We all start somewhere and the first competition (2012 Competition) organized by the Teach-Discover-Teach Initiative (TDTi) was announced at the San Diego ACS meeting (spring 2012; right below this section). The winning projects and awards were presented at the New Orleans ACS meeting (spring 2013; further down the page).
We are excited about the computational chemistry community's embrace of our first competition. The ability to provide excellent teaching materials (tutorials, workflows and protocols) based on drug discovery research that marries computational and bench experiments in the discovery of new compounds to battle neglected diseases is the main focus of TDTi. The projects presented below are truly the power of collaborative efforts.
We are excited about the computational chemistry community's embrace of our first competition. The ability to provide excellent teaching materials (tutorials, workflows and protocols) based on drug discovery research that marries computational and bench experiments in the discovery of new compounds to battle neglected diseases is the main focus of TDTi. The projects presented below are truly the power of collaborative efforts.
Initiative launched on March 25, 2012 (San Diego, California; Spring 2012 ACS Meeting)
Teach-Discover-Treat: A COMP initiative to provide high quality computational chemistry tutorials that impact education and drug discovery for neglected diseases
Johanna M Jansen, Yufeng J Tseng and Rommie E Amaro.
Distributed Drug Discovery (D3): Enabling computational and synthetic chemists to work together to educate students while discovering drug-leads for neglected diseases
William L Scott and Martin J O'Donnell
Open source QSAR models with IP-sensitive SAR data: POCs in secure online environments for collaborative drug discovery showing CDK with SMARTS keys are statistically equivalent (κ = .43)...and open call for all industry and academic projects
Barry A. Bunin and Sean Ekins
It doesn't have to be a one-way street: Open-source software for drug discovery from big pharma
Gregory Landrum, Yiqun Cao and Andrew Palmer
Collaborative drug discovery and structural genomics: Positive impact for neglected disease research
Aled Edwards, Raymond Hui, James Sacchettini, Amy Wernimont, Peter Brown.
Teach-Discover-Treat: A COMP initiative to provide high quality computational chemistry tutorials that impact education and drug discovery for neglected diseases
Johanna M Jansen, Yufeng J Tseng and Rommie E Amaro.
Distributed Drug Discovery (D3): Enabling computational and synthetic chemists to work together to educate students while discovering drug-leads for neglected diseases
William L Scott and Martin J O'Donnell
Open source QSAR models with IP-sensitive SAR data: POCs in secure online environments for collaborative drug discovery showing CDK with SMARTS keys are statistically equivalent (κ = .43)...and open call for all industry and academic projects
Barry A. Bunin and Sean Ekins
It doesn't have to be a one-way street: Open-source software for drug discovery from big pharma
Gregory Landrum, Yiqun Cao and Andrew Palmer
Collaborative drug discovery and structural genomics: Positive impact for neglected disease research
Aled Edwards, Raymond Hui, James Sacchettini, Amy Wernimont, Peter Brown.
