CD ComputaBio provides polar surface area (PSA) and topological polar surface area (TPSA) analysis for compound screening, analog optimization, and conformational polarity studies. Send molecular structures and your research question; receive comparable property data, an explanation of relevant differences, and recommendations for the next selection or validation step.
A single TPSA value is a starting point. The useful comparison connects a defined molecular structure, a consistent calculation method, and the experimental decision your team needs to make.
Begin with the application matrix below. It shows what to provide and what you can expect to receive for library profiling, analog selection, permeability investigations, and conformation-dependent questions.
Explore your analysis options →The IUPHAR/BPS Guide to PHARMACOLOGY lists a TPSA of 115.54 Ų for its parent tiotropium record, calculated using the Chemistry Development Kit (CDK). This is a computed descriptor for the represented structure.
| Chemical form / record | TPSA (Ų) | Method / source |
|---|---|---|
| Tiotropium — parent compound record | 115.54 | CDK-generated descriptor; IUPHAR/BPS, ligand 367 ↗ |
| Tiotropium bromide | Not verified here | Confirm the salt representation and calculation settings before assigning a value. |
| Tiotropium bromide hydrate | Not verified here | Confirm hydration state and whether disconnected components are retained. |
Comparing different TPSA values? Match chemical form, structure preparation, and descriptor implementation first. This reference value is not a measurement of permeability or oral bioavailability.
Request a structure-specific TPSA comparison →From library filtering to method reconciliation
Topology-based and three-dimensional analysis
Data, figures, and an interpretation report
From your question to the next-test plan
Compound library filtering before screening
Select compounds for purchase or experimental testing.
A library contains more compounds than the team can test. Property values from different sources may also use inconsistent structures or methods.
Compound IDs and SMILES or SDF structures; screening objective and test capacity.
HelpfulProperty criteria, availability constraints, and existing activity data.
Checked structure list; TPSA with agreed companion descriptors; filter labels and QC flags.
Hit-to-lead analog prioritization
Choose which structural changes to synthesize next.
An active series needs a better property balance. The team must understand whether a modification changes polarity, size, charge, or several factors together.
Parent and proposed analog structures; optimization objective.
HelpfulPotency, selectivity, solubility, and permeability data with units and assay conditions.
Analog-by-analog property comparison, descriptor changes relative to the parent, and a documented selection rationale.
Investigation of poor or inconsistent permeability
Plan the right follow-up experiment.
Compounds with similar TPSA have different assay results, or a low-TPSA compound still performs poorly. A single descriptor does not explain the behavior.
Structures and available permeability results, including endpoint, units, assay type, and conditions.
HelpfulpH, solubility, logD, recovery, efflux ratios, and replicate information where available.
Comparable-assay subset, property–assay comparison, missing-data flags, and ranked explanations.
Macrocycle and cyclic peptide polarity assessment
Investigate whether conformation changes polar exposure.
Connectivity-based TPSA cannot distinguish open and shielded conformations of the same molecule. Flexible scaffolds may need a structure-based comparison.
Complete structures with stereochemistry, comparison goal, and relevant environment.
HelpfulConformers, NMR constraints, trajectories, and matched permeability data.
For an agreed 3D study: conformer-level polar surface values, distributions, representative structures, and possible shielding or intramolecular hydrogen-bond patterns.
PROTAC linker and degrader comparison
Compare polarity during linker redesign.
Linker changes can alter size, flexibility, and exposed polarity at the same time. TPSA alone is insufficient to select a degrader with suitable cellular behavior.
Complete degrader structures, linker variants, and the comparison objective.
HelpfulCellular degradation, biochemical activity, solubility, and permeability measurements.
A property comparison across variants; optional conformational exposure analysis when feasible.
Reconciliation of conflicting PSA or TPSA results
Make internal and external datasets comparable.
The same compound name gives different values across databases or software, making filtering and interpretation unreliable.
Exact structures, reported values, and their sources.
HelpfulSoftware versions, salt/hydrate handling, and atom-inclusion or surface settings.
Identity and method comparison, documented causes of discrepancies where identifiable, and a consistent recalculation protocol.
A routine TPSA batch, a 3D exposure study, and an assay interpretation project require different inputs and levels of analysis.
For libraries and analog series
Calculate a topology-based polarity descriptor from molecular connectivity. Combine TPSA with molecular weight, formal charge, hydrogen-bond donor/acceptor counts, and selected lipophilicity estimates when useful.
Best when the immediate need is a consistent property table, comparison, or filter.
For conformation-dependent questions
Generate or review conformations, define the geometric surface and polar atom selection, and compare exposure across suitable structures. Add molecular dynamics when an environment or dynamic question justifies the work.
Best when flexible scaffolds need more than a connectivity-based descriptor.
For explaining a research observation
Compare calculated properties with compatible assay data. Separate supported patterns from hypotheses and identify the measurements that could resolve uncertainty.
Best when the team needs to decide what to modify or test next.
What PSA can tell you: TPSA and geometric polar surface descriptors provide complementary views of molecular polarity. Neither establishes oral absorption, brain penetration, or membrane permeability by itself. Charge, lipophilicity, solubility, transport processes, and the experimental system also matter.
Traceable compound data, clear comparisons, and a report that connects molecular polarity to your next research decision.
