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ChemLib
© 2026 Rubén Prieto-Díaz
Structure drawing powered by Ketcher, © EPAM Systems, licensed under the Apache License 2.0.
Library
Filters
Assay type
Target
Unit
Value range
–
Chart type
Style
Low
High
Shape stays per-group — only fill color is driven by the property.
pt
–
pt
pt
X axis
Y axis
X axis
Y axis
Z axis
Drag to rotate, scroll to zoom.
Value (Y axis)
Value
Properties
Axes are fixed: TPSA (x) vs WLogP (y). White region = high probability of
passive GI absorption; yolk region = high probability of BBB penetration.
Region boundaries from Daina & Zoete, ChemMedChem 11, 1117–1121 (2016).
Value (Y axis)
One box per group (Ungrouped + your defined groups) — assign compounds to groups in the sidebar to compare distributions. Whiskers are 1.5×IQR; dots beyond them are outliers.
Value (Y axis)
One violin per group, shape from a kernel density estimate of its values (needs 2+ per group). The line marks the median.
Select compounds
Project
Assign group
Computational
Structure viewer
Load structure
Appearance
Components & docking grid
Binding site
Within
Å
Heuristic proximity contacts
Chains
Ligands / heteroatoms
· grouped by type
Center (Å)
Size (Å)
Flexible residues
Click "Detect in grid" once the box is positioned
Review models, chains and components before preparation.
No structure loaded
Type a PDB code (e.g. 6LU7) or a UniProt accession in the sidebar and press Enter
Docking
Select a receptor or a docking job from the list to see its details here.
Ligand preparation
Select a preparation, or create one with + New, to review its charge and chemical state before docking.
ADME
ADME profile from SMILES
For molecules you are designing — nothing is saved. The same profile as a Library compound's ADME profile: drug-likeness rules, PAINS/Brenk alerts, solubility, synthetic accessibility and BOILED-Egg absorption. One structure per line, optionally followed by a name.
ADME profileEnter or draw structures in the sidebar to calculate their profiles.
QM / DFT is coming soon
Generate quantum-chemistry input decks for external submission (Gaussian, ORCA…).
ML property prediction is coming soon
Predicted ADMET/activity properties from structure, once a model is in place.
Run docking
Advanced
A structure that is not in the Library. Add a row, then type its name and SMILES.
Ligands reviewed and approved in Ligand preparation: their charge and chemical state were checked, and they are docked exactly as approved.
To dock
No ligands added yet
Receptor selection
Import external docking results
For results computed outside ChemLib (Glide, GOLD, a Vina run on another machine…) — no docking is run here, this just brings the files into the pose viewer/2D interaction map like a normal job.
Coordinates can be imported without a score. Proprietary scoring fields are not converted to Vina energies.
A file with multiple MODEL/ENDMDL blocks is read as multiple poses of that one ligand (same as a Vina output) — ligand name comes from the filename. A "REMARK VINA RESULT: -x.xx" line per pose is picked up as its score if present.
Docking performance
How many CPU cores Vina/OpenBabel are allowed to use per docking job run on this server. One core is always left free for the app itself.
Search structures
Searches RCSB (deposited experimental structures) and UniProt (for an AlphaFold predicted model when there's no experimental one) at once.
2D interaction map
Schematic, not to scale — residues colored by amino-acid property, connecting lines colored/styled by interaction type, curved ribbons show sequence-adjacent residues.
Preparing receptor…
Stripping ligand/waters, adding hydrogens, assigning Gasteiger charges (OpenBabel)
Export image
Workspace
Select a project
Pick one from the list, or click + New to start one
Calendar
Dissemination
Type
Workflow
Year
Person
Project
RecordsAll records
Resources
Beta
Equipment
Category
Status
Reservation
Shared by connected laboratories
Open this view to load shared equipment.
No rooms yet
Ask an admin to create one
Filter by status
Room equipment
Designated areas
Safety equipment
Superusers
Select a piece of equipment to view its schedule
Pick an instrument card above to see and make bookings
Urgency
Filters
Period
Filters
Funding scope
Status
Lock
Funding scope
Category
Expense log kind
Order requests
Active in ChemInventory
New request
— or a new reagent: identify it by CAS or structure and PubChem fills the rest —
Project economics — operational cost, commercial pipeline and collections
Shown only when Business & Finance is enabled. This is project control, not statutory accounting.
Budget line health — spent vs. available, projected exhaustion at current pace
By category
By supplier
By requester (reagent requests)
Monthly trend
Spend heatmap — month × category
Top expenses — largest individual purchases in this range
By project — for grant justification
By budget line
Expense log — every PO cost and manual entry, chronologically
Select a request or order sheet
Choose one from the list on the left
New supplier invoice
Register the document exactly as issued by the supplier.
New supplier
Tax breakdownNet bases and tax must reproduce the printed total.
+=
Payment schedule
Plan several due dates. The instalments must equal the invoice total.
Allocate invoice
Split the invoice exactly across projects and funding lines.
Allocated€0.00
Remaining€0.00
Review PDF suggestions
Confirm only values that match the original invoice. This does not verify or post the invoice.
AmountsNet, tax and total are applied together and validated before saving.
Human review requiredSuggestions may be incomplete or wrong. The original PDF remains unchanged and no data leaves this ChemLib instance.
Record payment
Register a full or partial payment. Corrections are made by reversal, never deletion.
Supplier
Fiscal identity and default payment details.
Review statement import
Reconciliation rules
Use familiar bank text to rank the correct customer or supplier. ChemLib still asks before recording a payment.
Split bank movement
Select at least two documents and distribute the exact movement total.