Challenge Files
Challenge 1: Workflow to analyze HTS data & build models for further hit finding
Challenge 2: Structure-based design workflow, new chemotypes
Challenge 3: Structure-based design workflow, medicinal chemistry strategy
Challenge 4: Call for innovative drug discovery workflows
Challenge 1: Workflow to analyze HTS data & build models for further hit finding
Challenge 2: Structure-based design workflow, new chemotypes
Challenge 3: Structure-based design workflow, medicinal chemistry strategy
Challenge 4: Call for innovative drug discovery workflows
2012 Challenge Winners
Overall winner, addressing challenge 2
TDT 2012 Grand Champion: 3D-QSAR-boosted SBVS
Paolo Tosco – Department of Drug Science and Technology, Torino (Italy)
First runner-up, addressing challenge 2
Cresset Award: Teaching molecular interactions with online interactive pharmacophore modeling
David Ryan Koes and Carlos J. Camacho – Department of Computational and Systems Biology, University of Pittsburgh
Second runner-up, addressing challenge 4
OpenEye Award: Public domain chemical databases for malaria drug discovery
George Nicola, Tiqing Liu, Michael Gilson – University of California, San Diego
Third runner-up, addressing challenge 3
KNIME Award: Structure-based drug design for trypanosomal PDEB1
Khaled M. Elokely, Robert J. Doerksen – University of Mississippi School of Pharmacy
Overall winner, addressing challenge 2
TDT 2012 Grand Champion: 3D-QSAR-boosted SBVS
Paolo Tosco – Department of Drug Science and Technology, Torino (Italy)
First runner-up, addressing challenge 2
Cresset Award: Teaching molecular interactions with online interactive pharmacophore modeling
David Ryan Koes and Carlos J. Camacho – Department of Computational and Systems Biology, University of Pittsburgh
Second runner-up, addressing challenge 4
OpenEye Award: Public domain chemical databases for malaria drug discovery
George Nicola, Tiqing Liu, Michael Gilson – University of California, San Diego
Third runner-up, addressing challenge 3
KNIME Award: Structure-based drug design for trypanosomal PDEB1
Khaled M. Elokely, Robert J. Doerksen – University of Mississippi School of Pharmacy
Judging Criteria
The steering committee and judging panel greatly appreciate the contribution and efforts of all six groups who submitted tutorials and materials toward furthering both computational drug discovery and open science. The tutorials were rated on a scale of 1-10 for the following 4 criteria:
Scientific content
The steering committee and judging panel greatly appreciate the contribution and efforts of all six groups who submitted tutorials and materials toward furthering both computational drug discovery and open science. The tutorials were rated on a scale of 1-10 for the following 4 criteria:
Scientific content
- What is the quality of the underlying science?
- Is the tutorial relevant to drug discovery?
- Are the objectives of the tutorial clearly defined?
- Does the tutorial provide a logical workflow?
- Does the tutorial provide sufficient background?
- Will the tutorial stimulate interest in computational chemistry and molecular modeling?
- Does the tutorial provide a gateway to further research?
- Can the work be easily reproduced?
- Is all of the software readily available?
- Does the tutorial utilize commercial software?
- Does the tutorial require a complex installation?
Award Symposium Presentations (New Orleans, Louisiana; Spring 2013 ACS Meeting)
Judging the ACS Teach-Discover-Treat initiative: Lessons learned and directions for the future
W Patrick Walters
Structural plasticity of malarial dihydroorotate dehydrogenases demonstrated by X-ray structural analysis of inhibitor bound complexes
Xiaoyi Deng, Farah El Mazouni, Elizabeth J Goldsmith, Pradipsinh K Rathod and Margaret A Phillips
TDT 2012 Grand Champion: 3D-QSAR-boosted SBVS
Paolo Tosco
Cresset Award: Teaching molecular interactions with online interactive pharmacophore modeling
David R Koes and Carlos J Camacho
KNIME Award: Computational workflow for human African trypanosomiasis phosphodiesterase inhibitor identification
Khaled M Elokely and Robert J Doerksen
OpenEye Award: Public domain chemical databases for neglected disease drug discovery
George Nicola, Tiqing Liu and Michael Gilson
Judging the ACS Teach-Discover-Treat initiative: Lessons learned and directions for the future
W Patrick Walters
Structural plasticity of malarial dihydroorotate dehydrogenases demonstrated by X-ray structural analysis of inhibitor bound complexes
Xiaoyi Deng, Farah El Mazouni, Elizabeth J Goldsmith, Pradipsinh K Rathod and Margaret A Phillips
TDT 2012 Grand Champion: 3D-QSAR-boosted SBVS
Paolo Tosco
Cresset Award: Teaching molecular interactions with online interactive pharmacophore modeling
David R Koes and Carlos J Camacho
KNIME Award: Computational workflow for human African trypanosomiasis phosphodiesterase inhibitor identification
Khaled M Elokely and Robert J Doerksen
OpenEye Award: Public domain chemical databases for neglected disease drug discovery
George Nicola, Tiqing Liu and Michael Gilson