The construction of an amino acid network for understanding protein structure and function
Amino acid networks (AANs) are undirected networks consisting of amino acid residues and
their interactions in three-dimensional protein structures. The analysis of AANs provides …
their interactions in three-dimensional protein structures. The analysis of AANs provides …
Soft computing methods for the prediction of protein tertiary structures: A survey
AE Márquez-Chamorro, G Asencio-Cortés… - Applied Soft …, 2015 - Elsevier
The problem of protein structure prediction (PSP) represents one of the most important
challenges in computational biology. Determining the three dimensional structure of proteins …
challenges in computational biology. Determining the three dimensional structure of proteins …
Residue interaction network analysis of Dronpa and a DNA clamp
Topology is an essential aspect of protein structure. The network paradigm is increasingly
used to describe the topology and dynamics of proteins. In this paper, the effect of topology …
used to describe the topology and dynamics of proteins. In this paper, the effect of topology …
Node-weighted amino acid network strategy for characterization and identification of protein functional residues
The study of functional residues (FRs) is essential for understanding protein functions and
biological processes. The amino acid network (AAN) has become an emerging paradigm for …
biological processes. The amino acid network (AAN) has become an emerging paradigm for …
[HTML][HTML] Protein structure quality assessment based on the distance profiles of consecutive backbone cα atoms
S Chakraborty, R Venkatramani, BJ Rao… - …, 2013 - ncbi.nlm.nih.gov
Predicting the three dimensional native state structure of a protein from its primary sequence
is an unsolved grand challenge in molecular biology. Two main computational approaches …
is an unsolved grand challenge in molecular biology. Two main computational approaches …
ANCA: A web server for amino acid networks construction and analysis
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 …
functions by describing a protein 3D structure as a graph, where nodes represent residues …
Amino acid contact energy networks impact protein structure and evolution
One of the most challenging tasks in structural proteomics is to understand the relationship
between protein structure, biological function, and evolution. An understanding of amino …
between protein structure, biological function, and evolution. An understanding of amino …
Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals
Motivation Elucidation of protein native states from amino acid sequences is a primary
computational challenge. Modern computational and experimental methodologies, such as …
computational challenge. Modern computational and experimental methodologies, such as …
Amino acid network for prediction of catalytic residues in enzymes: a comparison survey
Catalytic residues play a significant role in enzyme functions. With the recent accumulation
of experimentally determined enzyme 3D structures and network theory on protein …
of experimentally determined enzyme 3D structures and network theory on protein …
An information gain-based approach for evaluating protein structure models
For three decades now, knowledge-based scoring functions that operate through the
“potential of mean force”(PMF) approach have continuously proven useful for studying …
“potential of mean force”(PMF) approach have continuously proven useful for studying …