| Chapter title |
A Discontinuous Potential Model for Protein–Protein Interactions
|
|---|---|
| Chapter number | 1 |
| Book title |
Foundations of Molecular Modeling and Simulation
|
| Published in |
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.), January 2016
|
| DOI | 10.1007/978-981-10-1128-3_1 |
| Pubmed ID | |
| Book ISBNs |
978-9-81-101126-9, 978-9-81-101128-3
|
| Authors |
Qing Shao, Carol K. Hall, Shao, Qing, Hall, Carol K. |
| Abstract |
Protein-protein interactions play an important role in many biologic and industrial processes. In this work, we develop a two-bead-per-residue model that enables us to account for protein-protein interactions in a multi-protein system using discontinuous molecular dynamics simulations. This model deploys discontinuous potentials to describe the non-bonded interactions and virtual bonds to keep proteins in their native state. The geometric and energetic parameters are derived from the potentials of mean force between sidechain-sidechain, sidechain-backbone, and backbone-backbone pairs. The energetic parameters are scaled with the aim of matching the second virial coefficient of lysozyme reported in experiment. We also investigate the performance of several bond-building strategies. |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 8 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 2 | 25% |
| Professor | 2 | 25% |
| Lecturer | 1 | 13% |
| Student > Doctoral Student | 1 | 13% |
| Student > Master | 1 | 13% |
| Other | 1 | 13% |
| Readers by discipline | Count | As % |
|---|---|---|
| Chemical Engineering | 2 | 25% |
| Materials Science | 2 | 25% |
| Pharmacology, Toxicology and Pharmaceutical Science | 1 | 13% |
| Engineering | 1 | 13% |
| Unknown | 2 | 25% |