Frank Dimaio (Frank DiMaio, F DiMaio)

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 50

Top Topics

Protein Protein

Saccharomyces Cerevisiae

Top Venues

Science (New York, N.Y.)

This page only lists publications with an associated author ORCID identifier.

Publications

Qinqin Zhao, Savannah Bertolli, Young-Jun Park, Yongjun Tan, Kevin J Cutler, Pooja Srinivas, Kyle L Asfahl, Citlali Fonesca-García, Larry A Gallagher, Yaqiao Li, Yaxi Wang, Devin Coleman-Derr, Frank Dimaio, Dapeng Zhang, S Brook Peterson, David J Veesler, Joseph D Mougous
Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore Pintilie, Stephen Burley, Jiri Cerny, Vincent Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael Prisant, Randy J Read, Jane S Richardson, Alexis Rohou, Bohdan Schneider, Benjamin Sellers, Chenghua Chao, Elizabeth Sourial, Chris Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel Moriarty, Andrew Muenks, Garib Murshudov, Robert Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar Pothula, Christopher Rowley, Daipayan Sarkar, Luisa Schäfer, Christopher Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea Vaiana, Sundeep Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen Berman, Wah Chiu
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Research square (2024)
Qinqin Zhao, Savannah Bertolli, Young-Jun Park, Yongjun Tan, Kevin J Cutler, Pooja Srinivas, Kyle L Asfahl, Citlali Fonesca-García, Larry A Gallagher, Yaqiao Li, Yaxi Wang, Devin Coleman-Derr, Frank Dimaio, Dapeng Zhang, S Brook Peterson, David J Veesler, Joseph D Mougous
Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 629 (8010) (2024)
Qinqin Zhao, Savannah Bertolli, Young-Jun Park, Yongjun Tan, Kevin J Cutler, Pooja Srinivas, Kyle L Asfahl, Citlali Fonesca-García, Larry A Gallagher, Yaqiao Li, Yaxi Wang, Devin Coleman-Derr, Frank Dimaio, Dapeng Zhang, S Brook Peterson, David J Veesler, Joseph D Mougous
Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature (2024)
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet, Gyu Rie Lee, Felix S Morey-Burrows, Ivan Anishchenko, Ian R Humphreys, Ryan McHugh, Dionne K Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, Christopher Neil Hunter, Alex Kang, Evans Brackenbrough, Asim K Bera, Minkyung Baek, Frank Dimaio, Julien S Baker
Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science (New York, N.Y.) 384 (6693) (2024)
Guangfeng Zhou, Domnita-Valeria Rusnac, Hahnbeom Park, Daniele Canzani, Hai Minh Nguyen, Lance J Stewart, Matthew F Bush, Phuong Tran Nguyen, Heike Wulff, Vladimir Yarov-Yarovoy, Ning Zheng, Frank Dimaio
An artificial intelligence accelerated virtual screening platform for drug discovery. Nature communications 15 (1) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature methods 21 (7) (2024)
Qinqin Zhao, Savannah Bertolli, Young-Jun Park, Yongjun Tan, Kevin J Cutler, Pooja Srinivas, Kyle L Asfahl, Citlali Fonesca-García, Larry A Gallagher, Yaqiao Li, Yaxi Wang, Devin Coleman-Derr, Frank Dimaio, Dapeng Zhang, S Brook Peterson, David J Veesler, Joseph D Mougous
Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 629 (8010) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Research square (2024)
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet, Gyu Rie Lee, Felix S Morey-Burrows, Ivan Anishchenko, Ian R Humphreys, Ryan McHugh, Dionne K Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, Christopher Neil Hunter, Alex Kang, Evans Brackenbrough, Asim K Bera, Minkyung Baek, Frank Dimaio, Julien S Baker
Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science (New York, N.Y.) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature methods 21 (7) (2024)
