Journal ArticleDOI
Aminonet-a tool to construct and visualize amino acid networks, and to calculate topological parameters
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AMINONET is a Java-based software tool to construct different protein contact networks (unweighted and weighted; long range, short range and any range; hydrophobic, hydrophilic, charged or all-amino-acid networks).Abstract:
AMINONET is a Java-based software tool to construct different protein contact networks (unweighted and weighted; long range, short range and any range; hydrophobic, hydrophilic, charged or all-amino-acid networks). The networks thus constructed can be visualized. The software will also help in the calculation of the values of the different topological parameters of the constructed networks. The user can either provide a PDB ID or upload a structure file in PDB format as input. If necessary, the user can also do the same for a large number of proteins, uploading a batch file as input (details described in the document available online).read more
Citations
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The self-assembly, aggregation and phase transitions of food protein systems in one, two and three dimensions
Raffaele Mezzenga,Peter Fischer +1 more
TL;DR: This review will tackle the current understanding of protein aggregation in the framework of foods, which is possibly one of the broadest contexts, yet is of tremendous daily relevance.
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NAPS: Network Analysis of Protein Structures.
Broto Chakrabarty,Nita Parekh +1 more
TL;DR: A web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative analysis of residue–residue interactions in single chains, protein complex, modelled protein structures and trajectories and provides insights into structure-function relationship.
Journal ArticleDOI
Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization.
Dhriti Sengupta,Sudip Kundu +1 more
TL;DR: An extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales is presented and is able to capture several known properties of protein structure as well as can unravel several new features.
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Inferring Ancestral Pueblo Social Networks from Simulation in the Central Mesa Verde
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Journal ArticleDOI
The Topology and Dynamics of Protein Complexes: Insights from Intra– Molecular Network Theory
TL;DR: This work reviews the recent advances in the use of network theory to study the topology and dynamics of protein- ligand and protein-nucleic acid complexes and describes some web-based resources for protein complexes.
References
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Journal ArticleDOI
New amino acid indices based on residue network topology.
TL;DR: In this study, residue networks are constructed from the PDB structures of 640 representative proteins based on the distance between Calpha atoms with an 8 A cutoff, indicating that the network property based amino acid indices can be useful complements to the existing physicochemical property based Amino acid indices.
Journal ArticleDOI
Analysis of protein folds using protein contact networks
Pankaj Barah,Somdatta Sinha +1 more
TL;DR: Using the network representation of protein structures and their 2D contact maps, this results suggest that this direct and computationally simple methodology can be used to infer about the presence of specific folds from the protein’s contact map alone.