Rosen Center for Advanced Computing
Purdue Logo
Quick links
Helpful links

Charles W Christoffer

Charles William Christoffer's Profile Photo

Computational Life Sciences Lead

Education

  • Ph.D., Computer Science, Purdue University (2023)
    • Dissertation: "Flexible and Data-Driven Modeling of 3D Protein Complex Structures"
  • M.S., Computer Science, Purdue University (2018).
  • B.S., Computer Science & Applied Mathematics, Purdue University (2015).

Selected Presentations

  • Responding to NIH Requirements for Controlled-Access Data. 2025 NSF Cybersecurity Summit. Boulder, CO. Plenary session (October 21, 2025).

Selected Publications

  • Zicong Zhang, Jacob Verburgt, Yuki Kagaya, Charles Christoffer, & Daisuke Kihara, Learning with Privileged Knowledge Distillation for Improved Peptide-Protein Docking, ACS Omega, 10: 26684-26693, (2025)

  • Charles W. Christoffer, Tsukasa Nakamura, Xusi Han, Woong-Hee Shin, Genki Terashi, Lyman Monroe, Lukasz Kurgan, & Daisuke Kihara, Study of the Variability of the Native Protein Structure, Encyclopedia of Bioinformatics and Computational Biology 2nd Edition, 6: 107-122 (2025)

  • Charles Christoffer, Yuki Kagaya, Jacob Verburgt, Genki Terashi, Woong-Hee Shin, Anika Jain, Daipayan Sarkar, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Xiao Wang, Zicong Zhang, Yuanyuan Zhang, & Daisuke Kihara, Integrative Protein Assembly With LZerD and Deep Learning in CAPRI 47-55, Proteins, Online ahead of print (2025)

  • Charles Christoffer, Kannan Harini, Gupta Archit, & Daisuke Kihara, Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints, Journal of Molecular Biology, 436: 168486 (2024)

  • M.F. Lensink, ,,, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, ,,, Kihara D, ,,, & S.J. Wodak (113 authors), Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment, Proteins, 91: 1658-1683 (2023)

  • Kannan Harini, Charles Christoffer, M Michael Gromiha, & Daisuke Kihara, Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server, Methods in Molecular Biology, 2690: 355-373 (2023)

  • Hugo Schweke, ,,, Xiao Wang, Genki Terashi, Daipayan Sarkar, Charles Christoffer, Tunde Aderinwale, Jacob Verburgt, Daisuke Kihara, ,,, Emmanuel D. Levy & Shoshana J. Wodak (56 authors), Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study, Proteomics, 23: e2200323 (2023)

  • Jennifer J. Lee, Swetha Ramadesikan, Adrianna F. Black, Charles Christoffer, Andres F. Pacheco Pacheco, Sneha Subramanian, Claudia B. Hanna, Gillian Barth, Cynthia V. Stauffacher, Daisuke Kihara, & Ruben Claudio Aguilar, Heterogeneity in Lowe Syndrome: Mutations Affecting the Phosphatase Domain of OCRL1 Differ in Impact on Enzymatic Activity and Severity of Cellular Phenotypes, Biomolecules, 13: 615 (2023)

  • Charles Christoffer, & Daisuke Kihara, Modeling Protein-Nucleic Acid Complexes with Extremely Large Conformational Changes using Flex-LZerD, PROTEOMICS, 23: e2200322 (2023)

  • Charles Christoffer & Daisuke Kihara, Domain-Based Protein Docking with Extremely Large Conformational Changes, Journal of Molecular Biology, 434: 167820 (2022)

  • Tunde Aderinwale, Charles Christoffer, & Daisuke Kihara, RL-MLZerD: Multimeric Protein Docking Using Reinforcement Learning, Frontiers In Molecular Biosciences, 9: 969394 (2022)

  • Gagliardi L, Raffo A, Fugacci U, Biasotti S, Rocchia W, Huang H, Amor B, Fang Y, Yuanyuan Zhang, Xiao Wang, Charles Christoffer, Daisuke Kihara, Axenopoulos A, Mylonas S, & Daras P, SHREC 2022: Protein-ligand binding site recognition, Computers & Graphics, 107: 20-31 (2022)