Qinqin Zhao, Savannah Bertolli, Young-Jun Park, Yongjun Tan, Kevin J Cutler, Pooja Srinivas, Kyle L Asfahl, Citlali Fonesca-García, Larry A Gallagher, Yaqiao Li, Yaxi Wang, Devin Coleman-Derr, Frank Dimaio, Dapeng Zhang, S Brook Peterson, David J Veesler, Joseph D Mougous
Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 629 (8010) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature methods (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Research square (2024)
Qinqin Zhao, Savannah Bertolli, Young-Jun Park, Yongjun Tan, Kevin J Cutler, Pooja Srinivas, Kyle L Asfahl, Citlali Fonesca-García, Larry A Gallagher, Yaqiao Li, Yaxi Wang, Devin Coleman-Derr, Frank Dimaio, Dapeng Zhang, S Brook Peterson, David J Veesler, Joseph D Mougous
Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 629 (8010) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore Pintilie, Stephen Burley, Jiri Cerny, Vincent Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael Prisant, Randy J Read, Jane S Richardson, Alexis Rohou, Bohdan Schneider, Benjamin Sellers, Chenghua Chao, Elizabeth Sourial, Chris Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel Moriarty, Andrew Muenks, Garib Murshudov, Robert Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar Pothula, Christopher Rowley, Daipayan Sarkar, Luisa Schäfer, Christopher Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea Vaiana, Sundeep Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen Berman, Wah Chiu
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Research square (2024)
Qinqin Zhao, Savannah Bertolli, Young-Jun Park, Yongjun Tan, Kevin J Cutler, Pooja Srinivas, Kyle L Asfahl, Citlali Fonesca-García, Larry A Gallagher, Yaqiao Li, Yaxi Wang, Devin Coleman-Derr, Frank Dimaio, Dapeng Zhang, S Brook Peterson, David J Veesler, Joseph D Mougous
Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 629 (8010) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature methods 21 (7) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Research square (2024)
Qinqin Zhao, Savannah Bertolli, Young-Jun Park, Yongjun Tan, Kevin J Cutler, Pooja Srinivas, Kyle L Asfahl, Citlali Fonesca-García, Larry A Gallagher, Yaqiao Li, Yaxi Wang, Devin Coleman-Derr, Frank Dimaio, Dapeng Zhang, S Brook Peterson, David J Veesler, Joseph D Mougous
Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 629 (8010) (2024)
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet, Gyu Rie Lee, Felix S Morey-Burrows, Ivan Anishchenko, Ian R Humphreys, Ryan McHugh, Dionne K Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, Christopher Neil Hunter, Alex Kang, Evans Brackenbrough, Asim K Bera, Minkyung Baek, Frank Dimaio, Julien S Baker
Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science (New York, N.Y.) 384 (6693) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature methods (2024)
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet, Gyu Rie Lee, Felix S Morey-Burrows, Ivan Anishchenko, Ian R Humphreys, Ryan McHugh, Dionne K Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, Christopher Neil Hunter, Alex Kang, Evans Brackenbrough, Asim K Bera, Minkyung Baek, Frank Dimaio, Julien S Baker
Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science (New York, N.Y.) 384 (6693) (2024)
Stephen A Rettie, Katelyn V Campbell, Asim K Bera, Alex Kang, Simon Kozlov, Joshmyn De La Cruz, Victor Adebomi, Guangfeng Zhou, Frank Dimaio, Sergey Ovchinnikov, Gaurav Bhardwaj
Cyclic peptide structure prediction and design using AlphaFold. bioRxiv : the preprint server for biology (2023)
