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CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

James B. Dunbar, Richard D. Smith, Chao-Yie Yang, Peter Man-Un Ung, Katrina W. Lexa, Nickolay A. Khazanov, Jeanne A. Stuckey, Shaomeng Wang, Heather A. Carlson
2011 Journal of Chemical Information and Modeling  
Here, we describe our process for creating the 2010 benchmark exercise data set that was used in the studies to follow.  ...  ' MODIFICATIONS TO THE DATASET, POST-MEETING EXERCISE: CSAR-NRC HIQ DATASET (SEPTEMBER 24, 2010 RELEASE) 2010 on the CSAR Web site as the CSAR_ NRC_HiQ_Set_24Sept2010.tar.  ... 
doi:10.1021/ci200082t pmid:21728306 pmcid:PMC3180202 fatcat:cqd3oezs2bbdrlpz7spd75lxoq

CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions

Richard D. Smith, James B. Dunbar, Peter Man-Un Ung, Emilio X. Esposito, Chao-Yie Yang, Shaomeng Wang, Heather A. Carlson
2011 Journal of Chemical Information and Modeling  
To learn what features are most important to address first, we devised our 2010 benchmark exercise.  ...  ' ACKNOWLEDGMENT We would like to thank all participants in the benchmark exercise!  ... 
doi:10.1021/ci200269q pmid:21809884 pmcid:PMC3186041 fatcat:o72lqwmrbbhgbh2pqtkxv6ifyq

Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function

Sheng-You Huang, Xiaoqin Zou
2011 Journal of Chemical Information and Modeling  
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

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

David Ryan Koes, Matthew P. Baumgartner, Carlos J. Camacho
2013 Journal of Chemical Information and Modeling  
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

Kelly L. Damm-Ganamet, Richard D. Smith, James B. Dunbar, Jeanne A. Stuckey, Heather A. Carlson
2013 Journal of Chemical Information and Modeling  
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  ...  Lastly, we found that minimizing the protein and correcting histidine tautomeric states positively trended with low RMSD for pose prediction but minimizing the ligand negatively trended.  ...  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 proteinligand complexes and (2) investigating  ... 
doi:10.1021/ci400025f pmid:23548044 pmcid:PMC3753884 fatcat:dxmgxmeerbh4xe4xyg7ynmnagi

A Diverse Benchmark Based on 3D Matched Molecular Pairs for Validating Scoring Functions

Lena Kalinowsky, Julia Weber, Shantheya Balasupramaniam, Knut Baumann, Ewgenij Proschak
2018 ACS Omega  
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.  ...  The prediction of protein-ligand interactions and their corresponding binding free energy is a challenging task in structure-based drug design and related applications.  ...  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

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

Heather A. Carlson, Richard D. Smith, Kelly L. Damm-Ganamet, Jeanne A. Stuckey, Aqeel Ahmed, Maire A. Convery, Donald O. Somers, Michael Kranz, Patricia A. Elkins, Guanglei Cui, Catherine E. Peishoff, Millard H. Lambert (+1 others)
2016 Journal of Chemical Information and Modeling  
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.  ...  Acknowledgments We would like to thank all participants in the benchmark exercise! We would also like to thank Dr.  ... 
doi:10.1021/acs.jcim.5b00523 pmid:27149958 pmcid:PMC5228621 fatcat:5kin36kdjrfndps4w3yhge3tla

Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets

Jui-Hua Hsieh, Shuangye Yin, Shubin Liu, Alexander Sedykh, Nikolay V. Dokholyan, Alexander Tropsha
2011 Journal of Chemical Information and Modeling  
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

Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation

Sergei Grudinin, Maria Kadukova, Andreas Eisenbarth, Simon Marillet, Frédéric Cazals
2016 Journal of Computer-Aided Molecular Design  
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

Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors

Damian Bartuzi, Agnieszka Kaczor, Katarzyna Targowska-Duda, Dariusz Matosiuk
2017 Molecules  
One of the key steps in such studies is proper computational reconstruction of actual ligand-receptor or protein-protein interactions, a process called molecular docking.  ...  The growing number of studies on G protein-coupled receptors (GPCRs) family are a source of noticeable improvement in our understanding of the functioning of these proteins.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules22020340 pmid:28241450 fatcat:xyytfxpfcvd43dyoefto4qr5pi

