Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Journal of Chemical Information and Modeling

• Publication date

  2016-06-27

• Fields of study

  Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1021/acs.jcim.5b00279PMID 26247231
• 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.

• Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

  2015cited by this paper
• Screen3D: A Novel Fully Flexible High-Throughput Shape-Similarity Search Method

  2014cited by this paper
• Molecular similarity in medicinal chemistry.

  2014cited by this paper
• SABRE: Ligand/Structure-Based Virtual Screening Approach Using Consensus Molecular-Shape Pattern Recognition

  2014cited by this paper
• Computational Methods in Drug Discovery

  2014cited by this paper
• Hierarchical virtual screening approaches in small molecule drug discovery

  2014cited by this paper
• Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set

  2014cited by this paper
• Identification of 1, 2, 5-Oxadiazoles as a New Class of SENP2 Inhibitors Using Structure Based Virtual Screening

  2014cited by this paper
• PLS and shape-based similarity analysis of maleimides – GSK-3 inhibitors

  2014cited by this paper
• Scaffold Hopping with Virtual Screening from IP3 to a Drug‐Like Partial Agonist of the Inositol Trisphosphate Receptor

  2014cited by this paper
• Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results

  2014cited by this paper
• CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys

  2013cited by this paper
• Scoring functions for prediction of protein-ligand interactions.

  2013cited by this paper
• CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series

  2013cited by this paper
• Virtual screening strategies in drug discovery: a critical review.

  2013cited by this paper
• The holistic integration of virtual screening in drug discovery.

  2013cited by this paper
• On exploring structure-activity relationships.

  2013cited by this paper
• Combination of ligand- and structure-based methods in virtual screening.

  2013cited by this paper
• Methods and applications of structure based pharmacophores in drug discovery.

  2013cited by this paper
• Latest developments in molecular docking: 2010–2011 in review

  2013cited by this paper
• Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking

  2013cited by this paper
• Enhanced ranking of PknB Inhibitors using data fusion methods

  2013cited by this paper
• Discovery of a novel and potent class of F. tularensis enoyl-reductase (FabI) inhibitors by molecular shape and electrostatic matching.

  2012cited by this paper
• From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling

  2012cited by this paper
• Machine learning techniques and drug design.

  2012cited by this paper
• Application of Consensus Scoring and Principal Component Analysis for Virtual Screening against β-Secretase (BACE-1)

  2012cited by this paper
• Recognizing Pitfalls in Virtual Screening: A Critical Review

  2012cited by this paper
• Application of Support Vector Machine to Three-Dimensional Shape-Based Virtual Screening Using Comprehensive Three-Dimensional Molecular Shape Overlay with Known Inhibitors

  2012cited by this paper
• Pharmacophore modelling: a forty year old approach and its modern synergies.

  2011cited by this paper
• SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening

  2011cited by this paper
• Challenges and advances in computational docking: 2009 in review

  2011cited by this paper
• Current trends in virtual high throughput screening using ligand-based and structure-based methods.

  2011cited by this paper
• DSX: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes

  2011cited by this paper
• CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions

  2011cited by this paper
• 3D QSAR studies on ketoamides of human cathepsin K inhibitors based on two different alignment methods.

  2010cited by this paper
• Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

  2010cited by this paper
• Rescoring ligand docking poses.

  2010cited by this paper
• De novo design: balancing novelty and confined chemical space

  2010cited by this paper
• Computational approaches for fragment-based and de novo design.

  2010cited by this paper
• Virtual screening: an endless staircase?

  2010cited by this paper
• Identification of a chemical probe for NAADP by virtual screening

  2009cited by this paper
• Machine learning in virtual screening.

  2009cited by this paper
• ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential

  2009cited by this paper
• AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

  2009cited by this paper
• SeleX-CS: A New Consensus Scoring Algorithm for Hit Discovery and Lead Optimization

  2009cited by this paper
• Comparative Assessment of Scoring Functions on a Diverse Test Set

  2009cited by this paper
• Structure-based drug screening and ligand-based drug screening with machine learning.

  2009cited by this paper
• Synergies of virtual screening approaches.

  2008cited by this paper
• Supervised Consensus Scoring for Docking and Virtual Screening

  2007cited by this paper
• Comparison of shape-matching and docking as virtual screening tools.

  2007cited by this paper
• A critical assessment of docking programs and scoring functions.

  2006cited by this paper
• Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein-Ligand Complexes

  2006cited by this paper
• Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.

  2006cited by this paper
• Advances in virtual screening

  2006cited by this paper
• A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction.

  2005cited by this paper
• Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

  2004cited by this paper
• Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.

  2004cited by this paper
• Gaussian docking functions.

  2003cited by this paper
• DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

  2001cited by this paper
• Virtual screening : an overview

  1998cited by this paper
• Flexible docking using tabu search and an empirical estimate of binding affinity

  1998cited by this paper
• Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

  1997cited by this paper
• Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

  1996cited by this paper
• Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming.

  1995cited by this paper
• The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

  1988cited by this paper
• The Protein Data Bank: a computer-based archival file for macromolecular structures.

  1977cited by this paper

• ClassyPose: A Machine‐Learning Classification Model for Ligand Pose Selection Applied to Virtual Screening in Drug Discovery

  2024cites this paper
• Novel hydrazone compounds with broad-spectrum antiplasmodial activity and synergistic interactions with antimalarial drugs

  2024cites this paper
• MultiPharm-DT: A Multi-Objective Decision Tool for Ligand-Based Virtual Screening Problems

  2021cites this paper
• Structure-Based Prediction of hERG-Related Cardiotoxicity: A Benchmark Study

  2021cites this paper
• Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound

  2020cites this paper
• Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches

  2020cites this paper
• Getting Docking into Shape Using Negative Image-Based Rescoring

  2019cites this paper
• SuCOS is Better than RMSD for Evaluating Fragment Elaboration and Docking Poses

  2019cites this paper
• Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model

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

  2019influential citation
• Combining Docking Pose Rank and Structure with Deep Learning Improves Protein-Ligand Binding Mode Prediction over a Baseline Docking Approach

  2019cites this paper
• Optimizing Electrostatic Similarity for Virtual Screening: A New Methodology

  2019cites this paper
• Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3

  2018cites this paper
• Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery

  2018cites this paper
• Do Fragments and Crystallization Additives Bind Similarly to Drug-like Ligands?

  2017cites this paper
• The impact of in silico screening in the discovery of novel and safer drug candidates.

  2017cites this paper
• Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2

  2017cites this paper
• Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2

  2017cites this paper
• Role of computational efficiency indices and pose clustering in effective decision making: An example of annulated furanones in Pf-DHFR space

  2017cites this paper
• Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015

  2016cites this paper
• CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

  2016cites this paper
• A pose prediction approach based on ligand 3D shape similarity

  2016cites this paper
• Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes

  2016cites this paper
• Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015

  2016cites this paper
• A Novel Scaffold for Developing Specific or Broad-Spectrum Chitinase Inhibitors

  2016cites this paper
• Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014

  2016cites this paper