Molecular graph convolutions: moving beyond fingerprints
Kearnes, Steven, McCloskey, Kevin, Berndl, Marc, Pande, Vijay, Riley, Patrick
Published in Journal of computer-aided molecular design (01.08.2016)
Published in Journal of computer-aided molecular design (01.08.2016)
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Guidelines for the analysis of free energy calculations
Klimovich, Pavel V., Shirts, Michael R., Mobley, David L.
Published in Journal of computer-aided molecular design (01.05.2015)
Published in Journal of computer-aided molecular design (01.05.2015)
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FreeSolv: a database of experimental and calculated hydration free energies, with input files
Mobley, David L., Guthrie, J. Peter
Published in Journal of computer-aided molecular design (01.07.2014)
Published in Journal of computer-aided molecular design (01.07.2014)
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Journal Article
TargetNet: a web service for predicting potential drug–target interaction profiling via multi-target SAR models
Yao, Zhi-Jiang, Dong, Jie, Che, Yu-Jing, Zhu, Min-Feng, Wen, Ming, Wang, Ning-Ning, Wang, Shan, Lu, Ai-Ping, Cao, Dong-Sheng
Published in Journal of computer-aided molecular design (01.05.2016)
Published in Journal of computer-aided molecular design (01.05.2016)
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Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
Shirts, Michael R., Klein, Christoph, Swails, Jason M., Yin, Jian, Gilson, Michael K., Mobley, David L., Case, David A., Zhong, Ellen D.
Published in Journal of computer-aided molecular design (01.01.2017)
Published in Journal of computer-aided molecular design (01.01.2017)
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The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations
Rizzi, Andrea, Jensen, Travis, Slochower, David R., Aldeghi, Matteo, Gapsys, Vytautas, Ntekoumes, Dimitris, Bosisio, Stefano, Papadourakis, Michail, Henriksen, Niel M., de Groot, Bert L., Cournia, Zoe, Dickson, Alex, Michel, Julien, Gilson, Michael K., Shirts, Michael R., Mobley, David L., Chodera, John D.
Published in Journal of computer-aided molecular design (01.05.2020)
Published in Journal of computer-aided molecular design (01.05.2020)
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D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
Gaieb, Zied, Liu, Shuai, Gathiaka, Symon, Chiu, Michael, Yang, Huanwang, Shao, Chenghua, Feher, Victoria A., Walters, W. Patrick, Kuhn, Bernd, Rudolph, Markus G., Burley, Stephen K., Gilson, Michael K., Amaro, Rommie E.
Published in Journal of computer-aided molecular design (01.01.2018)
Published in Journal of computer-aided molecular design (01.01.2018)
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Estimation of the size of drug-like chemical space based on GDB-17 data
Polishchuk, P. G., Madzhidov, T. I., Varnek, A.
Published in Journal of computer-aided molecular design (01.08.2013)
Published in Journal of computer-aided molecular design (01.08.2013)
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Journal Article
D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings
Gaieb, Zied, Parks, Conor D., Chiu, Michael, Yang, Huanwang, Shao, Chenghua, Walters, W. Patrick, Lambert, Millard H., Nevins, Neysa, Bembenek, Scott D., Ameriks, Michael K., Mirzadegan, Tara, Burley, Stephen K., Amaro, Rommie E., Gilson, Michael K.
Published in Journal of computer-aided molecular design (01.01.2019)
Published in Journal of computer-aided molecular design (01.01.2019)
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Journal Article
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
Parks, Conor D., Gaieb, Zied, Chiu, Michael, Yang, Huanwang, Shao, Chenghua, Walters, W. Patrick, Jansen, Johanna M., McGaughey, Georgia, Lewis, Richard A., Bembenek, Scott D., Ameriks, Michael K., Mirzadegan, Tara, Burley, Stephen K., Amaro, Rommie E., Gilson, Michael K.
Published in Journal of computer-aided molecular design (01.02.2020)
Published in Journal of computer-aided molecular design (01.02.2020)
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Journal Article
Overview of the SAMPL6 host–guest binding affinity prediction challenge
Rizzi, Andrea, Murkli, Steven, McNeill, John N., Yao, Wei, Sullivan, Matthew, Gilson, Michael K., Chiu, Michael W., Isaacs, Lyle, Gibb, Bruce C., Mobley, David L., Chodera, John D.
Published in Journal of computer-aided molecular design (01.10.2018)
Published in Journal of computer-aided molecular design (01.10.2018)
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Journal Article
Ligand docking and binding site analysis with PyMOL and Autodock/Vina
Seeliger, Daniel, de Groot, Bert L.
Published in Journal of computer-aided molecular design (01.05.2010)
Published in Journal of computer-aided molecular design (01.05.2010)
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Journal Article
D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
Gathiaka, Symon, Liu, Shuai, Chiu, Michael, Yang, Huanwang, Stuckey, Jeanne A., Kang, You Na, Delproposto, Jim, Kubish, Ginger, Dunbar, James B., Carlson, Heather A., Burley, Stephen K., Walters, W. Patrick, Amaro, Rommie E., Feher, Victoria A., Gilson, Michael K.
Published in Journal of computer-aided molecular design (01.09.2016)
Published in Journal of computer-aided molecular design (01.09.2016)
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Journal Article
Artificial intelligence in chemistry and drug design
Brown, Nathan, Ertl, Peter, Lewis, Richard, Luksch, Torsten, Reker, Daniel, Schneider, Nadine
Published in Journal of computer-aided molecular design (01.07.2020)
Published in Journal of computer-aided molecular design (01.07.2020)
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