ArticleBioinformatics (Oxford, England)2018
MODE-TASK: large-scale protein motion tools.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed.
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- Application of chemical similarity and bioisosteres to find allosteric inhibitors of type 2 lipid kinase γ.Scientific reports · 2025Article
- Naringenin and its structural analogues inhibit CDK2: a combined MD-MMGBSA and protein-ligand interaction study for colon cancer.In silico pharmacology · 2025Article
- Using residue interaction networks to understand protein function and evolution and to engineer new proteins.Current opinion in structural biology · 2024Review
- Molecular Mechanism of Cynodon dactylon Phytosterols Targeting MAPK3 and PARP1 to Combat Epithelial Ovarian Cancer: A Multifaceted Computational Approach.Cell biochemistry and biophysics · 2024Article
- Fragment-based Drug Discovery Strategy and its Application to the Design of SARS-CoV-2 Main Protease Inhibitor.Current medicinal chemistry · 2024Review
- Boosting the Full Potential of PyMOL with Structural Biology Plugins.Biomolecules · 2022Review
- Protein Function Analysis through Machine Learning.Biomolecules · 2022Review
- Collective variable discovery in the age of machine learning: reality, hype and everything in between.RSC advances · 2022Review
- TIRAP-mediated activation of p38 MAPK in inflammatory signaling.Scientific reports · 2022Article
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- Effects of the Nature of the Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM Studies.Chemphyschem : a European journal of chemical physics and physical chemistry · 2021Article
- A Novel Therapeutic Peptide Blocks SARS-CoV-2 Spike Protein Binding with Host Cell ACE2 Receptor.Drugs in R&D · 2021Article
- JEDi: java essential dynamics inspector - a molecular trajectory analysis toolkit.BMC bioinformatics · 2021Article
- MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics.Computational and structural biotechnology journal · 2021Article
- Molecular Modeling Study of c-KIT/PDGFRα Dual Inhibitors for the Treatment of Gastrointestinal Stromal Tumors.International journal of molecular sciences · 2020Article
- Side-by-side comparison of Notch- and C83 binding to γ-secretase in a complete membrane model at physiological temperature.RSC advances · 2020Article
- FoldamerDB: a database of peptidic foldamers.Nucleic acids research · 2020Article
- A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs.Frontiers in molecular biosciences · 2020Article
- Probing the Structural Dynamics of theFrontiers in molecular biosciences · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Summary: MODE-TASK, a novel and versatile software suite, comprises Principal Component Analysis, Multidimensional Scaling, and t-Distributed Stochastic Neighbor Embedding techniques using Molecular Dynamics trajectories. MODE-TASK also includes a Normal Mode Analysis tool based on Anisotropic Network Model so as to provide a variety of ways to analyse and compare large-scale motions of protein complexes for which long MD simulations are prohibitive. Beside the command line function, a GUI has been developed as a PyMOL plugin. Availability and implementation: MODE-TASK is open source, and available for download from https://github.com/RUBi-ZA/MODE-TASK. It is implemented in Python and C++. It is compatible with Python 2.x and Python 3.x and can be installed by Conda. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.