D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
出版年份 2020 全文链接
标题
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
作者
关键词
-
出版物
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume 34, Issue 2, Pages 99-119
出版商
Springer Science and Business Media LLC
发表日期
2020-01-23
DOI
10.1007/s10822-020-00289-y
参考文献
相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。- D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings
- (2019) Zied Gaieb et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Ensemble Docking in Drug Discovery
- (2018) Rommie E. Amaro et al. BIOPHYSICAL JOURNAL
- Most Ligand-Based Classification Benchmarks Reward Memorization Rather than Generalization
- (2018) Izhar Wallach et al. Journal of Chemical Information and Modeling
- KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks
- (2018) José Jiménez et al. Journal of Chemical Information and Modeling
- Multiscale weighted colored graphs for protein flexibility and rigidity analysis
- (2018) David Bramer et al. JOURNAL OF CHEMICAL PHYSICS
- Convolutional neural network scoring and minimization in the D3R 2017 community challenge
- (2018) Jocelyn Sunseri et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
- (2018) Zixuan Cang et al. PLoS Computational Biology
- Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3
- (2018) Panagiotis I. Koukos et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges
- (2018) Duc Duy Nguyen et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3
- (2018) Ashutosh Kumar et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3
- (2018) Polo C.-H. Lam et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3
- (2018) Bing Xie et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Calculate protein–ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3
- (2018) Xibing He et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations
- (2018) Ludovic Chaput et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Monte Carlo on the manifold and MD refinement for binding pose prediction of protein–ligand complexes: 2017 D3R Grand Challenge
- (2018) Mikhail Ignatov et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction
- (2017) Zixuan Cang et al. International Journal for Numerical Methods in Biomedical Engineering
- Rigidity Strengthening: A Mechanism for Protein–Ligand Binding
- (2017) Duc D. Nguyen et al. Journal of Chemical Information and Modeling
- Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
- (2017) Zoe Cournia et al. Journal of Chemical Information and Modeling
- Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets
- (2017) Haoyu S. Yu et al. Journal of Chemical Theory and Computation
- Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2
- (2017) Christina Athanasiou et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations
- (2017) Edithe Selwa et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking
- (2017) Martin A. Olsson et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method
- (2017) Hervé Hogues et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2
- (2017) Eko Aditya Rifai et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling
- (2017) Soumendranath Bhakat et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor
- (2017) Rui Duan et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations
- (2017) Antonia S. J. S. Mey et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations
- (2017) Oleksandr Yakovenko et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2
- (2017) Priscila da Silva Figueiredo Celestino Gomes et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
- (2017) Zeynep Kurkcuoglu et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- CDOCKER and $$\lambda$$ λ -dynamics for prospective prediction in D3R Grand Challenge 2
- (2017) Xinqiang Ding et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2
- (2017) Veronica Salmaso et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort
- (2017) Ying-Duo Gao et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016
- (2017) Xavier Fradera et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2
- (2017) Maria Kadukova et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study
- (2017) Manon Réau et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP+
- (2017) Christina Schindler et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges
- (2017) Bentley M. Wingert et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- A cross docking pipeline for improving pose prediction and virtual screening performance
- (2017) Ashutosh Kumar et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2
- (2017) Matthew P. Baumgartner et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
- (2017) Zied Gaieb et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Protein–ligand docking using FFT based sampling: D3R case study
- (2017) Dzmitry Padhorny et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach
- (2017) Polo C.-H. Lam et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions
- (2017) Zixuan Cang et al. PLoS Computational Biology
- Role of BACE1 in Alzheimer’s synaptic function
- (2017) Brati Das et al. Translational Neurodegeneration
- Lessons Learned over Four Benchmark Exercises from the Community Structure–Activity Resource
- (2016) Heather A. Carlson Journal of Chemical Information and Modeling
- CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma
- (2016) Heather A. Carlson et al. Journal of Chemical Information and Modeling
- Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics
- (2016) Evangelos A. Coutsias et al. Journal of Chemical Theory and Computation
- D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
- (2016) Symon Gathiaka et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Docking Screens for Novel Ligands Conferring New Biology
- (2016) John J. Irwin et al. JOURNAL OF MEDICINAL CHEMISTRY
- The ChEMBL database in 2017
- (2016) Anna Gaulton et al. NUCLEIC ACIDS RESEARCH
- Role of computer-aided drug design in modern drug discovery
- (2015) Stephani Joy Y. Macalino et al. ARCHIVES OF PHARMACAL RESEARCH
- CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge
- (2015) Richard D. Smith et al. Journal of Chemical Information and Modeling
- eFindSite: Enhanced Fingerprint-Based Virtual Screening Against Predicted Ligand Binding Sites in Protein Models
- (2014) Wei P. Feinstein et al. Molecular Informatics
- Accuracy Assessment and Automation of Free Energy Calculations for Drug Design
- (2013) Clara D. Christ et al. Journal of Chemical Information and Modeling
- CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
- (2013) Kelly L. Damm-Ganamet et al. Journal of Chemical Information and Modeling
- Potential and Limitations of Ensemble Docking
- (2012) Oliver Korb et al. Journal of Chemical Information and Modeling
- Perspective: Alchemical free energy calculations for drug discovery
- (2012) David L. Mobley et al. JOURNAL OF CHEMICAL PHYSICS
- Alchemical free energy methods for drug discovery: progress and challenges
- (2011) John D Chodera et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Software and resources for computational medicinal chemistry
- (2011) Chenzhong Liao et al. Future Medicinal Chemistry
- Open Babel: An open chemical toolbox
- (2011) Noel M O'Boyle et al. Journal of Cheminformatics
- Protein Kinases: Docking and Homology Modeling Reliability
- (2010) Tiziano Tuccinardi et al. Journal of Chemical Information and Modeling
- Macrocyclic peptidomimetic β-secretase (BACE-1) inhibitors with activity in vivo
- (2009) Rainer Machauer et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss
- (2009) Pascal Bonnet et al. Journal of Chemical Information and Modeling
- AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
- (2009) Oleg Trott et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
- (2009) Garrett M. Morris et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria
- (2008) William L. Jorgensen et al. Journal of Chemical Theory and Computation
- An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
- (2008) Rommie E. Amaro et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles
- (2008) Sidhartha Chaudhury et al. JOURNAL OF MOLECULAR BIOLOGY
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started