  • Tunde Aderinwale, Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh, Yuki Kagaya, & Daisuke Kihara, Real-time structure search and structure classification for AlphaFold protein models, Communications Biology, 5: 316 (2022)

  • Florent Langenfeld, Tunde Aderinwale, Charles Christoffer, Woong-Hee Shin, Genki Terashi, Xiao Wang, Daisuke Kihara, Halim Benhabiles, Karim Hammoudi, Adnane Cabani, Feryal Windal, Mahmoud Melkemi, Ekpo Otu, Reyer Zwiggelaar, David Hunter, Yonghuai Liu, Léa Sirugue, Huu-Nghia H Nguyen, Tuan-Duy H Nguyen, Vinh-Thuyen Nguyen-Truong, Danh Le, Hai-Dang Nguyen, Minh-Triet Tran, & Matthieu Montès, Surface-based protein domains retrieval methods from a SHREC2021 challenge, Journal of Molecular Graphics & Modelling, 111: 108103 (2022)

  • Kryshtafovych A., Moult J.,, & CASP-COVID paricipants (including Charles Christoffer, Genki Terashi, Daipayan Sarkar, & Daisuke Kihara), Modeling SARS-CoV-2 proteins in the CASP-commons experiment, Proteins, 89: 1987-1996 (2021)

  • M.F. Lensink, ,, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, ,, & S.J. Wodak (108 authors), Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment, Proteins, 89: 1800-1823 (2021)

  • Charles Christoffer, Vijay Bharadwaj, Ryan Luu, & Daisuke Kihara, LZerD protein-protein docking webserver enhanced with de novo structure prediction, Frontiers in Molecular Biosciences, 8: 724947 (2021)

  • A. Raffo, U. Fugacci, S. Biasotti, W. Rocchia, Y. Liu, E. Otu, R. Zwiggelaar, D. Hunter, E.I. Zacharaki, E. Psatha, D. Laskos, G. Arvanitis, K. Moustakas, Tunde Aderinwale, Charles Christoffer, Woong-Hee Shin, Daisuke Kihara, A. Giachetti, H.-N. Nguyen, T.-D. Nguyen, V.-T. Nguyen-Truong, D. Le-Thanh, H.-D. Ngyuen, & M.-T. Tran, SHREC 2021: Retrieval and classification of protein surfaces equipped with physical and chemical properties, Computers & Graphics, 99: 1-21 (2021)

  • Charles Christoffer, Siyang Chen, Vijay Bharadwaj, Tunde Aderinwale, Vidhur Kumar, Matin Hormati, & Daisuke Kihara, LZerD webserver for pairwise and multiple protein-protein docking, Nucleic Acid Research, 49: W359-W365 (2021)

  • Anwesha Sanyal, Erica A. Zbornik, Ben G. Watson, Charles Christoffer, Jia Ma, Daisuke Kihara, & Seema Mattoo, Kinetic and structural parameters governing Fic-mediated adenylylation/AMPylation of the Hsp70 chaperone, BiP/GRP78, Cell Stress & Chaperones, 26: 639-656 (2021)

  • Xusi Han#, Genki Terashi#, Charles Christoffer, Siyang Chen, & Daisuke Kihara (# co-first authors), VESPER: global and local cryo-EM map alignment using local density vectors, Nature Communications, 12: 2090 (2021)

  • Aashish Jain, Genki Terashi, Yuki Kagaya, Sai Raghavendra Venkata Maddhuri Subramaniya, Charles Christoffer, & Daisuke Kihara, Analyzing effect of quadraple multiple sequence alignments on deep learning based protein inter-residue distance prediction, Scientific Reports, 11: 7574 (2021)

  • Daisuke Kihara, Charles Christoffer, Siyang Chen, Vijay Bharadwaj, & Tunde Aderinwale, LZerD: Software for protein docking modeling, Jikken Igaku (Experimental Medicine), 38: 3271-3276 (in Japanese) (2020)

