ArticleNucleic acids research2019
NAPS update: network analysis of molecular dynamics data and protein-nucleic acid complexes.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Exploring proteins and protein-ligand complexes through residue interaction networks.Nature protocols · 2026Review
- Insights into human TLR9 structural dynamics and recognition of pathogen-associated CpG DNA using molecular dynamics simulation.iScience · 2026Article
- Allostery between Distant Structural Regions Dictates Selectivity in GPCR:G Protein Coupling.Biochemistry · 2026Article
- Protein contact network explorer: topological analysis of protein structures.Frontiers in bioinformatics · 2026Article
- Computational studies on the functional and structural impact of pathogenic mutations in enzymes.Protein science : a publication of the Protein Society · 2025Review
- Elucidating the structural dynamics induced by active site mutations in 3C protease of foot-and-mouth disease virus.PloS one · 2025Article
- Using residue interaction networks to understand protein function and evolution and to engineer new proteins.Current opinion in structural biology · 2024Review
- BaNDyT: Bayesian Network modeling of molecular Dynamics Trajectories.bioRxiv : the preprint server for biology · 2024Article
- The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors.Mini reviews in medicinal chemistry · 2024Review
- Distinct or Overlapping Areas of Mitochondrial Thioredoxin 2 May Be Used for Its Covalent and Strong Non-Covalent Interactions with Protein Ligands.Antioxidants (Basel, Switzerland) · 2023Article
- AQcalc: A web server that identifies weak molecular interactions in protein structures.Protein science : a publication of the Protein Society · 2023Article
- A comparative study on structural proteins of viruses that belong to the identical family.The European physical journal. Special topics · 2023Article
- Molecular dynamics of the ERRγ ligand-binding domain bound with agonist and inverse agonist.PloS one · 2023Article
- Mechanistic Studies on the Stereoselectivity of FFAR1 Modulators.Journal of chemical information and modeling · 2022Article
- Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant.International journal of molecular sciences · 2022Article
- PSNtools for standalone and web-based structure network analyses of conformational ensembles.Computational and structural biotechnology journal · 2022Article
- SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations.PloS one · 2022Article
- Review
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- Connecting the dots: A practical evaluation of web-tools for describing protein dynamics as networks.Frontiers in bioinformatics · 2022Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Network theory is now a method of choice to gain insights in understanding protein structure, folding and function. In combination with molecular dynamics (MD) simulations, it is an invaluable tool with widespread applications such as analyzing subtle conformational changes and flexibility regions in proteins, dynamic correlation analysis across distant regions for allosteric communications, in drug design to reveal alternative binding pockets for drugs, etc. Updated version of NAPS now facilitates network analysis of the complete repertoire of these biomolecules, i.e., proteins, protein-protein/nucleic acid complexes, MD trajectories, and RNA. Various options provided for analysis of MD trajectories include individual network construction and analysis of intermediate time-steps, comparative analysis of these networks, construction and analysis of average network of the ensemble of trajectories and dynamic cross-correlations. For protein-nucleic acid complexes, networks of the whole complex as well as that of the interface can be constructed and analyzed. For analysis of proteins, protein-protein complexes and MD trajectories, network construction based on inter-residue interaction energies with realistic edge-weights obtained from standard force fields is provided to capture the atomistic details. Updated version of NAPS also provides improved visualization features, interactive plots and bulk execution. URL: http://bioinf.iiit.ac.in/NAPS/.
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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.