Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2
出版年份 2017 全文链接
标题
Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2
作者
关键词
Protein–ligand docking, Ensemble docking, Flexible docking, D3R, Scoring function
出版物
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume 32, Issue 1, Pages 151-162
出版商
Springer Nature
发表日期
2017-09-14
DOI
10.1007/s10822-017-0062-1
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。- Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization
- (2017) Maria Kadukova et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Blinded predictions of binding modes and energies of HSP90-α ligands for the 2015 D3R grand challenge
- (2016) Antonia S.J.S. Mey et al. BIOORGANIC & MEDICINAL CHEMISTRY
- Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates
- (2016) Maria Kadukova et al. Journal of Chemical Information and Modeling
- Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise
- (2016) Regina Politi et al. 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- CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma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
- Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015
- (2016) Diogo Santos-Martins JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Docking-undocking combination applied to the D3R Grand Challenge 2015
- (2016) Sergio Ruiz-Carmona et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Improved pose and affinity predictions using different protocols tailored on the basis of data availability
- (2016) Philip Prathipati et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Yada: a novel tool for molecular docking calculations
- (2016) S. Piotto et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015
- (2016) Veronica Salmaso et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation
- (2016) Sergei Grudinin et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015
- (2016) Inna Slynko et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- A D3R prospective evaluation of machine learning for protein-ligand scoring
- (2016) Jocelyn Sunseri et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge
- (2016) Zhaofeng Ye et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015
- (2016) Nanjie Deng et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations
- (2016) Majda Misini Ignjatović et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets
- (2016) Edithe Selwa et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
- (2016) Symon Gathiaka et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015
- (2016) Ashutosh Kumar et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Integration of Ligand and Structure Based Approaches for CSAR-2014
- (2015) Philip Prathipati et al. Journal of Chemical Information and Modeling
- Blind Pose Prediction, Scoring, and Affinity Ranking of the CSAR 2014 Dataset
- (2015) Virginie Y. Martiny et al. Journal of Chemical Information and Modeling
- Evaluation of the Wilma-SIE Virtual Screening Method in Community Structure–Activity Resource 2013 and 2014 Blind Challenges
- (2015) Hervé Hogues et al. Journal of Chemical Information and Modeling
- CSAR Benchmark of Flexible MedusaDock in Affinity Prediction and Nativelike Binding Pose Selection
- (2015) Praveen Nedumpully-Govindan et al. Journal of Chemical Information and Modeling
- Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks
- (2015) Chengfei Yan et al. Journal of Chemical Information and Modeling
- Predicting Binding Poses and Affinities in the CSAR 2013–2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential
- (2015) Sergei Grudinin et al. Journal of Chemical Information and Modeling
- Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein–Ligand Binding Prediction in CSAR 2013 and 2014
- (2015) Xiaolei Zhu et al. Journal of Chemical Information and Modeling
- Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment
- (2015) Matthew P. Baumgartner et al. Journal of Chemical Information and Modeling
- 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
- Evaluation of GalaxyDock Based on the Community Structure–Activity Resource 2013 and 2014 Benchmark Studies
- (2015) Woong-Hee Shin et al. Journal of Chemical Information and Modeling
- HybridDock: A Hybrid Protein–Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches
- (2015) Sheng-You Huang et al. Journal of Chemical Information and Modeling
- Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise
- (2015) Ashutosh Kumar et al. Journal of Chemical Information and Modeling
- Target-Specific Native/Decoy Pose Classifier Improves the Accuracy of Ligand Ranking in the CSAR 2013 Benchmark
- (2014) Denis Fourches 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
- Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches
- (2013) Denis Fourches et al. Journal of Chemical Information and Modeling
- Domain enhanced lookup time accelerated BLAST
- (2012) Grzegorz M Boratyn et al. Biology Direct
- Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
- (2012) Marcus D Hanwell et al. Journal of Cheminformatics
- Optimization of a novel class of benzimidazole-based farnesoid X receptor (FXR) agonists to improve physicochemical and ADME properties
- (2011) Hans G.F. Richter et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions
- (2011) Richard D. Smith et al. Journal of Chemical Information and Modeling
- Open Babel: An open chemical toolbox
- (2011) Noel M O'Boyle et al. Journal of Cheminformatics
- AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
- (2009) Garrett M. Morris et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Improved prediction of protein side-chain conformations with SCWRL4
- (2009) Georgii G. Krivov et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now