BEAR, a Novel Virtual Screening Methodology for Drug Discovery

BEAR (binding estimation after refinement) is a new virtual screening technology based on the conformational refinement of docking poses through molecular dynamics and prediction of binding free energies using accurate scoring functions. Here, the authors report the results of an extensive benchmark of the BEAR performance in identifying a smaller subset of known inhibitors seeded in a large (1.5 million) database of compounds. BEAR performance proved strikingly better if compared with standard docking screening methods. The validations performed so far showed that BEAR is a reliable tool for drug discovery. It is fast, modular, and automated, and it can be applied to virtual screenings against any biological target with known structure and any database of compounds.

• Publication year

  2011

• Venue

  Journal of biomolecular screening

• Publication date

  2011-01-01

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1177/1087057110388276PMID 21084717
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA

  2009cited by this paper
• Binding Estimation after Refinement, a New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening

  2009cited by this paper
• AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

  2009cited by this paper
• Design and Discovery of Plasmepsin II Inhibitors Using an Automated Workflow on Large‐Scale Grids

  2009cited by this paper
• Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors.

  2007cited by this paper
• Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring.

  2006cited by this paper
• Benchmarking sets for molecular docking.

  2006influential reference
• The Amber biomolecular simulation programs

  2005cited by this paper
• ZINC - A Free Database of Commercially Available Compounds for Virtual Screening

  2005cited by this paper
• ZINC ? A Free Database of Commercially Available Compounds for Virtual Screening.

  2005cited by this paper
• Insights into antifolate resistance from malarial DHFR-TS structures

  2003cited by this paper
• Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

  2001cited by this paper
• A Ligand That Is Predicted to Bind Better to Avidin than Biotin: Insights from Computational Fluorine Scanning

  2000cited by this paper
• Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.

  2000cited by this paper

• Computational Studies in Dermo-cosmetics: In silico Discovery of Therapeutic Agents Targeting a Variety of Proteins for Skin Diseases.

  2024cites this paper
• Synthesis-accessibility-oriented design of c-Jun N-terminal kinase 1 inhibitor.

  2023cites this paper
• Lead identification against Mycobacterium tuberculosis using highly enriched active molecules against pantothenate synthetase

  2023cites this paper
• Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA

  2022cites this paper
• Molecular Docking: Principles, Advances, and its Applications in Drug Discovery

  2022cites this paper
• Promising Non-cytotoxic Monosubstituted Chalcones to Target Monoamine Oxidase-B

  2021cites this paper
• Virtual Screening: Practical Application of Docking, Consensus Scoring and Rescoring Using Binding Free Energy

  2021cites this paper
• DREAM-in-CDM Approach and Identification of a New Generation of Anti-inflammatory Drugs Targeting mPGES-1

  2020cites this paper
• Benchmarking the performance of MM/PBSA in virtual screening enrichment using the GPCR-Bench dataset

  2020cites this paper
• Refinement and Rescoring of Virtual Screening Results

  2019cites this paper
• Comparison Study of Computational Prediction Tools for Drug-Target Binding Affinities

  2019cites this paper
• Molecular Docking: Shifting Paradigms in Drug Discovery

  2019cites this paper
• Computational elucidation of the binding mechanisms of curcumin analogues as bacterial RecA inhibitors

  2019cites this paper
• Selection of protein conformations for structure-based polypharmacology studies.

  2018cites this paper
• Hit-to-Lead: Hit Validation and Assessment.

  2018cites this paper
• The Use of Dynamic Pharmacophore in Computer-Aided Hit Discovery: A Case Study.

  2018cites this paper
• Selective inhibitors of human mPGES-1 from structure-based computational screening.

  2017cites this paper
• Computational Modeling in Bioprocess Development

  2017cites this paper
• Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 1: High-Throughput Screening and Preliminary Exploration.

  2017cites this paper
• RATIONAL DESIGN, SYNTHESIS, AND CHARACTERIZATION OF NOVEL mPGES-1 INHIBITORS AS NEXT GENERATION OF ANTI-INFLAMMATORY DRUGS

  2017cites this paper
• Structure-based Virtual Screening Approaches in Kinase-directed Drug Discovery.

  2017cites this paper
• Virtual screening: an in silico tool for interlacing the chemical universe with the proteome.

  2015cites this paper
• Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis.

  2015cites this paper
• Structure-based discovery of the first allosteric inhibitors of cyclin-dependent kinase 2

  2014cites this paper
• g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations

  2014cites this paper
• Virtual Screening of PRK1 Inhibitors: Ensemble Docking, Rescoring Using Binding Free Energy Calculation and QSAR Model Development

  2014cites this paper
• Emerging Topics in Structure-Based Virtual Screening

  2013cites this paper
• BEAR, a Molecular Docking Refinement and Rescoring Method

  2013cites this paper
• Free Energy Methods in Ligand Design

  2013cites this paper
• Prediction of Binding Free Energy Calculation Using Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) Method in Drug Discovery: A Short Review

  2012cites this paper
• Novel tyrosinase inhibitors from natural resources - their computational studies.

  2012cites this paper
• Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations.

  2012cites this paper
• Advances and applications of binding affinity prediction methods in drug discovery.

  2012cites this paper
• MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies

  2012cites this paper