Differences

This shows you the differences between two versions of the page.

--- applications [2013/02/24 21:09] – rkiss
+++ applications [2014/01/16 18:40] – flack
@@ Line 1: / Line 1: @@
-====== 1-Click Applications ======
+{{ :icon_big.png?65|}}
-{{:app.png|}}
+====== LEAD OPTIMIZATION ======
-Continuously growing set of simple, ready-to use modeling applications specifically designed to evaluate and generate ideas in the lead optimization process.
-**[[1clickdocking|1-Click Docking]]**
+Mcule offers a continuously growing set of intuitive, easy-to-use modeling applications specifically designed to evaluate and generate ideas in the hit/lead optimization process. In the course of a drug discovery project, after identifying a hit or lead molecule, the next step is the optimization of multiple properties of the hit/lead. Some of the properties that typically need further optimization are binding affinity to the target, selectivity (affinity to off-targets) and [[http://en.wikipedia.org/wiki/ADME|ADMET]] properties.
-  * Single ligand docking into a single target
+===== 1-CLICK DOCKING =====
-  * Visualize or download the best binding poses
-  * Rank your ideas based on docking scores and the formation of critical interactions
-**[[1clickscaffoldhop|1-Click Scaffold Hop]]**
+Molecular docking simulations predict the binding orientation and affinity of a ligand to a target. 1-Click Docking is the easiest molecular docking solution online. It has been designed to quickly test and rank-order ideas of medicinal chemists. Ideas can be prioritized based on the docking scores (predicted binding affinity) and interactions can be visualized between the ligand and the target.
-  * Draw a reference structure and discover new scaffolds in just a few seconds
+**[[1clickdocking|Learn more »]]**
-  * Generate new ideas to replace toxic, IP protected and other problematic substructures
+===== 1-CLICK SCAFFOLD HOP =====
-  * Intuitive visualization helps to understand the similarity between the query and the identified scaffold
-**[[propcalc|Property calculator]]**
+Scaffold hopping is about finding novel active ligands structurally different from a reference ligand (Query). Scaffold hopping can be particularly useful during lead optimization, when certain parts of lead molecules need to be replaced to fix IP, toxicity, selectivity or pharmacokinetic issues. 1-Click Scaffold Hop utilizes the powerful FTrees Visual Similarities algorithm (link), which can identify structurally different scaffolds that are still active.
-  * Create a physicochemical property profile for your compound in a second
+**[[1clickscaffoldhop|Learn more »]]**
-  * Reject compounds with unsuitable logP, insufficient number of H-bond acceptors/donors, too many rotatable bonds, etc.
+===== PROPERTY CALCULATOR =====
-  * Prioritize compounds with highest ligand efficiency (low number of heavy atoms and logP)
-**[[toxicitychecker|Toxicity checker]]**
+ADMET properties heavily depend on physicochemical properties. For example, high logP (> 5) and molecular weight (> 500 g/mol) are typically associated with unsuitable ADMET profile. Property calculator creates a physicochemical property profile for your compound in seconds. You can reject compounds with unsuitable logP, insufficient number of H-bond acceptors/donors, too many rotatable bonds, etc.
-  * Searching for substructures commonly found in toxic and promiscuous ligands
+**[[propcalc|Learn more »]]**
-  * Based on more than 100 SMARTS toxic matching rules
+===== TOXICITY CHECKER =====
-  * Reject problematic compounds to avoid toxicity, selectivity and pharmacokinetic issues in further development
-**[[Ideaval|Idea validator]]**
+Certain structural elements of a molecule can be responsible for toxicity. In fact, some substructural motifs occur more frequently in toxic compounds than in non-toxic ones. It therefore makes sense to eliminate such structural motifs from hits/leads as early as possible. Toxicity checker is based on more than 100 toxic and promiscuous scaffolds. It displays an alert, when such a motif is found, and it displays the incriminated part of the molecule.
-  * Fully customizable solution to validate and prioritize synthetic ideas
+**[[toxicitychecker|Learn more »]]**
-  * Business rules can be easily applied
+===== IDEA VALIDATOR =====
-  * Features: activity prediction, target profiling, physicochemical property alerts, toxic alerts, commercial availability check
+Idea validator offers a fully customizable solution to validate and prioritize synthetic ideas. Business rules can be easily implemented. Feature set that can be integrated includes: activity prediction, target profiling, physicochemical property alerts, toxic alerts, commercial availability check
+**[[Ideaval|Learn more »]]**