ArticleComputational and structural biotechnology journal2021
MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics.
Article in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 49 citations in OpenAlex.
- Exploring proteins and protein-ligand complexes through residue interaction networks.Nature protocols · 2026Review
- 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
- Stage-dependent role of NEK7 in the inactive-to-active conformational transition of NLRP3 monomer.PLoS computational biology · 2026Article
- Clustering and Analyzing Ensembles of Residue Interaction Networks from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- DynamiSpectra: A Python Software Package and Web Platform for Molecular Dynamics Data Analysis in Computational Biology.Journal of chemical information and modeling · 2025Article
- Deep learning-based dipeptidyl peptidase IV inhibitor screening, experimental validation, and GaMD/LiGaMD analysis.BMC biology · 2025Article
- Exploration of Natural Products for Targeting IDH1/2 Mutations in Acute Myeloid Leukemia Through Ligand-Based Pharmacophore Screening, Docking, ADME-T, and Molecular Dynamic Simulation Approaches.Bioinformatics and biology insights · 2025Article
- Computational Development of Transmission-Blocking Vaccine Candidates Based on Fused Antigens of Pre- and Post-fertilization Gametocytes AgainstBioinformatics and biology insights · 2025Article
- Allosteric modulation of Plasmodium falciparum Isoleucyl tRNA synthetase by South African natural compounds.PloS one · 2025Article
- Transfer learning towards predicting viral missense mutations: A case study on SARS-CoV-2.Computational and structural biotechnology journal · 2025Article
- Using residue interaction networks to understand protein function and evolution and to engineer new proteins.Current opinion in structural biology · 2024Review
- Revealing SARS-CoV-2 MComputational and structural biotechnology journal · 2024Article
- Toll-like receptor 4 pathway evolutionary trajectory and functional emergence.Frontiers in immunology · 2024Article
- The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors.Mini reviews in medicinal chemistry · 2024Review
- MDiGest: A Python package for describing allostery from molecular dynamics simulations.The Journal of chemical physics · 2023Article
- Investigation of Multi-SubunitInternational journal of molecular sciences · 2023Article
- Deciphering Isoniazid Drug Resistance Mechanisms on DimericACS omega · 2022Article
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- Slipknot or Crystallographic Error: A Computational Analysis of theInternational journal of molecular sciences · 2022Article
- Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins.Computational and structural biotechnology journal · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The web server, MDM-TASK-web, combines the MD-TASK and MODE-TASK software suites, which are aimed at the coarse-grained analysis of static and all-atom MD-simulated proteins, using a variety of non-conventional approaches, such as dynamic residue network analysis, perturbation-response scanning, dynamic cross-correlation, essential dynamics and normal mode analysis. Altogether, these tools allow for the exploration of protein dynamics at various levels of detail, spanning single residue perturbations and weighted contact network representations, to global residue centrality measurements and the investigation of global protein motion. Typically, following molecular dynamic simulations designed to investigate intrinsic and extrinsic protein perturbations (for instance induced by allosteric and orthosteric ligands, protein binding, temperature, pH and mutations), this selection of tools can be used to further describe protein dynamics. This may lead to the discovery of key residues involved in biological processes, such as drug resistance. The server simplifies the set-up required for running these tools and visualizing their results. Several scripts from the tool suites were updated and new ones were also added and integrated with 2D/3D visualization via the web interface. An embedded work-flow, integrated documentation and visualization tools shorten the number of steps to follow, starting from calculations to result visualization. The Django-powered web server (available at https://mdmtaskweb.rubi.ru.ac.za/) is compatible with all major web browsers. All scripts implemented in the web platform are freely available at https://github.com/RUBi-ZA/MD-TASK/tree/mdm-task-web and https://github.com/RUBi-ZA/MODE-TASK/tree/mdm-task-web.
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Registered trials
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.