Literature DB >> 27345761

Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource.

Heather A Carlson1.   

Abstract

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Year:  2016        PMID： 27345761      PMCID： PMC5217176          DOI： 10.1021/acs.jcim.6b00182

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN： 1549-9596            Impact factor:   4.956


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  21 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function.

Authors:  Sheng-You Huang; Xiaoqin Zou
Journal:  J Chem Inf Model       Date:  2011-08-31       Impact factor: 4.956

3.  The Uppsala Electron-Density Server.

Authors:  Gerard J Kleywegt; Mark R Harris; Jin Yu Zou; Thomas C Taylor; Anders Wählby; T Alwyn Jones
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-11-26

4.  Decoys for docking.

Authors:  Alan P Graves; Ruth Brenk; Brian K Shoichet
Journal:  J Med Chem       Date:  2005-06-02       Impact factor: 7.446

5.  Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide.

Authors:  Matthew P Repasky; Robert B Murphy; Jay L Banks; Jeremy R Greenwood; Ivan Tubert-Brohman; Sathesh Bhat; Richard A Friesner
Journal:  J Comput Aided Mol Des       Date:  2012-05-11       Impact factor: 3.686

6.  CSAR scoring challenge reveals the need for new concepts in estimating protein-ligand binding affinity.

Authors:  Fedor N Novikov; Alexey A Zeifman; Oleg V Stroganov; Viktor S Stroylov; Val Kulkov; Ghermes G Chilov
Journal:  J Chem Inf Model       Date:  2011-06-03       Impact factor: 4.956

7.  Check your confidence: size really does matter.

Authors:  Heather A Carlson
Journal:  J Chem Inf Model       Date:  2013-08-08       Impact factor: 4.956

8.  Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.

Authors:  Michael M Mysinger; Michael Carchia; John J Irwin; Brian K Shoichet
Journal:  J Med Chem       Date:  2012-07-05       Impact factor: 7.446

9.  CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series.

Authors:  Kelly L Damm-Ganamet; Richard D Smith; James B Dunbar; Jeanne A Stuckey; Heather A Carlson
Journal:  J Chem Inf Model       Date:  2013-05-10       Impact factor: 4.956

10.  CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.

Authors:  Richard D Smith; James B Dunbar; Peter Man-Un Ung; Emilio X Esposito; Chao-Yie Yang; Shaomeng Wang; Heather A Carlson
Journal:  J Chem Inf Model       Date:  2011-08-29       Impact factor: 4.956
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  11 in total

1.  D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Authors:  Zied Gaieb; Shuai Liu; Symon Gathiaka; Michael Chiu; Huanwang Yang; Chenghua Shao; Victoria A Feher; W Patrick Walters; Bernd Kuhn; Markus G Rudolph; Stephen K Burley; Michael K Gilson; Rommie E Amaro
Journal:  J Comput Aided Mol Des       Date:  2017-12-04       Impact factor: 3.686

2.  Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method.

Authors:  Hervé Hogues; Traian Sulea; Francis Gaudreault; Christopher R Corbeil; Enrico O Purisima
Journal:  J Comput Aided Mol Des       Date:  2017-10-05       Impact factor: 3.686

3.  The role of human in the loop: lessons from D3R challenge 4.

Authors:  Oleg V Stroganov; Fedor N Novikov; Michael G Medvedev; Artem O Dmitrienko; Igor Gerasimov; Igor V Svitanko; Ghermes G Chilov
Journal:  J Comput Aided Mol Des       Date:  2020-01-21       Impact factor: 3.686

4.  D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings.

Authors:  Zied Gaieb; Conor D Parks; Michael Chiu; Huanwang Yang; Chenghua Shao; W Patrick Walters; Millard H Lambert; Neysa Nevins; Scott D Bembenek; Michael K Ameriks; Tara Mirzadegan; Stephen K Burley; Rommie E Amaro; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2019-01-10       Impact factor: 3.686

5.  Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking.

Authors:  Jeffrey R Wagner; Christopher P Churas; Shuai Liu; Robert V Swift; Michael Chiu; Chenghua Shao; Victoria A Feher; Stephen K Burley; Michael K Gilson; Rommie E Amaro
Journal:  Structure       Date:  2019-06-27       Impact factor: 5.006

6.  Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015.

Authors:  Diogo Santos-Martins
Journal:  J Comput Aided Mol Des       Date:  2016-08-22       Impact factor: 3.686

7.  D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Authors:  Conor D Parks; Zied Gaieb; Michael Chiu; Huanwang Yang; Chenghua Shao; W Patrick Walters; Johanna M Jansen; Georgia McGaughey; Richard A Lewis; Scott D Bembenek; Michael K Ameriks; Tara Mirzadegan; Stephen K Burley; Rommie E Amaro; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2020-01-23       Impact factor: 3.686

8.  Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2.

Authors:  Priscila da Silva Figueiredo Celestino Gomes; Franck Da Silva; Guillaume Bret; Didier Rognan
Journal:  J Comput Aided Mol Des       Date:  2017-08-01       Impact factor: 3.686

9.  Convolutional neural network scoring and minimization in the D3R 2017 community challenge.

Authors:  Jocelyn Sunseri; Jonathan E King; Paul G Francoeur; David Ryan Koes
Journal:  J Comput Aided Mol Des       Date:  2018-07-10       Impact factor: 3.686

Review 10.  Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges.

Authors:  Isabella A Guedes; Felipe S S Pereira; Laurent E Dardenne
Journal:  Front Pharmacol       Date:  2018-09-24       Impact factor: 5.810
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