Journal ArticleDOI
Aminonet-a tool to construct and visualize amino acid networks, and to calculate topological parameters
Reads0
Chats0
TLDR
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
More filters
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
Inferring Ancestral Pueblo Social Networks from Simulation in the Central Mesa Verde
TL;DR: In this article, the authors use computer simulation to explore the extent to which food-sharing practices would have been instrumental for the survival of Ancestral Pueblo people across the patchy landscape of the Prehispanic American Southwest and suggest that we can see direct evidence of exchange through the aggregation of households into clustered settlements.
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
More filters
Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Inference of macromolecular assemblies from crystalline state.
E. Krissinel,Kim Henrick +1 more
TL;DR: A new method, based on chemical thermodynamics, is developed for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments, as found, biological units may be recovered at 80-90% success rate, which makesX-ray crystallography an important source of experimental data on macromolescular complexes and protein-protein interactions.
Journal ArticleDOI
Network biology: understanding the cell's functional organization
TL;DR: This work states that rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize the view of biology and disease pathologies in the twenty-first century.
Posted Content
Evolution of Networks: From Biological Nets to the Internet and WWW
TL;DR: The principles of the complex organization and evolution of networks, natural and artificial, are discussed in this paper, which is addressed to all involved researchers and students, and the ideas are presented in a clear and a pedagogical way, with minimal mathematics, so even students without a deep knowledge of mathematics and statistical physics can rely on this as a reference.