Zepyros: A webserver to evaluate the shape complementarity of protein-protein interfaces (2402.06960v1)
Abstract: Shape complementarity of molecular surfaces at the interfaces is a well-known characteristic of protein-protein binding regions, and it is critical in influencing the stability of the complex. Measuring such complementarity is at the basis of methods for both the prediction of possible interactions and for the design/optimization of speficic ones. However, only a limited number of tools are currently available to efficiently and rapidly assess it. Here, we introduce Zepyros, a webserver for fast measuring of the shape complementarity between two molecular interfaces of a given protein-protein complex using structural information. Zepyros is implemented as a publicly available tool with a user-friendly interface. Our server can be found at the following link (all major browser supported): https://zepyros.bio-groups.com
- Hamid Hadi-Alijanvand. Complex stability is encoded in binding patch softness: A monomer-based approach to predict inter-subunit affinity of protein dimers. Journal of proteome research, 19(1):409–423, 2019.
- Spatial organization of hydrophobic and charged residues affects protein thermal stability and binding affinity. Scientific Reports, 12(1), July 2022.
- Computational approaches to therapeutic antibody design: established methods and emerging trends. Briefings in bioinformatics, 21(5):1549–1567, 2020.
- Protein folding and binding can emerge as evolutionary spandrels through structural coupling. Proceedings of the National Academy of Sciences, 112(6):1797–1802, 2015.
- The role of shape complementarity in the protein-protein interactions. Scientific reports, 3(1):3271, 2013.
- Electrostatic complementarity at the interface drives transient protein-protein interactions. Scientific Reports, 13(1), June 2023.
- Fast dynamic docking guided by adaptive electrostatic bias: The md-binding approach. Journal of Chemical Theory and Computation, 14(3):1727–1736, January 2018.
- Insights on protein thermal stability: a graph representation of molecular interactions. Bioinformatics, 35(15):2569–2577, December 2018.
- Thermometer: a webserver to predict protein thermal stability. Bioinformatics, 38(7):2060–2061, January 2022.
- 2d zernike polynomial expansion: Finding the protein-protein binding regions. Computational and Structural Biotechnology Journal, 19:29–36, 2021.
- A computational approach to investigate tdp-43 rna-recognition motif 2 c-terminal fragments aggregation in amyotrophic lateral sclerosis. Biomolecules, 11(12):1905, December 2021.
- Inferring the stabilization effects of sars-cov-2 variants on the binding with ace2 receptor. Communications Biology, 5(1), January 2022.
- Lactoferrin inhibition of the complex formation between ace2 receptor and sars cov-2 recognition binding domain. International Journal of Molecular Sciences, 23(10):5436, May 2022.
- Investigating the competition between ace2 natural molecular interactors and sars-cov-2 candidate inhibitors. Chemico-Biological Interactions, 374:110380, April 2023.
- Differences in the organization of interface residues tunes the stability of the sars-cov-2 spike-ace2 complex. Frontiers in Molecular Biosciences, 10, June 2023.
- Two receptor binding strategy of sars-cov-2 is mediated by both the n-terminal and receptor-binding spike domain. The Journal of Physical Chemistry B, 128(2):451–464, January 2024.
- Computational optimization of angiotensin-converting enzyme 2 for sars-cov-2 spike molecular recognition. Computational and Structural Biotechnology Journal, 19:3006–3014, 2021.
- Shape complementarity optimization of antibody–antigen interfaces: The application to SARS-CoV-2 spike protein. Frontiers in Molecular Biosciences, 9, May 2022.
- Computational structural-based gpcr optimization for user-defined ligand: Implications for the development of biosensors. Computational and Structural Biotechnology Journal, 21:3002–3009, 2023.
- Design of protein-binding peptides with controlled binding affinity: the case of sars-cov-2 receptor binding domain and angiotensin-converting enzyme 2 derived peptides. Frontiers in Molecular Biosciences, 10, January 2024.
Paper Prompts
Sign up for free to create and run prompts on this paper using GPT-5.
Top Community Prompts
Collections
Sign up for free to add this paper to one or more collections.