Program

Protein Surface Printer (PSP)

Protein surfaces play a vital role role in protein-protein, protein-therapeutic interactions.

Features of PSP:

Distributions (local and global) of surface amino acids
Probabilities of surface amino acids
Single-frame analysis, and MD simulation trajectory
Support numerous MD software (Gromacs, NAMD, AMBER, OpenMM)
Support various all-atom potentials (CHARMM, AMBER, OPLS-AA, AMOEBA)

References:

Protein Surface Printer for Exploring Protein Domains

Y. Li, B. Qiao,* and M. Olvera de la Cruz,* J. Chem. Inf. Model. 2020, 60, 5255.

Water Follows Polar and Nonpolar Protein Surface Domains

B. Qiao, F. Jiménez-Ángeles, T. Nguyen, and M. Olvera de la Cruz, PNAS 2019, 116, 19274.

3. Efficient encapsulation of proteins with random copolymers

T. Nguyen, B. Qiao, and M. Olvera de la Cruz, PNAS, 2018, 115, 6578.

4. Random Heteropolymer Enables Protein Function in Foreign Environments

B. Panganiban, B. Qiao, T. Jiang, C. DelRe, M. Obadia, T. Nguyen, A. Smith, A. Hall, I. Sit, M. Crosby, P. B. Dennis, E. Drockenmuller, M. Olvera de la Cruz, and T. Xu, Science 2018, 359, 1239.

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