chemistry

LiSiCA

LiSiCA is a chemistry topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand LiSiCA rather than just read about it. In short: LiSiCA (Ligand Similarity using Clique Algorithm) is a ligand-based virtual screening software that searches for 2D and 3D similarities between a reference compound and a database of target compounds which should be represented in a Mol2 format. The similarities are expressed using the Tanimoto coefficients and the target compounds are ranked accordingly.

Key takeaways

LiSiCA belongs to chemistry; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect LiSiCA to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of LiSiCA from memory before moving on to harder problems.

Reference excerpt

LiSiCA (Ligand Similarity using Clique Algorithm) is a ligand-based virtual screening software that searches for 2D and 3D similarities between a reference compound and a database of target compounds which should be represented in a Mol2 format. The similarities are expressed using the Tanimoto coefficients and the target compounds are ranked accordingly. LiSiCA is also available as LiSiCA PyMOL plugin both on Linux and Windows operating systems.

Description As an input LiSiCA requires at least one reference compound and database of target compounds. For 3D screening this database has to be a pregenerated database of conformations of target and for 2D screening a topology, that is, a list of atoms and bonds, for each target compound. On each step the algorithm compares reference compound to one of the compounds from target compounds based on their 2D or 3D representation. Both compounds(molecules) are converted to molecular graphs. In 2D and 3D screening the molecular graph vertices represent atoms. In 2D screening edges of molecular graph represent covalent bonds while in 3D screening edges are drawn between every pair of vertices and have no chemical meaning. A product graph generated from molecular graphs is then searched using fast maximum clique algorithm to find the largest substructure common to both compounds. The similarity between compounds is calculated using Tanimoto coefficients and target compounds are ranked according to their Tanimoto coefficients.

Feature overview

LiSiCA can search 2D and 3D similarities between a reference compound and a database of target compounds. It takes as an input at least one reference compound and a database of target compounds. By default it returns only the compound most similar to the reference compound out of all compounds in database of target compounds. Other optional parameters LiSiCA uses are:

Number of CPU threads to useDefault value: the default is to try to detect the number of CPUs and use all of them or, failing that, use 1 Product graph dimensionPossible input: 2, 3Default value: 2 Maximum allowed atom spatial distance difference for the 3D product graph measured in angstromsDefault value: 1.0 Maximum allowed shortest path difference for the 2D product graph measured in the number of covalent bonds between atomsDefault value: 1 Consider hydrogensDefault value: False Number of highest ranked molecules to write to outputDefault value: 0 Maximum allowed number of highest scoring conformations to be outputtedDefault value: 1 In addition LiSiCA PyMOL plugin also offers to load saved results.

History LiSiCA Software (March 2015) LiSiCA PyMOL plugin (March 2016)

Interesting fact The Slovene word lisica means 'fox', which is why the logo of LiSiCA software is a fox holding two molecules.

References

External links LiSiCA software LiSiCA plugin

Illustrations

Worked examples

Example 1 — a first encounter with LiSiCA

Start with the simplest possible case. Write down what LiSiCA claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In chemistry, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to LiSiCA before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about LiSiCA ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of LiSiCA

In research: LiSiCA appears in chemistry research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses LiSiCA in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: LiSiCA is common in secondary-school and first-year university syllabi. It links to neighbouring topics Chemistry software, Molecular modelling, so understanding it makes those chapters shorter.
In everyday life: Look for LiSiCA outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study LiSiCA in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what LiSiCA means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain LiSiCA out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is LiSiCA in simple terms?

Why does LiSiCA matter?

Because it connects several chemistry ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study LiSiCA?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on LiSiCA.