RIP-MD: a tool to study residue interaction networks in protein molecular dynamics
Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given the data-intensive nature of the tech...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2018-12-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/5998.pdf |
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| author | Sebastián Contreras-Riquelme Jose-Antonio Garate Tomas Perez-Acle Alberto J.M. Martin |
| author_facet | Sebastián Contreras-Riquelme Jose-Antonio Garate Tomas Perez-Acle Alberto J.M. Martin |
| author_sort | Sebastián Contreras-Riquelme |
| collection | DOAJ |
| description | Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given the data-intensive nature of the technique, gathering relevant information from MD simulations is a complex and time consuming process requiring several computational tools to perform these analyses. Among different approaches, the study of residue interaction networks (RINs) has proven to facilitate the study of protein structures. In a RIN, nodes represent amino-acid residues and the connections between them depict non-covalent interactions. Here, we describe residue interaction networks in protein molecular dynamics (RIP-MD), a visual molecular dynamics (VMD) plugin to facilitate the study of RINs using trajectories obtained from MD simulations of proteins. Our software generates RINs from MD trajectory files. The non-covalent interactions defined by RIP-MD include H-bonds, salt bridges, VdWs, cation-π, π–π, Arginine–Arginine, and Coulomb interactions. In addition, RIP-MD also computes interactions based on distances between Cαs and disulfide bridges. The results of the analysis are shown in an user friendly interface. Moreover, the user can take advantage of the VMD visualization capacities, whereby through some effortless steps, it is possible to select and visualize interactions described for a single, several or all residues in a MD trajectory. Network and descriptive table files are also generated, allowing their further study in other specialized platforms. Our method was written in python in a parallelized fashion. This characteristic allows the analysis of large systems impossible to handle otherwise. RIP-MD is available at http://www.dlab.cl/ripmd. |
| first_indexed | 2024-03-09T06:38:04Z |
| format | Article |
| id | doaj.art-3ad3ab31d89547b594d94cf0a787aabf |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:38:04Z |
| publishDate | 2018-12-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-3ad3ab31d89547b594d94cf0a787aabf2023-12-03T10:55:24ZengPeerJ Inc.PeerJ2167-83592018-12-016e599810.7717/peerj.5998RIP-MD: a tool to study residue interaction networks in protein molecular dynamicsSebastián Contreras-Riquelme0Jose-Antonio Garate1Tomas Perez-Acle2Alberto J.M. Martin3Computational Biology Laboratory (DLab), Fundacion Ciencia & Vida, Santiago, ChileCentro Interdisciplinario de Neurociencia de Valparaíso, Valparaíso, ChileComputational Biology Laboratory (DLab), Fundacion Ciencia & Vida, Santiago, ChileNetwork Biology Laboratory, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, ChileProtein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given the data-intensive nature of the technique, gathering relevant information from MD simulations is a complex and time consuming process requiring several computational tools to perform these analyses. Among different approaches, the study of residue interaction networks (RINs) has proven to facilitate the study of protein structures. In a RIN, nodes represent amino-acid residues and the connections between them depict non-covalent interactions. Here, we describe residue interaction networks in protein molecular dynamics (RIP-MD), a visual molecular dynamics (VMD) plugin to facilitate the study of RINs using trajectories obtained from MD simulations of proteins. Our software generates RINs from MD trajectory files. The non-covalent interactions defined by RIP-MD include H-bonds, salt bridges, VdWs, cation-π, π–π, Arginine–Arginine, and Coulomb interactions. In addition, RIP-MD also computes interactions based on distances between Cαs and disulfide bridges. The results of the analysis are shown in an user friendly interface. Moreover, the user can take advantage of the VMD visualization capacities, whereby through some effortless steps, it is possible to select and visualize interactions described for a single, several or all residues in a MD trajectory. Network and descriptive table files are also generated, allowing their further study in other specialized platforms. Our method was written in python in a parallelized fashion. This characteristic allows the analysis of large systems impossible to handle otherwise. RIP-MD is available at http://www.dlab.cl/ripmd.https://peerj.com/articles/5998.pdfResidue interaction networksMolecular dynamicsVMD pluginTrajectory analysis |
| spellingShingle | Sebastián Contreras-Riquelme Jose-Antonio Garate Tomas Perez-Acle Alberto J.M. Martin RIP-MD: a tool to study residue interaction networks in protein molecular dynamics PeerJ Residue interaction networks Molecular dynamics VMD plugin Trajectory analysis |
| title | RIP-MD: a tool to study residue interaction networks in protein molecular dynamics |
| title_full | RIP-MD: a tool to study residue interaction networks in protein molecular dynamics |
| title_fullStr | RIP-MD: a tool to study residue interaction networks in protein molecular dynamics |
| title_full_unstemmed | RIP-MD: a tool to study residue interaction networks in protein molecular dynamics |
| title_short | RIP-MD: a tool to study residue interaction networks in protein molecular dynamics |
| title_sort | rip md a tool to study residue interaction networks in protein molecular dynamics |
| topic | Residue interaction networks Molecular dynamics VMD plugin Trajectory analysis |
| url | https://peerj.com/articles/5998.pdf |
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