ArticleJournal of chemical information and modeling2012
ALiBERO: evolving a team of complementary pocket conformations rather than a single leader.
Article in Journal of chemical information and modeling, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Optimization of First-in-Class Dual-Acting FFAR1/FFAR4 Allosteric Modulators with Novel Mode of Action.ACS medicinal chemistry letters · 2022Article
- Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles.Journal of chemical information and modeling · 2018Article
- Structure-Activity Investigations and Optimisations of Non-metabolite Agonists for the Succinate Receptor 1.Scientific reports · 2018Article
- Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange.Journal of chemical information and modeling · 2018Article
- Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.Journal of computer-aided molecular design · 2018Article
- Improving virtual screening of G protein-coupled receptors via ligand-directed modeling.PLoS computational biology · 2017Article
- The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening.Journal of chemical information and modeling · 2017Article
- Structure-Based Discovery of New Antagonist and Biased Agonist Chemotypes for the Kappa Opioid Receptor.Journal of medicinal chemistry · 2017Article
- From Homology Models to a Set of Predictive Binding Pockets-a 5-HTJournal of chemical information and modeling · 2017Article
- Identifying ligands at orphan GPCRs: current status using structure-based approaches.British journal of pharmacology · 2016Review
- SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice.Nature chemical biology · 2015Article
- DOCK 6: Impact of new features and current docking performance.Journal of computational chemistry · 2015Article
- Structure-based predictions of activity cliffs.Journal of chemical information and modeling · 2015Article
- Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations.Biochemistry · 2014Article
- In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α.Toxicological sciences : an official journal of the Society of Toxicology · 2014Article
- Modelling three-dimensional protein structures for applications in drug design.Drug discovery today · 2014Review
- Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.Nature chemistry · 2014Article
- Identification of novel serotonin transporter compounds by virtual screening.Journal of chemical information and modeling · 2014Article
- The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers.Molecular pharmacology · 2014Article
- Integration of ligand-based drug screening with structure-based drug screening by combining maximum volume overlapping score with ligand docking.Pharmaceuticals (Basel, Switzerland) · 2012Article
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3 authors.
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Abstract
Docking and virtual screening (VS) reach maximum potential when the receptor displays the structural changes needed for accurate ligand binding. Unfortunately, these conformational changes are often poorly represented in experimental structures or homology models, debilitating their docking performance. Recently, we have shown that receptors optimized with our LiBERO method (Ligand-guided Backbone Ensemble Receptor Optimization) were able to better discriminate active ligands from inactives in flexible-ligand VS docking experiments. The LiBERO method relies on the use of ligand information for selecting the best performing individual pockets from ensembles derived from normal-mode analysis or Monte Carlo. Here we present ALiBERO, a new computational tool that has expanded the pocket selection from single to multiple, allowing for automatic iteration of the sampling-selection procedure. The selection of pockets is performed by a dual method that uses exhaustive combinatorial search plus individual addition of pockets, selecting only those that maximize the discrimination of known actives compounds from decoys. The resulting optimized pockets showed increased VS performance when later used in much larger unrelated test sets consisting of biologically active and inactive ligands. In this paper we will describe the design and implementation of the algorithm, using as a reference the human estrogen receptor alpha.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.