AutoT&T v2.0

A versatile computational tool for automatic lead optimization as well as lead discovery

Running AutoT&T v.2 on-line as Demonstration
Through the interface below, the user can conduct on-line lead optimization jobs by running the AutoT&T2 software at the server end. To submit a job through this web interface, the user is required to upload the necessary inputs, including the structure files of a target protein, a lead molecule, and a reference library. Note that both the lead molecule and the whole reference library need to be docked into the binding site on the target protein in prior. Then, the user may set the parameters included here. Once the job is completed at the server end, a new web page will be displayed for the user to download the results.

Click here for the input files for running the p38 MAPK test case: [Input files for running the p38 MAPK test case]

Note that the interface below is designed for the users to test AutoT&T2 in the standard running mode only, i.e. structural optimization based on a single lead molecule. To use the full functions of AutoT&T2, the user has to download the complete AutoT&T2 suite and run it on a local computer. The full functions of AutoT&T2 are described in the user's manual. [User manual of AutoT&T2]

Upload Structure Files
Target Protein:	(* in PDB Format)
Lead Compound:	(* in Mol2/SDF Format)
Reference Library:	(* in Mol2/SDF Format)
Optional Parameters
Optimization Parameters	Standard optimization on single lead
	Maximal rounds of optimization
	Method for searching matched bonds:
	distance cutoff for matching bond (Angstrom)
	Angle cutoff for matching bond (degree)
	Maximal molecules retained after each round
	Consider A-H bonds in matching
	Use RECAP rules to filter matched bonds
Internal Scoring Function	PLP scoring function
Final Energy Minimization [Optional]	Enable energy minimization
	Force Field:
	Method for minimization:
	Maximal steps for energy minimization
	Ignore electrostatic energy
Final Clustering Parameters	Method for computing similarity:
Final Clustering Parameters	Method for clustering:
Final Druglikeness Filtering Parameters	- Molecular weight
	- Hydrogen bond acceptors
	- Hydrogen bond donors
	- Number of rotatable bonds
	- Number of rings
	- Number of heavy atoms
	- LogP value
	Ignore molecules with multi-fragments