One-step Retrosynthesis

Examine one-step precursors for a target molecule, purely based on retro templates


This module allows you to look at suggested disconnections based solely on retrosynthetic templates. Candidate precursors are returned sorted by a heuristic scoring function that (1) heavily favors buyable chemicals, (2) favors smaller compounds with fewer rings and fewer chiral centers, and/or (3) prefers precursors generated by templates perceived to be relevant to the target chemical. For each suggestion, you can click on the reactant SMILES to perform another search using that new compound as a target. You can also click on the forward arrow (→ ?) to open the Content Recommendation page. Clicking on the images of the suggested reactants will show the list of retrosynthetic transforms upon which the suggestion is based. You can click through to look at the details of the transform, including a list of the precedent reactions that led to that template.

Tree Builder

Generate and view possible synthesis plans, with manual step-wise evaluation


This module allows you to run a time-limited tree expansion that will recursively apply retrosynthetic transforms in a parallelized best-first tree search until it reaches either (a) a buyable chemical, or (b) the maximum depth. Once the expansion time has elapsed and (ideally) candidate pathways are found and displayed, you can interact with those suggestions by hovering over the reaction nodes to evaluate the reaction using the Forward Prediction tool or to see the transform rules upon which the suggestion is based. It is also possible to "hide all" of the tree suggestions that use a certain reaction if you know that reaction to be improbable. A more extreme option is to "blacklist" that reaction, which will add it to a user-specific list of forbidden reactions. Any subsequent tree expansions you perform will exclude that reaction. The same can be done for chemicals if a particular intermediate should be avoided. You can access your blacklisted reactions or chemicals and activate/deactivate/delete them by clicking your username in the upper-right corner of the screen.

Context Recommendation

Get ideas for reaction conditions for an attempted transformation


This module allows you to use trained context recommendation models to get suggestions for reagents, catalysts, solvents, and temperature for any attempted transformation. There is both a nearest neighbor model (based on reaction fingerprints) and a neural network model that makes a direct prediction of condition. The latter is significantly faster and seemingly more accurate.

Forward Prediction

Predict the outcome of a chemical reaction by specifying the reactants and context


This module allows you to use the Reaxys-trained template-based or USPTO-trained template-free forward predictor to anticipate the outcomes of an arbitrary chemical reaction. While the models are trained to be condition-dependent, this is a work-in-progress. The results of a forward enumeration can be exported to a .csv for offline processing or copying/pasting into Chemdraw.

Reaction Evaluation

Predict if a reaction will succeed by specifying the reactants and intended product


This module allows you to estimate the probability that a given reaction (defined by reactants and products) will succeed. The program will use a nearest-neighbor reaction condition recommendation model to find a list of possible reaction conditions. Up to ten conditions will be attempted and the most promising one reported back to you. If you already have a good idea of the reaction conditions, it may be more productive to use the Forward Prediction tool and then see if the expected product is ranked highly.

SCScore Evaluator

Analyze a chemical's perceived synthetic complexity


This module is a utility to evaluate the SCScore (a learned synthetic complexity metric) for arbitrary target chemicals. The model was trained on reactions in Reaxys in an attempt to understand the nuance of synthetic complexity, e.g., when protections and deprotections are constructive. It is designed to perceive a monotonic increase in complexity throughout a linear synthesis.

Buyable Look-up

Check to see if a chemical is in the buyables database


This module is a utility to check if a certain compound is contained in our very-imperfect database of buyable compounds. Currently, we have approximately 175,000 chemicals (not all unique) from eMolecules, Sigma Aldrich with prices up to $100 per gram.

Drawing

Draw molecules, reactions, or templates from SMILES/SMARTS strings


This module is a utility to draw SMILES strings describing chemicals, reactions, or SMARTS strings describing templates. Note that you can also copy a SMILES string and "Paste special" in Chemdraw (highly recommended), although this does not work very well for templates.

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