Minkyung Baek, Ryan McHugh, David Baker, Hanlun Jiang, Julien S Baker, Frank Dimaio
Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA. Nature methods (2023)
Stephen A Rettie, Katelyn V Campbell, Asim K Bera, Alex Kang, Simon Kozlov, Joshmyn De La Cruz, Victor Adebomi, Guangfeng Zhou, Frank Dimaio, Sergey Ovchinnikov, Gaurav Bhardwaj
Cyclic peptide structure prediction and design using AlphaFold. bioRxiv : the preprint server for biology (2023)
Min Zhang, Anna Jungblut, Franziska Kunert, Luis Hauptmann, Thomas Hoffmann, Olga Kolesnikova, Felix J Metzner, Manuela Moldt, Felix Weis, Frank Dimaio, Karl-Peter Hopfner, Sebastian Eustermann
Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling. Science (New York, N.Y.) (2023)
Stephen A Rettie, Katelyn V Campbell, Asim K Bera, Alex Kang, Simon Kozlov, Joshmyn De La Cruz, Victor Adebomi, Guangfeng Zhou, Frank Dimaio, Sergey Ovchinnikov, Gaurav Bhardwaj
Cyclic peptide structure prediction and design using AlphaFold. bioRxiv : the preprint server for biology (2023)
Zhaoqian Wang, Moushimi Amaya, Amin Addetia, Ha V Dang, Gabriella Reggiano, Lianying Yan, Andrew C Hickey, Frank Dimaio, Christopher C Broder, David J Veesler
Architecture and antigenicity of the Nipah virus attachment glycoprotein. Science (New York, N.Y.) 375 (6587) (2022)
Basile I M Wicky, Lukas F Milles, Alexis Courbet, Robert J Ragotte, Justas Dauparas, E Kinfu, S Tipps, Ryan D Kibler, Minkyung Baek, Frank Dimaio, Xinting Li, Lauren Carter, Alex Kang, Hannah Nguyen, Asim K Bera, Julien S Baker
Hallucinating symmetric protein assemblies. Science (New York, N.Y.) 378 (6615) (2022)
Jue Wang, Sidney Lisanza, David C Juergens, Doug K Tischer, Joseph L Watson, Karla M Castro, Robert J Ragotte, Amijai Saragovi, Lukas F Milles, Minkyung Baek, David Baker, Wei Yang, Derrick R Hicks, Marc Expòsit, Thomas Schlichthaerle, Jung-Ho Chun, Justas Dauparas, Nathaniel R Bennett, Basile I M Wicky, Andrew Muenks, Frank Dimaio, Bruno E Correia, Sergey Ovchinnikov, Julien S Baker
Scaffolding protein functional sites using deep learning. Science (New York, N.Y.) 377 (6604) (2022)
Manoj K Rathinaswamy, Udit Dalwadi, Kaelin D Fleming, Carson Adams, Jordan T B Stariha, Els Pardon, Minkyung Baek, Oscar Vadas, Frank Dimaio, Jan Steyaert, Scott D Hansen, Calvin K Yip, John E Burke
Structure of the phosphoinositide 3-kinase (PI3K) p110γ-p101 complex reveals molecular mechanism of GPCR activation. Science advances 7 (35) (2021)
Minkyung Baek, Frank Dimaio, David Baker, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Nick V Grishin, Lisa N Kinch, R Dustin Schaeffer, Claudia Millán, Hahnbeom Park, Carson Adams, Caleb R Glassman, Andy DeGiovanni, Jose Henrique Pereira, Andria V Rodrigues, Alberdina A van Dijk, Ana C Ebrecht, Diederik Johannes Opperman, Theo Sagmeister, Christoph Buhlheller, Tea Pavkov-Keller, Manoj K Rathinaswamy, Udit Dalwadi, Calvin K Yip, John E Burke, K Christopher Garcia, Nick V Grishin, Paul D Adams, Randy J Read, Julien S Baker
Accurate prediction of protein structures and interactions using a three-track neural network. Science (New York, N.Y.) 373 (6557) (2021)
Cassie M Bryan, Gabriel J Rocklin, Matthew J Bick, Alex Ford, Sonia S Majri-Morrison, Ashley V Kroll, Chad J Miller, Lauren Carter, Inna Goreshnik, Alex Kang, Frank Dimaio, Kristin V Tarbell, Julien S Baker
Computational design of a synthetic PD-1 agonist. Proceedings of the National Academy of Sciences of the United States of America 118 (29) (2021)
Jesse M Hansen, Avital Horowitz, Eric M Lynch, Daniel P Farrell, Joel Quispe, Frank Dimaio, Justin M Kollman
Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation. eLife 10 (2021)
Hahnbeom Park, Guangfeng Zhou, Minkyung Baek, David Baker, Frank Dimaio
Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein-Ligand Docking. Journal of chemical theory and computation 17 (3) (2021)
Patrick R Stoddard, Eric M Lynch, Daniel P Farrell, Annie M Dosey, Frank Dimaio, Tom A Williams, Justin M Kollman, Andrew W Murray, Ethan C Garner
Polymerization in the actin ATPase clan regulates hexokinase activity in yeast. Science (New York, N.Y.) 367 (6481) (2020)
Daniel P Farrell, Ivan Anishchenko, Shabih Shakeel, Anna Lauko, Lori A Passmore, David Baker, Frank Dimaio
Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM. IUCrJ 7 (Pt 5) (2020)
Zibo Chen, Matthew C Johnson, Jiajun Chen, Matthew J Bick, Scott E Boyken, Baihan Lin, James J De Yoreo, Justin M Kollman, David Baker, Frank Dimaio
Self-Assembling 2D Arrays with de Novo Protein Building Blocks. Journal of the American Chemical Society 141 (22) (2019)
Shoukai Kang, Kristian Davidsen, Luis Gomez-Castillo, Huayi Jiang, Xiaonan Fu, Zengpeng Li, Yu Liang, Molly Jahn, Mahmoud Moussa, Frank Dimaio, Liangcai Gu
COMBINES-CID: An Efficient Method for De Novo Engineering of Highly Specific Chemically Induced Protein Dimerization Systems. Journal of the American Chemical Society 141 (28) (2019)
Elizabeth H Kellogg, Nisreen M A Hejab, Simon Poepsel, Kenneth H Downing, Frank Dimaio, Eva Nogales
Near-atomic model of microtubule-tau interactions. Science (New York, N.Y.) 360 (6394) (2018)
Hahnbeom Park, Sergey Ovchinnikov, David E Kim, Frank Dimaio, Julien S Baker
Protein homology model refinement by large-scale energy optimization. Proceedings of the National Academy of Sciences of the United States of America 115 (12) (2018)
Peilong Lu, Duyoung Min, Frank Dimaio, Kathy Y Wei, Michael D Vahey, Scott E Boyken, Zibo Chen, Jorge A Fallas, George Ueda, William Sheffler, Vikram Khipple Mulligan, Wenqing Xu, James U Bowie, Julien S Baker
Accurate computational design of multipass transmembrane proteins. Science (New York, N.Y.) 359 (6379) (2018)
Andrew J Borst, Connor E Weidle, Matthew D Gray, Brandon Frenz, Joost Snijder, M Gordon Joyce, Ivelin S Georgiev, Guillaume Be Stewart-Jones, Peter D Kwong, Andrew T McGuire, Frank Dimaio, Leonidas Stamatatos, Marie Pancera, David J Veesler
Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core. eLife 7 (2018)
Gülsima D Usluer, Frank Dimaio, Shun Kai Yang, Jesse M Hansen, Jessica K Polka, R Dyche Mullins, Justin M Kollman
Cryo-EM structure of the bacterial actin AlfA reveals unique assembly and ATP-binding interactions and the absence of a conserved subdomain. Proceedings of the National Academy of Sciences of the United States of America 115 (13) (2018)
Sergey Ovchinnikov, Hahnbeom Park, David E Kim, Frank Dimaio, David Baker
Protein structure prediction using Rosetta in CASP12. Proteins (2017)
Peter M Kasson, Frank Dimaio, Xiong Yu, Soizick Lucas-Staat, Mart Krupovic, Stefan Schouten, David Prangishvili, Edward H Egelman
Model for a novel membrane envelope in a filamentous hyperthermophilic virus. eLife 6 (2017)
Hahnbeom Park, David E Kim, Sergey Ovchinnikov, David Baker, Frank Dimaio
Automatic structure prediction of oligomeric assemblies using Robetta in CASP12. Proteins (2017)
Gregory M Martin, Balamurugan Kandasamy, Frank Dimaio, Craig Yoshioka, Show-Ling Shyng
Anti-diabetic drug binding site in a mammalian KATP channel revealed by Cryo-EM. eLife 6 (2017)
Ray Yu-Ruei Wang, Yifan Song, Benjamin A Barad, Yifan Cheng, Brian K Shoichet, Frank Dimaio
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5 (2016)