D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
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Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2.A cross docking pipeline for improving pose prediction and virtual screening performance.Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2.Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015.Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain.CADD medicine: design is the potion that can cure my disease.Protein-Ligand Scoring with Convolutional Neural Networks.Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors.Predicting Binding Free Energies: Frontiers and Benchmarks.Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges.Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization.D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation.Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo.Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor.Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations.Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2.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.Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method.CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2.Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2.Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP.Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study.Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration.Application of Assisted Design of Antibody and Protein Therapeutics (ADAPT) improves efficacy of a Clostridium difficile toxin A single-domain antibody.Overview of Methods and Strategies for Conducting Virtual Small Molecule Screening.Computer-aided drug design: time to play with novel chemical matter.RosettaLigandEnsemble: A Small-Molecule Ensemble-Driven Docking Approach.Quantum Chemical Approaches in Structure-Based Virtual Screening and Lead Optimization.Assessing the stability of free-energy perturbation calculations by performing variations in the method.Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges
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P2860
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
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2016 nî lūn-bûn
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2016年の論文
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2016年学术文章
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2016年学术文章
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2016年学术文章
@zh-hans
2016年学术文章
@zh-my
2016年学术文章
@zh-sg
2016年學術文章
@yue
2016年學術文章
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2016年學術文章
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name
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
@en
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
@nl
type
label
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
@en
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
@nl
prefLabel
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
@en
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
@nl
P2093
P2860
P50
P1476
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
@en
P2093
Ginger Kubish
Heather A Carlson
Huanwang Yang
James B Dunbar
Jeanne A Stuckey
Jim Delproposto
Michael K Gilson
Rommie E Amaro
Symon Gathiaka
P2860
P2888
P304
P356
10.1007/S10822-016-9946-8
P577
2016-09-30T00:00:00Z