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The Identification of Sea Lamprey Pheromones Using Bioassay-Guided Fractionation

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SEABED: Small molEcule activity scanner weB servicE baseD.

Carlos Fenollosa¹, Marcel Otón¹, Pau Andrio²

¹Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain.

Bioinformatics (Oxford, England)

|October 29, 2014

Summary

This summary is machine-generated.

The SEABED web server offers advanced drug discovery tools, integrating docking and Quantitative Structure-Activity Relationship (QSAR) methods. It provides a flexible platform for virtual screening, receptor preparation, and analysis of protein mutants.

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Area of Science:

Computational chemistry
Cheminformatics
Drug discovery

Background:

The SEABED web server integrates diverse molecular docking and Quantitative Structure-Activity Relationship (QSAR) techniques.
It offers a user-friendly environment beyond basic web tools, incorporating advanced functionalities.

Purpose of the Study:

To present the SEABED web server as a comprehensive platform for computational drug discovery.
To highlight its extended functionalities for complex research scenarios.

Main Methods:

Implementation of various docking algorithms and QSAR modeling techniques.
Development of extended functionalities including receptor preparation, library editing, flexible ensemble docking, and hybrid docking/QSAR experiments.
Support for virtual screening on protein mutants.

Main Results:

SEABED provides a Software as a Service (SaaS) platform, not a monolithic workflow tool.
It enables complex computational tasks in an accessible web-based environment.

Conclusions:

SEABED enhances virtual screening and drug design capabilities through integrated computational tools.
The platform's flexibility and advanced features support diverse research needs in drug discovery.