Inside your delivery package
Editable results mapped to your compound IDs and analyzed structures, with descriptor values, units, chemical-form notes, and records requiring review.
Inspect property distributions and analog differences. Where a 3D module is agreed, receive selected conformers, surface views, and exposure summaries.
Understand the relevant differences, selection criteria, and remaining uncertainties, with a recommended next synthesis or experimental question.
Illustrative research scenarios
We examine TPSA, charge, size, lipophilicity estimates, assay conditions, and available solubility data.
You can decide which matched analog or focused solubility/transport test would help evaluate the polarity hypothesis.
We examine defined polar exposure metrics across sampled conformations, alongside matched experimental data.
You can decide which conformational hypothesis to take forward for structural or permeability validation.
Scope is agreed before calculation. Deliverable depth follows the selected analysis. Descriptor-only work does not include a validated permeability model; experimental EPSA measurements require a separate scope.
Four stages keep the analysis focused on the decision that matters to your team.
Define the compound set, selection or optimization objective, relevant assay endpoint, and next experimental step.
Compound structures or representative examples, approximate library size, and the selection or optimization question. Add relevant assay endpoints and conditions where available.
The comparison groups, intended use of the results, and which decision the analysis needs to support—for example, library triage, analog prioritization, or investigation of a polarity-related hypothesis.
An agreed research question, an initial input checklist, and the proposed analysis boundaries. Missing information is identified before detailed calculation is scoped.
Review structures, salts, charges, stereochemistry, and available assay conditions. Agree the descriptor panel or 3D sampling plan, deliverables, timeline, and quotation.
Check structure readability, identifiers, duplicates, salt forms, formal charges, and stereochemistry. Flag unresolved chemical identities or missing assay context for clarification.
Define structure preparation and the TPSA descriptor implementation. Where justified, agree conformer generation, sampling assumptions, and the 3D polar-exposure analysis protocol.
A documented analysis scope covering required inputs, preparation rules, methods, deliverables, timeline, and quotation. Optional work is identified separately.
Run the agreed analysis, inspect problematic structures and outliers, and compare compounds under one documented protocol.
Calculate the agreed descriptors under a consistent protocol. For a scoped 3D analysis, evaluate the agreed conformations and retain the relevant sampling and calculation settings.
Inspect failed calculations, unusual values, and differences associated with chemical representation. Compare compounds within the agreed groups and review trends alongside available experimental data.
A reviewed result set linked to submitted identifiers, with calculation status, QC flags, and comparison figures where applicable. Unresolved records and interpretation limits are documented.
Provide editable data, figures, and an interpretation report. Identify the strongest conclusions, unresolved questions, and recommended follow-up work.
Receive editable compound-level results and comparison figures, with original identifiers and the agreed method documentation. Flagged or excluded records remain traceable where applicable.
The report explains the supported comparisons, assumptions, and remaining uncertainties. Descriptor trends are considered alongside charge, solubility, assay context, and other available evidence.
Identify which compounds or hypotheses warrant follow-up and which additional measurements could resolve the remaining uncertainty. Additional modeling or experimental work requires an agreed scope.
Assess the service through the structure checks, method documentation, and decision support included in your project.
We compare the analyzed structure, rather than relying on a compound name. Salt handling, formal charge, and relevant chemical-state assumptions are recorded so differences can be checked.
Use fast topology-based profiling for a library; add conformational analysis when exposure matters. This makes the scope responsive to the decision instead of adding modeling by default.
Keep submitted identifiers connected to calculated values, exclusions, and QC flags. Your team can inspect which structures entered the comparison and why others need attention.
A ranking is accompanied by a rationale and specific next questions. Broader screening, modeling, or ADMET work can be scoped around those questions.
Practical details for starting a project and interpreting its results.
No. TPSA can be calculated from a valid molecular connectivity representation such as SMILES or SDF. A 3D surface analysis requires suitable conformations, which may be supplied or generated within the project.
Send compound IDs and structures in SMILES or SDF, plus the purpose of the comparison. If you only have names or database identifiers, identity resolution must be included before calculation.
It can help investigate a polarity-related hypothesis, but the answer also depends on charge, solubility, transporters, assay conditions, and other factors. Matched experimental data make the interpretation more useful.
Defined structures can be reviewed for feasibility. Flexible and larger molecules may need conformational analysis rather than a standard TPSA filter. Polarity analysis does not establish peptide permeability or PROTAC degradation activity.
The inputs may represent different salts, hydrates, charges, or chemical states. Implementations may also include different atom contributions. We compare the exact structures and settings before proposing a common protocol.
The IUPHAR/BPS Guide to PHARMACOLOGY reports 115.54 Ų for its parent tiotropium record using CDK-generated properties. The value belongs to that represented structure and method; confirm chemical form and calculation settings before comparing it with a tiotropium bromide or hydrate record.
No. Computed polar surface descriptors and a chromatography-derived experimental EPSA measurement are different outputs. Experimental testing requires a separately agreed scope.
They depend on molecule count, input quality, descriptor coverage, conformational sampling, and reporting depth. The quotation confirms deliverables, milestones or delivery date, and any optional analysis before work begins.
Start with your structures and objective. We will review the inputs and define an analysis scope around the output your team needs.
Confidentiality arrangements can be discussed before proprietary structures are shared. Send sensitive files through the agreed project channel.
Scientific background for polar surface descriptors and their interpretation.
For research use only.
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