LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening

Virtual screening is a powerful methodology to search for new small molecule inhibitors against a desired molecular target. Usually, it involves evaluating thousands of compounds (derived from large databases) in order to select a set of potential binders that will be tested in the wet-lab. The numb...

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Autores principales:	Radusky, L., Ruiz-Carmona, S., Modenutti, C., Barril, X., Turjanski, A.G., Martí, M.A.
Formato:	JOUR
Materias:	Binders Bins Proteins Enrichment factors Large database Large datasets Molecular targets Potential ligand Protein domains Small molecule inhibitor Virtual Screening Ligands ligand protein protein binding binding site chemistry computer interface drug database Internet metabolism preclinical study procedures software Binding Sites Databases, Pharmaceutical Drug Evaluation, Preclinical Protein Binding Software User-Computer Interface
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_15499596_v57_n8_p1741_Radusky
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_15499596_v57_n8_p1741_Radusky
record_format	dspace
spelling	todo:paper_15499596_v57_n8_p1741_Radusky2023-10-03T16:23:15Z LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening Radusky, L. Ruiz-Carmona, S. Modenutti, C. Barril, X. Turjanski, A.G. Martí, M.A. Binders Bins Proteins Enrichment factors Large database Large datasets Molecular targets Potential ligand Protein domains Small molecule inhibitor Virtual Screening Ligands ligand protein protein binding binding site chemistry computer interface drug database Internet metabolism preclinical study procedures software Binding Sites Databases, Pharmaceutical Drug Evaluation, Preclinical Internet Ligands Protein Binding Proteins Software User-Computer Interface Virtual screening is a powerful methodology to search for new small molecule inhibitors against a desired molecular target. Usually, it involves evaluating thousands of compounds (derived from large databases) in order to select a set of potential binders that will be tested in the wet-lab. The number of tested compounds is directly proportional to the cost, and thus, the best possible set of ligands is the one with the highest number of true binders, for the smallest possible compound set size. Therefore, methods that are able to trim down large universal data sets enriching them in potential binders are highly appreciated. Here we present LigQ, a free webserver that is able to (i) determine best structure and ligand binding pocket for a desired protein, (ii) find known binders, as well as potential ligands known to bind to similar protein domains, (iii) most importantly, select a small set of commercial compounds enriched in potential binders, and (iv) prepare them for virtual screening. LigQ was tested with several proteins, showing an impressive capacity to retrieve true ligands from large data sets, achieving enrichment factors of over 10%. LigQ is available at http://ligq.qb.fcen.uba.ar/. © 2017 American Chemical Society. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_15499596_v57_n8_p1741_Radusky
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Binders Bins Proteins Enrichment factors Large database Large datasets Molecular targets Potential ligand Protein domains Small molecule inhibitor Virtual Screening Ligands ligand protein protein binding binding site chemistry computer interface drug database Internet metabolism preclinical study procedures software Binding Sites Databases, Pharmaceutical Drug Evaluation, Preclinical Internet Ligands Protein Binding Proteins Software User-Computer Interface
spellingShingle	Binders Bins Proteins Enrichment factors Large database Large datasets Molecular targets Potential ligand Protein domains Small molecule inhibitor Virtual Screening Ligands ligand protein protein binding binding site chemistry computer interface drug database Internet metabolism preclinical study procedures software Binding Sites Databases, Pharmaceutical Drug Evaluation, Preclinical Internet Ligands Protein Binding Proteins Software User-Computer Interface Radusky, L. Ruiz-Carmona, S. Modenutti, C. Barril, X. Turjanski, A.G. Martí, M.A. LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening
topic_facet	Binders Bins Proteins Enrichment factors Large database Large datasets Molecular targets Potential ligand Protein domains Small molecule inhibitor Virtual Screening Ligands ligand protein protein binding binding site chemistry computer interface drug database Internet metabolism preclinical study procedures software Binding Sites Databases, Pharmaceutical Drug Evaluation, Preclinical Internet Ligands Protein Binding Proteins Software User-Computer Interface
description	Virtual screening is a powerful methodology to search for new small molecule inhibitors against a desired molecular target. Usually, it involves evaluating thousands of compounds (derived from large databases) in order to select a set of potential binders that will be tested in the wet-lab. The number of tested compounds is directly proportional to the cost, and thus, the best possible set of ligands is the one with the highest number of true binders, for the smallest possible compound set size. Therefore, methods that are able to trim down large universal data sets enriching them in potential binders are highly appreciated. Here we present LigQ, a free webserver that is able to (i) determine best structure and ligand binding pocket for a desired protein, (ii) find known binders, as well as potential ligands known to bind to similar protein domains, (iii) most importantly, select a small set of commercial compounds enriched in potential binders, and (iv) prepare them for virtual screening. LigQ was tested with several proteins, showing an impressive capacity to retrieve true ligands from large data sets, achieving enrichment factors of over 10%. LigQ is available at http://ligq.qb.fcen.uba.ar/. © 2017 American Chemical Society.
format	JOUR
author	Radusky, L. Ruiz-Carmona, S. Modenutti, C. Barril, X. Turjanski, A.G. Martí, M.A.
author_facet	Radusky, L. Ruiz-Carmona, S. Modenutti, C. Barril, X. Turjanski, A.G. Martí, M.A.
author_sort	Radusky, L.
title	LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening
title_short	LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening
title_full	LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening
title_fullStr	LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening
title_full_unstemmed	LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening
title_sort	ligq: a webserver to select and prepare ligands for virtual screening
url	http://hdl.handle.net/20.500.12110/paper_15499596_v57_n8_p1741_Radusky
work_keys_str_mv	AT raduskyl ligqawebservertoselectandprepareligandsforvirtualscreening AT ruizcarmonas ligqawebservertoselectandprepareligandsforvirtualscreening AT modenuttic ligqawebservertoselectandprepareligandsforvirtualscreening AT barrilx ligqawebservertoselectandprepareligandsforvirtualscreening AT turjanskiag ligqawebservertoselectandprepareligandsforvirtualscreening AT martima ligqawebservertoselectandprepareligandsforvirtualscreening
_version_	1807320479604670464

LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening

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