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Journal Articles
- 2023
[j18]Xuezhi Xie, Pedro A. Valiente
, Philip M. Kim:
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures. Bioinform. 39(1) (2023)- [j17]Jin Sub Lee, Jisun Kim, Philip M. Kim:
Score-based generative modeling for de novo protein design. Nat. Comput. Sci. 3(5): 382-392 (2023) - [j16]Mohammad Hassan Khatami, Udson C. Mendes, Nathan Wiebe, Philip M. Kim:
Gate-based quantum computing for protein design. PLoS Comput. Biol. 19(4) (2023) - 2022
- [j15]Pedro A. Valiente, Satra Nim, Jinah Lee, Seungtaek Kim, Philip M. Kim:
Targeting the Receptor-Binding Motif of SARS-CoV-2 with D-Peptides Mimicking the ACE2 Binding Helix: Lessons for Inhibiting Omicron and Future Variants of Concern. J. Chem. Inf. Model. 62(15): 3618-3626 (2022) - 2021
- [j14]Osama Abdin, Philip M. Kim:
Rapid protein model refinement by deep learning. Nat. Comput. Sci. 1(7): 456-457 (2021) - 2017
- [j13]Mark G. F. Sun, Philip M. Kim:
Data driven flexible backbone protein design. PLoS Comput. Biol. 13(8) (2017) - 2016
- [j12]Recep Colak, TaeHyung Kim, Hilal Kazan, Yoomi Oh, Miguel Cruz, Adan Valladares-Salgado, Jesus Peralta, Jorge Escobedo, Esteban J. Parra, Philip M. Kim, Anna Goldenberg:
JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis. Bioinform. 32(2): 203-210 (2016) - [j11]Daniel K. Witvliet, Alexey Strokach, Andrés Felipe Giraldo-Forero, Joan Teyra, Recep Colak, Philip M. Kim:
ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity. Bioinform. 32(10): 1589-1591 (2016) - [j10]Jouhyun Jeon, Roland Arnold, Fateh Singh, Joan Teyra, Tatjana Braun, Philip M. Kim:
PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies. BMC Bioinform. 17: 150 (2016) - 2013
- [j9]Recep Colak, TaeHyung Kim, Magali Michaut, Mark G. F. Sun, Manuel Irimia, Jeremy Bellay, Chad L. Myers, Benjamin J. Blencowe, Philip M. Kim:
Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing. PLoS Comput. Biol. 9(4) (2013) - 2012
- [j8]Mark G. F. Sun, Martin Sikora, Michael Costanzo, Charles Boone, Philip M. Kim:
Network Evolution: Rewiring and Signatures of Conservation in Signaling. PLoS Comput. Biol. 8(3) (2012) - 2011
- [j7]Chong Shou, Nitin Bhardwaj, Hugo Y. K. Lam, Koon-Kiu Yan, Philip M. Kim, Michael Snyder, Mark B. Gerstein:
Measuring the Evolutionary Rewiring of Biological Networks. PLoS Comput. Biol. 7(1) (2011) - 2010
- [j6]Hugo Y. K. Lam, Philip M. Kim, Janine Mok, Raffi Tonikian, Sachdev S. Sidhu, Benjamin E. Turk, Michael Snyder, Mark B. Gerstein:
MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains. BMC Bioinform. 11: 243 (2010) - 2009
- [j5]Kevin Y. Yip, Philip M. Kim, Drew McDermott, Mark Gerstein:
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. BMC Bioinform. 10 (2009) - 2008
- [j4]Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew McDermott, Mark Gerstein:
An integrated system for studying residue coevolution in proteins. Bioinform. 24(2): 290-292 (2008) - 2007
- [j3]Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein:
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinform. 23(8): 1048 (2007) - [j2]Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein:
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics. PLoS Comput. Biol. 3(4) (2007) - 2006
- [j1]Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein:
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinform. 22(23): 2968-2970 (2006)
Informal and Other Publications
- 2021
- [i1]Alexey Strokach, Philip M. Kim:
Deep Generative Modeling for Protein Design. CoRR abs/2109.13754 (2021)
Coauthor Index
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