Hotspot driven peptide design

Hotspot driven peptide design

@scienceguy
@scienceguy
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2 weeks ago 74

Hotspot driven peptide design

@scienceguy2 weeks ago

Preprint, Under review
HOTSPOT-DRIVEN PEPTIDE DESIGN VIA MULTIFRAGMENT AUTOREGRESSIVE EXTENSION
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Figure 1: Left: Hot spot residues are a small number of critical residues i…
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2 RELATED WORK
Generative Models for Protein Design Generative models have…
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Figure 2: Overview of our three-stage approach: In the first foudning stage…
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Algorithm 1: Peptide Sampling Outline
Data: Target protein T, peptide leng…
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residue types ensures that we transition from regions of low occurrence pro…
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Next, the backbone structure of the newly added residue Rij−1 is reconstruc…
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initial peptides for optimization—is often available. Therefore, we introdu…
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variability, calculated as the product of pairwise (1-TM-score) and (1-sequ…
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Figure 5: Examples of generated scaffolded peptides by PepHAR. PepHAR can s…
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6 CONCLUSION
In this work, we presented PepHAR, a hot-spot based autoregre…
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Andrew A Bogan and Kurt S Thorn. Anatomy of hot spots in protein interfaces…
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Oscar Davis, Samuel Kessler, Mircea Petrache, Avishek Joey Bose, et al. Fis…
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Preprint, Under review
Michael U Gutmann and Aapo Hyvarinen. Noise-contrastive estimation of unnor…
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Preprint, Under review
Bowen Jing, Gabriele Corso, Jeffrey Chang, Regina Barzilay, and Tommi Jaakk…
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Preprint, Under review
Julia Koehler Leman, Brian D Weitzner, Steven M Lewis, Jared Adolf-Bryfogle…
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Preprint, Under review
John B Matson and Samuel I Stupp. Self-assembling peptide scaffolds for reg…
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Preprint, Under review
Maxim V Shapovalov and Roland L Dunbrack. A smoothed backbone-dependent rot…
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Preprint, Under review
Mihaly Varadi, Stephen Anyango, Mandar Deshpande, Sreenath Nair, Cindy Nata…
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Preprint, Under review
Kevin E Wu, Kevin K Yang, Rianne van den Berg, Sarah Alamdari, James Y Zou,…
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Zaixi Zhang, Zepu Lu, Zhongkai Hao, Marinka Zitnik, and Qi Liu. Full-atom p…
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A HOT SPOT RESIDUES
In the context of protein interactions, hot spots refe…
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B ADJACENT RESIDUE RECONSTRUCTION
B.1 PEPTIDE BOND AND PLANAR
Peptide bon…
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The dihedral angle ϕiis calculated as the angle between the planes formed b…
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Translation Vector xi The translation vector xi defines the global position…
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Initial Reference Coordinates The initial reference coordinates for the pep…
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D.1 PROBABILITY DENSITY FUNCTION (PDF)
The probability density function (P…
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E PEPHAR IMPLEMENTATIONS
E.1 NETWORK DETAILS
The network used in our meth…
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F EXPERIMENTAL DETAILS
In each task, for every method, we generate 64 pept…
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across all generated peptides for a given target. A higher diversity score …
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G.2 CUMULATIVE ERROS
Figure 6: Scatter Plot of peptide length and RMSD val…
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Table 7: Evaluation of methods in the scaffold generation task. K = 1, 2, 3…
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G.4 CASE STUDY ON GPCR-PEPTIDE INTERACTION
Here, we present a case study o…
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