RIP-MD: A tool to study residue interaction networks in protein molecular dynamics

Sebastián Contreras-Riquelme, Jose Antonio Garate, Tomas Perez-Acle, Alberto J.M. Martin

Resultado de la investigación: Article

3 Citas (Scopus)

Resumen

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 Cas 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.

Idioma originalEnglish
Número de artículoe5998
PublicaciónPeerJ
Volumen2018
N.º12
DOI
EstadoPublished - 1 ene 2018

Huella dactilar

Protein Interaction Maps
molecular dynamics
Molecular Dynamics Simulation
Molecular dynamics
Proteins
proteins
trajectories
Trajectories
protein structure
Boidae
Python
Computer simulation
Systems Analysis
Coulomb interactions
sulfides
Disulfides
User interfaces
Cations
cations
Software

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Citar esto

Contreras-Riquelme, S., Garate, J. A., Perez-Acle, T., & Martin, A. J. M. (2018). RIP-MD: A tool to study residue interaction networks in protein molecular dynamics. PeerJ, 2018(12), [e5998]. https://doi.org/10.7717/peerj.5998
Contreras-Riquelme, Sebastián ; Garate, Jose Antonio ; Perez-Acle, Tomas ; Martin, Alberto J.M. / RIP-MD : A tool to study residue interaction networks in protein molecular dynamics. En: PeerJ. 2018 ; Vol. 2018, N.º 12.
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abstract = "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 Cas 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.",
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Contreras-Riquelme, S, Garate, JA, Perez-Acle, T & Martin, AJM 2018, 'RIP-MD: A tool to study residue interaction networks in protein molecular dynamics', PeerJ, vol. 2018, n.º 12, e5998. https://doi.org/10.7717/peerj.5998

RIP-MD : A tool to study residue interaction networks in protein molecular dynamics. / Contreras-Riquelme, Sebastián; Garate, Jose Antonio; Perez-Acle, Tomas; Martin, Alberto J.M.

En: PeerJ, Vol. 2018, N.º 12, e5998, 01.01.2018.

Resultado de la investigación: Article

TY - JOUR

T1 - RIP-MD

T2 - A tool to study residue interaction networks in protein molecular dynamics

AU - Contreras-Riquelme, Sebastián

AU - Garate, Jose Antonio

AU - Perez-Acle, Tomas

AU - Martin, Alberto J.M.

PY - 2018/1/1

Y1 - 2018/1/1

N2 - 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 Cas 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.

AB - 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 Cas 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.

KW - Molecular dynamics

KW - Residue interaction networks

KW - Trajectory analysis

KW - VMD plugin

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Contreras-Riquelme S, Garate JA, Perez-Acle T, Martin AJM. RIP-MD: A tool to study residue interaction networks in protein molecular dynamics. PeerJ. 2018 ene 1;2018(12). e5998. https://doi.org/10.7717/peerj.5998