Philip M. Kim

23 papers Journal 23
YearRankTypeTitle / Venue / Authors
2025 J jnl
FlowPacker: protein side-chain packing with torsional flow matching.
Bioinform.
Jin Sub Lee, Philip M. Kim
2024 J jnl
Antibody-SGM, a Score-Based Generative Model for Antibody Heavy-Chain Design.
J. Chem. Inf. Model.
Xuezhi Xie, Pedro A. Valiente, Jin Sub Lee, Jisun Kim, Philip M. Kim
2024 J jnl
Direct conformational sampling from peptide energy landscapes through hypernetwork-conditioned diffusion.
Nat. Mac. Intell.
Osama Abdin, Philip M. Kim
2024 J jnl
EuDockScore: Euclidean graph neural networks for scoring protein-protein interfaces.
Bioinform.
Matthew McFee, Jisun Kim, Philip M. Kim
2023 J jnl
Gate-based quantum computing for protein design.
PLoS Comput. Biol.
Mohammad Hassan Khatami, Udson C. Mendes, Nathan Wiebe, Philip M. Kim
2023 J jnl
HelixGAN a deep-learning methodology for conditional
Bioinform.
Xuezhi Xie, Pedro A. Valiente, Philip M. Kim
2023 J jnl
Score-based generative modeling for de novo protein design.
Nat. Comput. Sci.
Jin Sub Lee, Jisun Kim, Philip M. Kim
2022 J jnl
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.
Pedro A. Valiente, Satra Nim, Jinah Lee, SeungTaek Kim, Philip M. Kim
2021 J jnl
Deep Generative Modeling for Protein Design.
CoRR
Alexey Strokach, Philip M. Kim
2021 J jnl
Rapid protein model refinement by deep learning.
Nat. Comput. Sci.
Osama Abdin, Philip M. Kim
2017 J jnl
Data driven flexible backbone protein design.
PLoS Comput. Biol.
Mark G. F. Sun, Philip M. Kim
2016 J jnl
ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity.
Bioinform.
Daniel K. Witvliet, Alexey Strokach, Andrés Felipe Giraldo-Forero, Joan Teyra, Recep Colak, Philip M. Kim
2016 J jnl
JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis.
Bioinform.
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
2016 J jnl
PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies.
BMC Bioinform.
Jouhyun Jeon, Roland Arnold, Fateh Singh, Joan Teyra, Tatjana Braun, Philip M. Kim
2013 J jnl
Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing.
PLoS Comput. Biol.
Recep Colak, TaeHyung Kim, Magali Michaut, Mark G. F. Sun, Manuel Irimia, Jeremy Bellay, Chad L. Myers, Benjamin J. Blencowe, Philip M. Kim
2012 J jnl
Network Evolution: Rewiring and Signatures of Conservation in Signaling.
PLoS Comput. Biol.
Mark G. F. Sun, Martin Sikora, Michael Costanzo, Charles Boone, Philip M. Kim
2011 J jnl
Measuring the Evolutionary Rewiring of Biological Networks.
PLoS Comput. Biol.
Chong Shou, Nitin Bhardwaj, Hugo Y. K. Lam, Koon-Kiu Yan, Philip M. Kim, Michael Snyder, Mark B. Gerstein
2010 J jnl
MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains.
BMC Bioinform.
Hugo Y. K. Lam, Philip M. Kim, Janine Mok, Raffi Tonikian, Sachdev S. Sidhu, Benjamin E. Turk, Michael Snyder, Mark B. Gerstein
2009 J jnl
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.
BMC Bioinform.
Kevin Y. Yip, Philip M. Kim, Drew McDermott, Mark Gerstein
2008 J jnl
An integrated system for studying residue coevolution in proteins.
Bioinform.
Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew McDermott, Mark Gerstein
2007 J jnl
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics.
PLoS Comput. Biol.
Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein
2007 J jnl
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
Bioinform.
Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein
2006 J jnl
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
Bioinform.
Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein