`), click on the 'Forgot Password?' hyperlink.
Provide Account Email
Enter your registered email address and click the 'Send Recovery Link' or 'Request Code' button.
Extract Recovery Token
Check your email inbox. Copy the 6-digit recovery code from the system notification message.
Define New Password
Paste the code into the validation input field on PharmDex and type your new secure password.
Finalize Reset
Click 'Reset Password'. You will be returned to the login dashboard to sign in with your fresh credentials.
Navigate to the Profile Settings
Log in, click your avatar, and go to `/profile`.
Locate the Danger Zone
Scroll to the absolute bottom of the page to find the 'Danger Zone' card block.
Request Account Deactivation
Click the 'Deactivate Account' button.
Confirm Deactivation
Confirm your selection. This triggers a soft-deactivation: active user login tokens are destroyed and rate limits are suspended. Your past public contributions remain archived to maintain peer-reviewed citation integrity.
Open the Quota Portal
Log in and navigate to your Profile dashboard or go directly to `/quota-request`.
Fill Institutional Credentials
Specify your academic domain details, university department, supervising lab professor, and researcher tier level.
Provide Research Context
Describe your scientific study, drug development goals, or coursework excipient screening needs.
Submit and Await Verification
Click 'Submit Quota Request'. Our administrative team manually reviews and grants elevated daily quota limits for qualifying research teams.
Open the Bulk Request Portal
Select 'Bulk Requests' in the application menu or visit `/bulk-request`.
Download CSV Template
Click the 'Download Template CSV' link. The file contains two structured column headers: `api_smiles` and `excipient_smiles` (or `excipient_name`).
Populate Target Compound Pairs
Compile your screening pairs inside the CSV file using standard SMILES coordinates (up to 2,000 pairs max).
Upload and Request OTP
Drag-and-drop or select your CSV file in the upload pane, enter your verified institutional email, and click 'Send OTP'.
Validate and Finalize
Type the 6-digit OTP code sent to your email to prove authorization, and click 'Validate and Submit'.
Navigate to the Bulk Portal Tracker
Ensure you are logged in and navigate to `/bulk-request`.
Scroll to 'My Bulk Requests' Section
Scroll past the submission form to the 'My Bulk Requests' history table.
Check Status Badges
Monitor your file's progress row: `Pending` (awaiting screening approval), `Approved` (models executing), `Completed` (analysis done), or `Rejected` (denied).
Download Datasets
For completed runs, click the download icon to save the calculated physicochemical descriptors, probability scores, and overall verdicts as a local CSV.
Go to the Contribute Form
Navigate to the Contribution dashboard via `/contribute`.
Provide Chemical Identification
Enter the excipient's common IUPAC/scientific name and its PubChem CID number.
Define Molecular Coordinates
Paste the canonical SMILES string for the excipient (up to 2,000 characters).
Supply Scholarly Citation
Input a verified Peer-reviewed article DOI (Digital Object Identifier) reference that supports the compatibility boundary or stability constants of this compound.
Submit for Verification
Click 'Submit Excipient' to route it into the editorial verification review queue.
Navigate to the Contributions Dashboard
Log in and visit `/contributions`.
Review Submissions Grid
Observe the table containing all excipients you have contributed to PharmDex.
Monitor Editorial Tiers
Check the status tag: `Under Review` (editorial board checking structure), `Approved` (merged into master catalog, searchable by Deep Scan), or `Needs Revision` (requires correction).
Resolve Comments
If status is 'Needs Revision', click the details row to read the reviewer's feedback notes (e.g. broken reference DOI or invalid SMILES coordinates), correct the form, and resubmit.
support_agentStill need assistance?
If you have unique formulations questions, complex dataset errors, or need special research permissions, our team is ready to assist.