ArticlePeerJ2018
RIP-MD: a tool to study residue interaction networks in protein molecular dynamics.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- RinPy, a Python Package for Residue Interaction Network Model to Analyze Protein Structures and Predict Ligand Binding Sites.Journal of chemical information and modeling · 2026Article
- i-gRINN: a next-generation web server for protein energy network analysis of heterogeneous biomolecular systems with natural language-based data exploration.Nucleic acids research · 2026Article
- Untangling the Complexity of Binding Across Biomolecular Interfaces with Interaction Network Models.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Unravelling the role of key amino acid residues of the parainfluenza fusion peptide in membrane fusion.RSC chemical biology · 2025Article
- Application of Anomaly Detection to Identify Important Features of Protein Dynamics.ACS omega · 2025Article
- Using residue interaction networks to understand protein function and evolution and to engineer new proteins.Current opinion in structural biology · 2024Review
- The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors.Mini reviews in medicinal chemistry · 2024Review
- Protein and Peptide-Based Nanotechnology for Enhancing Stability, Bioactivity, and Delivery of Anthocyanins.Advanced healthcare materials · 2023Review
- Computational insight into stability-enhanced systems of anthocyanin with protein/peptide.Food chemistry. Molecular sciences · 2023Article
- SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations.Journal of chemical information and modeling · 2022Article
- Siah-1-interacting protein regulates mutated huntingtin protein aggregation in Huntington's disease models.Cell & bioscience · 2022Article
- SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations.PloS one · 2022Article
- SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility.Frontiers in medical technology · 2022Article
- Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations.Frontiers in immunology · 2022Article
- Exploring the dynamic mechanism of allosteric drug SHP099 inhibiting SHP2Molecular diversity · 2021Article
- MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics.Computational and structural biotechnology journal · 2021Article
- pyProGA-A PyMOL plugin for protein residue network analysis.PloS one · 2021Article
- Article
- Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering.International journal of molecular sciences · 2020Review
- ANCA: A Web Server for Amino Acid Networks Construction and Analysis.Frontiers in molecular biosciences · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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 C
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.