Related papers: The short-cut network within protein residue netwo…

We examined protein residue networks (PRNs) from a local search perspective to understand why PRNs are highly clustered when having short paths is important for protein functionality. We found that by adopting a local search perspective,…

Native shortcut networks (SCN0) are sub-graphs of native protein residue networks (PRN0). In this paper, we propose the Network Dynamics (ND) model, which reconstructs a PRN0 by adding back its edges according to some recipe, while its…

Machine learning (ML) is revolutionizing protein structural analysis, including an important subproblem of predicting protein residue contact maps, i.e., which amino-acid residues are in close spatial proximity given the amino-acid sequence…

A single protein molecule is regarded as a contact network of amino-acid residues. Some studies have indicated that this network is a small world network (SWN), while other results have implied that this is a fractal network (FN). However,…

A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…

Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…

The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…

The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…

Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…

Computer experiments are performed to investigate why protein contact networks (networks induced by spatial contacts between amino acid residues of a protein) do not have shorter average shortest path lengths in spite of their importance to…

The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…

Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…

Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…

A protein structure is represented as a network of residues whereby edges are determined by intra-molecular contacts. We introduce inhomogeneity into these networks by assigning each edge a weight that is determined by amino-acid pair…

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we…

It has been argued by Thom and Palm that sparsely-connected neural networks (SCNs) show improved performance over fully-connected networks (FCNs). Super-regular networks (SRNs) are neural networks composed of a set of stacked sparse layers…

Protein structural classification (PSC) is a supervised problem of assigning proteins into pre-defined structural (e.g., CATH or SCOPe) classes based on the proteins' sequence or 3D structural features. We recently proposed PSC approaches…

The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…

Real-world networks exhibit prominent hierarchical and modular structures, with various subgraphs as building blocks. Most existing studies simply consider distinct subgraphs as motifs and use only their numbers to characterize the…

In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…