MDN: A Web Portal for Network Analysis of Molecular Dynamics Simulations

Ribeiro, André A. S. T.; Ortiz, Vanessa

doi:10.1016/j.bpj.2015.06.013

Cited by 16 publications

(13 citation statements)

References 41 publications

(43 reference statements)

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“…Network analysis has the ability to abstract out such complexity while maintaining the inter-residue relationships, from which several centrality metrics derived from the social sciences, may be applied to investigate protein dynamics. Many research groups have applied residue interaction network (RIN) analysis on static structures, and have used multiple strategies and tools for summarizing the protein interactions using various edge and node modeling approaches [1][2][3][4] to minimize bias and maintain enough variance for recapitulating proteins topological changes. We previously proposed a post-hoc analysis approach of MD simulations using dynamic residue network (DRN) analysis to probe the impact of mutations [5,6] and allosteric effects [7] , before setting up the MD-TASK tool suite [8] in 2017.…”

Section: Introductionmentioning

confidence: 99%

MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics

Amamuddy

Glenister

Bishop

2021

Preprint

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MDM-TASK-web is the web server for the MD-TASK and MODE-TASK software suites. The web server simplifies the set-up for computing and visualizing results from dynamic residue networks, perturbation-response scanning, dynamic cross-correlation, essential dynamics, normal mode analysis and coordination-propensity. Upgrades and new functionalities to these software suites have also been introduced via the web server. An embedded work-flow, integrated documentation and 3D visualization functionality allow for a more intuitive and easy-to-use web platform.The web server is available at https://mdmtaskweb.rubi.ru.ac.za/. It is Django-based using a MySQL database and is compatible with all major web browsers.

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Section: Introductionmentioning

confidence: 99%

MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics

Amamuddy

Glenister

Bishop

2021

Preprint

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“…webPSN investigates structural communication in macromolecules by constructing static and dynamic AANs (Felline et al, 2020). Furthermore, AAN-based Web servers such as MDN (Ribeiro and Ortiz, 2015), NAPS (Chakrabarty and Parekh, 2016), and RIP-MD (Contreras-Riquelme et al, 2018) provide tools for quantifying protein dynamic based on MD simulation trajectories. More tools and Web servers for network can be found in a recent review (Liang et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

ANCA: A Web Server for Amino Acid Networks Construction and Analysis

Yan

Chen

et al. 2020

Front. Mol. Biosci.

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Amino acid network (AAN) models empower us to gain insights into protein structures and functions by describing a protein 3D structure as a graph, where nodes represent residues and edges as amino acid interactions. Here, we present the ANCA, an interactive Web server for Amino Acids Network Construction and Analysis based on a single structure or a set of structures from the Protein Data Bank. The main purpose of ANCA is to provide a portal for three types of an environment-dependent residue contact energy (ERCE)-based network model, including amino acid contact energy network (AACEN), node-weighted amino acid contact energy network (NACEN), and edgeweighted amino acid contact energy network (EACEN). For comparison, the C-alpha distance-based network model is also included, which can be extended to protein-DNA/RNA complexes. Then, the analyses of different types of AANs were performed and compared from node, edge, and network levels. The network and corresponding structure can be visualized directly in the browser. The ANCA enables researchers to investigate diverse concerns in the framework of AAN, such as the interpretation of allosteric regulation and functional residues. The ANCA portal, together with an extensive help, is available at http://sysbio.suda.edu.cn/anca/.

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“…Comprehensive analysis of the huge MD data is challenging and requires computationally efficient approaches for easy interpretation of the data. To the best of our knowledge, apart from MDN (18), majority of the resources for network analysis of MD trajectories are standalone software packages such as xPyder (19), PyInteraph (20), MD-TASK (21), gRINN (22) and PSN-Ensemble (23). xPyder is a PyMOL (https://www.pymol.org) plugin that constructs the network based on dynamic cross correlation between amino acid residues integrated with various features of PyMOL.…”

Section: Introductionmentioning

confidence: 99%

NAPS update: network analysis of molecular dynamics data and protein–nucleic acid complexes

Chakrabarty

Naganathan

Garg

et al. 2019

Nucleic Acids Research

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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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MDN: A Web Portal for Network Analysis of Molecular Dynamics Simulations

Cited by 16 publications

References 41 publications

MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics

MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics

ANCA: A Web Server for Amino Acid Networks Construction and Analysis

NAPS update: network analysis of molecular dynamics data and protein–nucleic acid complexes

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