PepMLM: Target Sequence-Conditioned Generation of Therapeutic Peptide Binders via Span Masked Language Modeling

Autor: Chen, Tianlai, Dumas, Madeleine, Watson, Rio, Vincoff, Sophia, Peng, Christina, Zhao, Lin, Hong, Lauren, Pertsemlidis, Sarah, Shaepers-Cheu, Mayumi, Wang, Tian Zi, Srijay, Divya, Monticello, Connor, Vure, Pranay, Pulugurta, Rishab, Kholina, Kseniia, Goel, Shrey, DeLisa, Matthew P., Truant, Ray, Aguilar, Hector C., Chatterjee, Pranam

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological

Externí odkaz: http://arxiv.org/abs/2310.03842

PepMLM: Target Sequence-Conditioned Generation of Therapeutic Peptide Binders via Span Masked Language Modeling.

Autor: Chen T; Department of Biomedical Engineering, Duke University., Dumas M; Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University.; Department of Microbiology, College of Agriculture and Life Sciences, Cornell University., Watson R; Department of Biomedical Engineering, Duke University., Vincoff S; Department of Biomedical Engineering, Duke University., Peng C; Department of Biochemistry and Biomedical Sciences, McMaster University., Zhao L; Department of Biomedical Engineering, Duke University., Hong L; Department of Biomedical Engineering, Duke University., Pertsemlidis S; Department of Biomedical Engineering, Duke University., Shaepers-Cheu M; Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University., Wang TZ; Department of Biomedical Engineering, Duke University., Srijay D; Department of Biomedical Engineering, Duke University., Monticello C; Department of Biochemistry and Biomedical Sciences, McMaster University., Vure P; Department of Biomedical Engineering, Duke University., Pulugurta R; Department of Biomedical Engineering, Duke University., Kholina K; Department of Biomedical Engineering, Duke University., Goel S; Department of Biomedical Engineering, Duke University., DeLisa MP; Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.; Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.; Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, USA., Truant R; Department of Biochemistry and Biomedical Sciences, McMaster University., Aguilar HC; Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University., Chatterjee P; Department of Biomedical Engineering, Duke University.; Department of Computer Science, Duke University.; Department of Biostatistics and Bioinformatics, Duke University.

Publikováno v: ArXiv [ArXiv] 2024 Aug 11. Date of Electronic Publication: 2024 Aug 11.

De Novo Design of Peptide Binders to Conformationally Diverse Targets with Contrastive Language Modeling.

Autor: Bhat S; Department of Biomedical Engineering, Duke University., Palepu K; Department of Biomedical Engineering, Duke University., Hong L; Department of Biomedical Engineering, Duke University., Mao J; Department of Cell Biology, Duke University., Ye T; Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA., Iyer R; Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Institute, San Diego, CA, USA., Zhao L; Department of Biomedical Engineering, Duke University., Chen T; Department of Biomedical Engineering, Duke University., Vincoff S; Department of Biomedical Engineering, Duke University., Watson R; Department of Biomedical Engineering, Duke University., Wang T; Department of Biomedical Engineering, Duke University., Srijay D; Department of Biomedical Engineering, Duke University., Kavirayuni VS; Department of Biomedical Engineering, Duke University., Kholina K; Department of Biomedical Engineering, Duke University., Goel S; Department of Biomedical Engineering, Duke University., Vure P; Department of Biomedical Engineering, Duke University., Desphande AJ; Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Institute, San Diego, CA, USA., Soderling SH; Department of Cell Biology, Duke University., DeLisa MP; Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.; Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.; Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, USA., Chatterjee P; Department of Biomedical Engineering, Duke University.; Department of Computer Science, Duke University.; Department of Biostatistics and Bioinformatics, Duke University.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Jul 22. Date of Electronic Publication: 2024 Jul 22.