Import historical invoices
Map your spreadsheet columns. Imported invoices remain drafts until reviewed.
Historical import runs
Every run and reversal remains auditable.
New quote
Create a reviewable commercial offer from Library catalogue items.
Quote lines
Add from Library
The scientific compound stays in Library; this adds commercial terms only.
Record stock shipment
Choose the physical Library stock used. ChemLib will deduct it and retain a reversible movement.
Traceable fulfilmentThe order quantity and selected stock use the catalogue sell unit. Partial shipments can be recorded in several passes.
Customer
Legal identity and commercial contact details.
Connect an online store
Bring checkout orders into the existing ChemLib sales and fulfilment flow.
One sales domainProducts match existing catalogue SKUs. Customers and accepted orders are imported; stock changes only when ChemLib records a shipment.
Biology
Select an experiment or request
Pick one from the sidebar, or click + New to create one
Sequence tools
Protein assay
Reference
Calculators — no experiment needed. Save a run to keep it as its own record, with the rest of your Biology work.
Saved runs
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Saved runs
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| Frame | Start | End | Length (aa) | First residues | Stop codon |
|---|
Saved runs
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Saved runs
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One representative codon per residue (common human codon usage) — a deterministic sequence, not real codon optimization.
Saved runs
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Nonpolar
Polar
Acidic
Basic
BCA is genuinely nonlinear across a wide concentration range — a straight line biases interpolated concentrations near the top of the curve. Use Quadratic unless your standards span a narrow, clearly linear range.
Standards
| Conc. (µg/µL) | Absorbance |
|---|
Samples
| Label | Absorbance | Conc. (µg/µL) |
|---|
Saved runs
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Manage targets
Rename a target to merge it with another — all results will be updated.
Rename or merge assay
Manage assay types
Rename to merge — all results and experiment columns will be updated.
New request
Collaborators
Add compounds
Type to search by compound ID or batch…
0 selected
Or free text (DMSO, Vehicle, controls…)
Log use —
Add stocks to experiment
Type to search by compound ID…
0 selected
Or add free text (DMSO, Vehicle, controls…)
New experiment
Edit compound
Protocol Templates
Version history
Name this cell
New plate
×
Copy plate layout
Copies the well roles, compounds and concentrations into a new plate on the target experiment. Readings and results are not copied.
New template
Result columns
Steps
Chemistry
Draw a structure to search
Structure
ChemInventory
Inventory
Library
Reactions (Notebook)
Remote files
Searches file names, independently of the chemical search mode.
| ID | Title | Researcher | Project | Date | Status | Yield |
|---|
Select an entry or create a new one
Click + New to write up your next reaction
This entry has been annulled and is read-only. Use Restore to reactivate it.
This entry has been submitted for review and is locked. Awaiting countersign from .
Note from the submitter:
Sent back to Draft by the reviewer: . Fix it and submit for review again.
This entry is completed and read-only. Use Request reopen if it needs editing again.
requested to reopen this entry: “”. Awaiting approval.
This entry belongs to a locked project (archived/completed) and cannot be edited.
Reagents
| Role | Name | CAS | MW g/mol |
Lim. | Mass | Equiv | mmol | Density g/mL |
Conc. mol/L |
Pur.% | Vol. |
|---|
Conditions
Procedure
Products
| Name | CAS | MW g/mol |
ρ g/mL |
Pur.% | mmol theo. |
Mass | Vol. | Yield% |
|---|
Risk assessment
Notes
Characterization ⓘ
Auto-generated report
Activity
Draw a structure to search
Structure
ChemInventory
Inventory
Select an experiment or create a new one
Click + New to start a combinatorial screen
This experiment has been annulled and is read-only. Use Restore to reactivate it.
This experiment has been submitted for review and is locked. Awaiting countersign from .
This experiment is completed and read-only. Use Back to Draft to edit it again.
Objective
Reagents
mmol per well (limiting reagent) — drives the equiv → volume hint below
Conditions
Procedure
Notes
Plates
Activity
Click a well to link a reagent (search, CAS, or draw) and set its stock concentration. Each well tracks how many times it's been picked for an Echo transfer.
New source plate
×
Well
Import into Reagent
Every filled well of the chosen source plate becomes one reagent in this column, stamped with its source well so an Echo pick list can be generated later.
Locations
Loaned out
Containers physically lent to other labs at the institution — still in the catalog and their own location, just marked out. From here: mark one returned, or see who has had what over time.
Returned history
Select an item
Search the catalogue on the left, or click + New to add a reagent
Mark as ordered
Mark as received
Leave blank for a common/communal reagent (e.g. gloves, deuterated chloroform) — it's received without adding a catalog entry
Add Reagent
ChemInventory is linked, so this creates a real container there (supplier, pack size and pack unit above are required) instead of a second, local-only catalog entry — ChemInventory stays the one place this bottle actually exists.
New ELN entry
New D2B experiment
New plate
×
Well
Click to draw the product structure
Structure
Reaction types
A reaction SMARTS (SMIRKS) transform used by each plate's Generate products button to auto-fill well products from assigned reagents — additive to manual entry, never overwrites a well that already has a product.
Add a new one
2 for a simple A+B coupling, 4 for an Ugi-style reaction — must match the SMARTS' reactant count; which column ends up in which slot is figured out automatically
Dose-response gradient planner
Designs a direct-dilution concentration series — each point's Echo transfer is computed straight from a stock, not by serial dilution, so rounding error never compounds across the ladder. Purely a planning calculator; nothing here is saved to the plate.
Available stocks
| # | Stock | Ideal (nL) | Transfer (nL) | Final | Plan | DMSO% | Status |
|---|
Admin
