14 Hits in 13.7 sec

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  
For each of the other 17 methods submitted, an optimal "core" score was chosen for our combined analysis across all participants.  ...  To learn what features are most important to address first, we devised our 2010 benchmark exercise.  ... 
doi:10.1021/ci200269q pmid:21809884 pmcid:PMC3186041 fatcat:o72lqwmrbbhgbh2pqtkxv6ifyq

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, for both sampling and ranking scoring functions, the use of the empirical scoring function appeared to trend positively with the RMSD.  ...  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CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

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  
The 2014 CSAR Benchmark Exercise was the last community-wide exercise that was conducted by the group at the University of Michigan, Ann Arbor.  ...  Methods that were able to dock well across all submitted systems include MDock 1 , Glide-XP 2 , PLANTS 3 , Wilma 4 , Gold 5 , SMINA 6 , Glide-XP 2 /PELE 7 , FlexX 8 , and MedusaDock 9 .  ...  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

Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge

Zhaofeng Ye, Matthew P. Baumgartner, Bentley M. Wingert, Carlos J. Camacho
2016 Journal of Computer-Aided Molecular Design  
In the 2010 Community Structure-Activity Resource (CSAR) Exercise, Carlson and collaborators analyzed the performance of different scoring functions on the CSAR-NRC data set [5, 24] .  ...  The results indicated that most of the scoring functions had comparable performance (R 2 =0.3-0.4) and the best R 2 were achieved by AutoDock and AutoDock Vina (R 2 =0.55) [5] .  ...  The work is funded by National Institution of Health 2GM097082.  ... 
doi:10.1007/s10822-016-9941-0 pmid:27573981 pmcid:PMC5079819 fatcat:65dh5fjdsvah7pe6qrfy7qw5qi

Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening

Qurrat Ul Ain, Antoniya Aleksandrova, Florian D. Roessler, Pedro J. Ballester
2015 Wiley Interdisciplinary Reviews. Computational Molecular Science  
The reliability of docking depends, however, on the accuracy of the adopted scoring function (SF).  ...  New SFs based on modern machine-learning regression models, which do not impose a predetermined functional form and thus are able to exploit effectively much larger amounts of experimental data, have recently  ...  the CSAR benchmark by a large margin.  ... 
doi:10.1002/wcms.1225 pmid:27110292 pmcid:PMC4832270 fatcat:6kkpyx7m3bgn5lxunyw7nga56i

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 present results have implications for methods development and future blind prediction exercises. * Despite the methodological differences, submission 5* is effectively a linear scaling of submission  ...  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

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  
Using the Danish National Registry of Patients, we identified all inpatient and outpatient diagnoses of VTE.  ...  We evaluated risk of ASD according to maternal and paternal IBD, and separately for maternal and paternal Crohn´s disease (CD) and ulcerative colitis (UC).  ...  Materials and methods: To evaluate the performance of SCORE in the primary prevention of CVD, we plan to review the medical records of all patients admitted for an AMI during 2010-2012 to the following  ... 
doi:10.1111/acps.12165 pmid:23799875 pmcid:PMC3819398 fatcat:laus7nv3kjdmhb54qwmigtuk2u

Full Pretoria Student Law Review (2020)14 2

Adelaide Chagopa, Kayla Thomas, Marcia van der Merwe, Nicholas Herd, Phenyo Sekati
2020 Pretoria Student Law Review  
As per Diageo SA and ABC v CSARS, the enquiry is whether a taxpayer has supplied a separate part, even though combined into a single supply.  ...  Notwithstanding that this procedure is used as a benchmark for the purposes of this article, it must be noted that a brief evaluation of the effectiveness of the procedure raised some shortcomings in its  ...  the 4 th IR, automation and artificial intelligence will disorganise the current model of demand for skills, ensuring rapid replacement of traditional jobs with new unknown ones. 2 These new jobs will  ... 
doi:10.29053/pslr.v14i2.1979 fatcat:ewto2xe4bvbspom5jupiv4wgjq

Design, development and first evaluation of a client/server system for managing and querying linguistic corpora Tesi presentata da: Eros Zanchetta Coordinatore dottorato Relatore

Marcello Soffritti, Marcello Soffritti
Then an analysis follows of how users actually interacted with corpora to complete the task they were assigned and what kind of queries they submitted.  ...  Chapter 3 describes the design of an experiment, carried out on a group of 58 students of translation, devised to evaluate the usability of the new system in comparison to another well-known corpus tool  ...  Martelli (2001) : "Words from Bononia Legal Corpus", in International Journal of Corpus Linguistics 6.Special Issue,  ... 

Volta : science, technology and society in Europe. 02 [article]

Institut Für Technikfolgenabschätzung Und Systemanalyse (ITAS)
(Catalonia) Subscriptions Newsletter and Print Legal deposit B-40368-2011 Volta was made possible by Volta is an initiative of fifteen technology assessment organisations  ...  citizens or the effective functioning of governments.  ...  Brain Pickings covers a wealth of disciplines across art, design, science and technology, empowering readers to 'combine them into original concepts that are stronger, smarter, richer, deeper and more  ... 
doi:10.5445/ir/1000035709 fatcat:u56oynbftfatjadihldt5obqgi

Cybersecurity | Special Report Technology-Norway

Sergio Bellucci -Ta, Katalin Fodor, Marianne Barland, Ingrid Geesink, Huup Dassen, Claartje Doorenbos, Philip Dröge, Emiliano Feresin, Jon Fixdal, Marlies Hanifer, Pascal Messer, Ann Maher (+1 others)
(Catalonia) Subscriptions Newsletter and Print Legal deposit B-40368-2011 Volta was made possible by Volta is an initiative of fifteen technology assessment organisations  ...  Brain Pickings covers a wealth of disciplines across art, design, science and technology, empowering readers to 'combine them into original concepts that are stronger, smarter, richer, deeper and more  ...  citizens or the effective functioning of governments.  ... 

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

to the targeting of a range of amyloid diseases.  ...  Aggregation of human islet amyloid polypeptide (IAPP) to form amyloid fibrils and plaques is implicated in the dysfunction and death of pancreatic beta cells in type 2 diabetes, a most common form of metabolic  ...  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

The Role of Italy in the development of a European security and defence policy

Claudio Catalano
The first objective of this research is to describe how Italy placed itself in the debate on the development of ESDP if compared to the Franco‐German couple and the British approach: two opposing views  ...  The thesis will define Italian contribution to European integration in the field of Security and Defence Policy.  ...  Air: a Combined Air component HQ), 26 Tornado and AMX combat aircraft, six CSAR helicopters, four C-130J transport aircraft (from 2003), nine tactical transport aircraft, two air refueling aircraft, three  ... 
doi:10.6092/imtlucca/e-theses/62 fatcat:ldwg7g4rf5go7i4rm6dizan7uq