Protein flexibility in docking and surface mapping

Katrina W. Lexa, Heather A. Carlson
2012 Quarterly Reviews of Biophysics (print)  
Typical protein-ligand docking efforts still rely on a single rigid receptor, which is an incomplete representation of potential binding conformations of the protein.  ...  As available structural information has increased, researchers have become increasingly aware of the importance of protein flexibility for accurate description of the native state.  ...  Acknowledgments This work has been supported by the National Institutes of Health (GM65372).  ... 
doi:10.1017/s0033583512000066 pmid:22569329 pmcid:PMC4272345 fatcat:s7voxcdb7zbyrgkt7kedvo3lky

Blind prediction of host–guest binding affinities: a new SAMPL3 challenge

Hari S. Muddana, C. Daniel Varnado, Christopher W. Bielawski, Adam R. Urbach, Lyle Isaacs, Matthew T. Geballe, Michael K. Gilson
2012 Journal of Computer-Aided Molecular Design  
The SAMPL3 community exercise included the first ever blind prediction challenge for host-guest binding affinities, through the incorporation of 11 new host-guest complexes.  ...  The computational prediction of protein-ligand binding affinities is of central interest in earlystage drug-discovery, and there is a widely recognized need for improved methods.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIGMS or the National Institutes of Health. We thank Drs.  ... 
doi:10.1007/s10822-012-9554-1 pmid:22366955 pmcid:PMC3383923 fatcat:rbmvxyxwvnbdpa7i3ogwdfxg7m

A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool

David Ryan Koes, Nicolas A. Pabon, Xiaoyi Deng, Margaret A. Phillips, Carlos J. Camacho, Robert W Sobol
2015 PLoS ONE  
The general approach entailed exhaustively building and screening sparse pharmacophore models comprising of a minimum of three features for each bound ligand in all available DHODH co-crystals and iteratively  ...  Pose prediction of compound 6. Receptor structure and binding site residues of 3I65 are shown in blue. Compound 6 is shown in magenta sticks. (a) Compound 6 aligned to the pharmacophore of Fig 1.  ...  We would also like to thank the students of the University of Pittsburgh TECBio REU and the UPCI Summer Academy. Author Contributions  ... 
doi:10.1371/journal.pone.0134697 pmid:26258606 pmcid:PMC4530941 fatcat:kae35r6vu5avlaaqdspdnawviy

Measuring psychotic depression

S. D. Østergaard, B. S. Meyers, A. J. Flint, B. H. Mulsant, E. M. Whyte, C. M. Ulbricht, P. Bech, A. J. Rothschild
2013 Acta Psychiatrica Scandinavica  
Methods: We conducted a registry-based nationwide cohort study including children born alive in Denmark from 1 January 1994 to 31 December 2009, with follow-up throughout 2010.  ...  Children with parents free of IBD were the comparison cohort.  ...  It is therefore only a subset of mitochondrial matrix proteins requiring Hsp60 for correct folding and maintenance of the native state.  ... 
doi:10.1111/acps.12165 pmid:23799875 pmcid:PMC3819398 fatcat:laus7nv3kjdmhb54qwmigtuk2u

Understanding the Structure, Toxicity and Inhibition of IAPP at the Nanoscale

EMILY HELEN PILKINGTON
2020
to the targeting of a range of amyloid diseases.  ...  Accordingly, this thesis investigated the amyloidosis of IAPP, its self-assembly into toxic aggregation states, and its interactions with proteins and lipids to acquire a 'protein corona', a concept pertinent  ...  The predictive power of MedusaScore has been validated in various benchmark studies, including recent community structure−activity resource (CSAR) blind ligand−receptor docking prediction exercises. 43  ... 
doi:10.26180/5ed4b0925ff3e fatcat:jzrcoxhcgzg7hfep6dnifu2dsu