  • F. Langenfeld, Y. Peng, Y.-K. Lai, P.L. Rosin, Tunde Aderinwale, Genki Terashi, Charles Christoffer, Daisuke Kihara, H. Benhabiles, K. Hammoudi, A. Cabani, F. Windal, M. Melkemi, A. Giachetti, S. Mylonas, A. Axenopoulos, P. Daras, E. Otu, R. Zwiggelaar, D. Hunter, Y. Liu, & M. Montes, SHREC2020: Multi-domain protein shape retrieval challenge, Computers & Graphics, 91: 189-198 (2020)

  • Charles Christoffer & Daisuke Kihara, IDP-LZerD: Software for modeling disordered protein interactions, Methods Mol. Biol., 2165: 231-244 (2020)

  • Tunde Aderinwale, Charles W. Christoffer, Daipayan Sarkar, Eman Alnabati, & Daisuke Kihara, Computational structure modeling for diverse categories of macromolecular interactions, Curr. Opin. Struct. Biol., 64: 1-8 (2020)

  • Genki Terashi, Charles Christoffer, & Daisuke Kihara, Path-LZerD: Predicting assembly order of multimeric protein complexes, Methods in Mol. Biol., 2074: 95-112 (2020)

  • Xiao Wang, Genki Terashi, Charles Christoffer, Mengmeng Zhu, & Daisuke Kihara, Protein docking model evaluation by 3D convolutional neural networks, Bioinformatics, 36: 2113-2118 (2020)

  • Charles Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Lenna Peterson, Jacob Verburgt, & Daisuke Kihara, Performance and enhancement of the LZerD protein asssembly pipeline in CAPRI 38-46, Proteins: Structure, Function, and Bioinformatics, 88: 948-961 (2020)

  • Mark F. Lensink,,, Charles Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Daisuke Kihara ,,,, & Shoshana J Wodak, Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment, Proteins: Structure, Function, and Bioinformatics, 87: 1200-1221 (2019)

  • Xusi Han, Atilla Sit, Charles Christoffer, Siyang Chen, & Daisuke Kihara, A global map of the protein shape universe, PloS Computational Biology, 15(4):e1006969 (2019)

  • Charles W. Christoffer & Daisuke Kihara, Modeling protein-protein interactions with intrinsically disordered proteins, Intrinsically Disordered Proteins, Nicola Salvi (ed.), pp. 189-206 Elsevier (2019)

  • Xusi Han, Woong-Hee Shin, Charles W. Christoffer, Genki Terashi, Lyman Monroe, & Daisuke Kihara, Study of the variability of the native protein structure, Encyclopedia of Bioinformatics and Computational Biology, 3: 606-619 (2019)

  • Lenna X. Peterson, Yoichiro Togawa, Juan Esquivel-Rodriguez, Genki Terashi, Charles Christoffer, Amitava Roy, Wooong-Hee Shin, & Daisuke Kihara, Modeling the assembly order of multimeric heteroprotein complexes, PLoS Comput. Biol., 14: e1005937 (2018)

  • Woong-Hee Shin*, Charles Christoffer*, & Daisuke Kihara (*co-first author), In silico structure-based approaches to discover protein-protein interaction targeting drugs, Methods, 131: 22-32 (2017)

  • Na Song, Daniela Craciun, Charles W. Christoffer, Xusi Han, Daisuke Kihara, Guillaume Levieux, Matthieu Montes, Hong Qin, Pranjal Sahu, Genki Terashi, & Haiguang Liu, SHREC'17 Track: Protein shape retrieval, Eurographics Workshop on 3D Object Retrieval, I. Pratikakis, F. Dupont, & M. Ovsjanikov (Eds.) (2017)

  • Lenna X. Peterson, Amitava Roy, Charles Christoffer, Genki Terashi, & Daisuke Kihara, Modeling disordered protein interactions from biophysical principles, PLoS Computational Biol., 13: e1005485 (2017)

  • Woong-Hee Shin, Charles Christoffer, Jibo Wang, & Daisuke Kihara, PL-PatchSurfer2: Improved local surface matching-based virtual screening method that is tolerant to target and ligand structure variation, J. Chem. Inf. Model, 56: 1676-1691 (2016)

  • Juan Esquivel-Rodriguez, Yi Xiong, Xusi Han, Shuomeng Gang, Charles Christoffer, & Daisuke Kihara, Navigating 3D Electron Microscopy Maps with EM-SURFER, BMC Bioinformatics, 16: 181 (2015)