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CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes
2011
Journal of Chemical Information and Modeling
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Here, we describe our process for creating the 2010 benchmark exercise data set that was used in the studies to follow. ...
This paper presents the process of developing the data set used in the 2010 CSAR exercise (flowchart in Figure 1 ). ...
doi:10.1021/ci200082t
pmid:21728306
pmcid:PMC3180202
fatcat:cqd3oezs2bbdrlpz7spd75lxoq
CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions
2011
Journal of Chemical Information and Modeling
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To learn what features are most important to address first, we devised our 2010 benchmark exercise. ...
We also thank the Chemical Computing Group and OpenEye Scientific Software for generously donating the use of their software. ' REFERENCES Special Issue: CSAR 2010 Scoring Exercise Received: June 14, 2011 ...
doi:10.1021/ci200269q
pmid:21809884
pmcid:PMC3186041
fatcat:o72lqwmrbbhgbh2pqtkxv6ifyq
Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise
2013
Journal of Chemical Information and Modeling
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scoring function and evaluated it in the context of the CSAR 2011 benchmarking exercise. ...
Using our general method, the unique capabilities of smina, a set of default interaction terms from AutoDock Vina, and the CSAR (Community Structure-Activity Resource) 2010 dataset, we created a custom ...
Acknowledgments This work was supported by grant R01GM097082-01 from the National Institutes of Health. ...
doi:10.1021/ci300604z
pmid:23379370
pmcid:PMC3726561
fatcat:5is3fcqvifbfpbf7ipx5kd2vue
CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
2013
Journal of Chemical Information and Modeling
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A total of 20 research groups submitted results for the benchmark exercise where the goal was to compare different improvements for pose prediction, enrichment, and relative ranking of congeneric series ...
The Community Structure-Activity Resource (CSAR) recently held its first blinded exercise based on data provided by Abbott, Vertex, and colleagues at the University of Michigan, Ann Arbor. ...
CSAR conducted its first benchmark exercise in 2010 with the goal of (1) evaluating the current ability of the field to predict the free energy of binding for protein−ligand complexes and (2) investigating ...
doi:10.1021/ci400025f
pmid:23548044
pmcid:PMC3753884
fatcat:dxmgxmeerbh4xe4xyg7ynmnagi
CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma
2016
Journal of Chemical Information and Modeling
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In Phase 1 of the CSAR 2014 Exercise, participants were given several protein-ligand complexes and asked to identify the one near-native pose from among 200 decoys provided by CSAR. ...
The 2014 CSAR Benchmark Exercise was the last community-wide exercise that was conducted by the group at the University of Michigan, Ann Arbor. ...
The CSAR Center is funded by the National Institute of General Medical Sciences (U01 GM086873). ...
doi:10.1021/acs.jcim.5b00523
pmid:27149958
pmcid:PMC5228621
fatcat:5kin36kdjrfndps4w3yhge3tla
Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function
2011
Journal of Chemical Information and Modeling
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The resulted scoring function, referred to as ITScore 2.0, has been tested with the CSAR (Community Structure-Activity Resource, 2009 release) benchmark of 345 diverse protein-ligand complexes. ...
Based on a statistical mechanics-based iterative method, we have extracted a set of distancedependent, all-atom pairwise potentials for protein-ligand interactions from the crystal structures of 1300 protein-ligand ...
The computations were performed on the HPC resources at the University of Missouri Bioinformatics Consortium (UMBC). ...
doi:10.1021/ci2000727
pmid:21830787
pmcid:PMC3190652
fatcat:sy75s3tlgnbo7jfyv4uqrgrzny
Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets
2011
Journal of Chemical Information and Modeling
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Special Issue: CSAR 2010 Scoring Exercise Received: March 28, 2011
Figure 1 . 1 Illustration of the method to derive PL/MCT-Tess descriptors using the tesselated proteinÀligand complex (3ERT, the ER/ ...
In this study, we employ the CSAR-NRC benchmark set to test two scoring functions of very different natures. ...
doi:10.1021/ci200146e
pmid:21780807
pmcid:PMC3183266
fatcat:a3mpg6litjffxoecillhubxqie
A Diverse Benchmark Based on 3D Matched Molecular Pairs for Validating Scoring Functions
2018
ACS Omega
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The prediction of protein-ligand interactions and their corresponding binding free energy is a challenging task in structure-based drug design and related applications. ...
This data set was used to study the predictive power of 13 commonly used scoring functions to demonstrate the applicability of the 3D-MMP data set as a valuable tool for benchmarking scoring functions. ...
Guido Kirsten, Chemical Computing Group, for the adaptation of the KNIME node to the Amber force field. ...
doi:10.1021/acsomega.7b01194
pmid:31458770
pmcid:PMC6641919
fatcat:kchkibqqbjaurorpje4u72ubni
Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures
2014
Nucleic Acids Research
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The improved user interface incorporates current thirdparty plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. ...
Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23 269 complexes and 8156 binding affinities. ...
ACKNOWLEDGEMENT We thank the many coworkers who have contributed to the Binding MOAD project, particularly Dr Mark Benson, PhD. ...
doi:10.1093/nar/gku1088
pmid:25378330
pmcid:PMC4383918
fatcat:vkrhl5ppizc4lnivd6nstpzewy
RosENet: Improving binding affinity prediction by leveraging molecular mechanics energies with a 3D Convolutional Neural Network
[article]
2020
bioRxiv
pre-print
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absolute binding affinity of protein - ligand complexes. ...
One key step in these approaches is the need for the rapid and accurate prediction of the binding affinity for potential leads. ...
This dataset was part of the CSAR 2010 exercise and was composed of two sets:
A2.2 FEP The FEP dataset was used for a Free Energy Perturbation study 32
A.2.3 PDBBind 2018 NMR structures Complexes ...
doi:10.1101/2020.05.12.090191
fatcat:ktsozvesc5hd7jsrtutrlbsf2q
ABS–Scan: In silico alanine scanning mutagenesis for binding site residues in protein–ligand complex
2014
F1000Research
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It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. ...
Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. ...
Acknowledgements We acknowledge all the members of the NSC lab for useful suggestions during the development of the web-server and visualization of the results. ...
doi:10.12688/f1000research.5165.1
pmid:25685322
pmcid:PMC4319546
fatcat:rs4nfm7tgzbz5borueyxw4h3ba
ABS–Scan: In silico alanine scanning mutagenesis for binding site residues in protein–ligand complex
2014
F1000Research
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It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. ...
Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. ...
Acknowledgements We acknowledge all the members of the NSC lab for useful suggestions during the development of the web-server and visualization of the results. ...
doi:10.12688/f1000research.5165.2
pmid:25685322
pmcid:PMC4319546
fatcat:chrxsu6jpzeizilkdzrfw4fi5i
Multipose Binding in Molecular Docking
2014
International Journal of Molecular Sciences
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., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. ...
Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity ...
Conflicts of Interest The authors declare no conflict of interest. ...
doi:10.3390/ijms15022622
pmid:24534807
pmcid:PMC3958872
fatcat:nvm46ljofrcddb5won76plkn6u
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
Journal of Computer-Aided Molecular Design
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provided an opportunity to test our new model for the binding free energy of small molecules, as well as to assess our protocol to predict binding poses for protein-ligand complexes. ...
Predicting binding poses and affinities for protein-ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimationAbstract The 2015 D3R Grand Challenge ...
Acknowledgments The authors thank Dr. Petr Popov from MIPT Moscow for the initial analysis of the HSP90 targets. ...
doi:10.1007/s10822-016-9976-2
pmid:27718029
fatcat:ofyasi7lzbbazl66nyh4e22jku
Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening
2015
Wiley Interdisciplinary Reviews. Computational Molecular Science
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The emerging picture from these studies is that the classical approach of using linear regression with a small number of expert-selected structural features can be strongly improved by a machine-learning ...
The reliability of docking depends, however, on the accuracy of the adopted scoring function (SF). ...
the CSAR benchmark by a large margin. ...
doi:10.1002/wcms.1225
pmid:27110292
pmcid:PMC4832270
fatcat:6kkpyx7m3bgn5lxunyw7nga56i
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