相关论文: Surveying the side-chain network approach to prote…

In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…

We investigate connectivity properties of the SARS-CoV2 spike protein-human ACE2-receptor complex employing a protein side chain-based network method that allows us to span a range from atomic to global protein scales. We analyze network…

The functionality of protein-protein complexes is closely tied to the strength of their interactions, making the evaluation of binding affinity a central focus in structural biology. However, the molecular determinants underlying binding…

Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from…

COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key…

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…

In this paper, we study the large-scale protein interaction network of yeast uti lizing a stochastic method based upon percolation of random graphs. In order to find the global features of connectivities in the network, we introduce numeric…

Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the case of SARS-CoV-2, we performed a structural analysis of the network of protein interactions obtained from the integration of three sources:…

The SARS-CoV-2 pandemic has led to a significant emergence of highly mutated forms of viruses with a great ability to adapt to the human host. Some mutations resulted in changes in the amino acid sequences of viral proteins, including the…

The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…

The availability of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus data post-COVID has reached exponentially to an enormous magnitude, opening research doors to analyze its behavior. Various studies are conducted by…

We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions of proteins surfaces. This innovative and general procedure, based on the representation of the molecular…

Proteins can exhibit dynamic structural flexibility as they carry out their functions, especially in binding regions that interact with other molecules. For the key SARS-CoV-2 spike protein that facilitates COVID-19 infection, studies have…

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major worldwide public health emergency that has infected over $1.5$ million people. The partially open state of S1 subunit in spike glycoprotein is considered…

Proteins play a key role in facilitating the infectiousness of the 2019 novel coronavirus. A specific spike protein enables this virus to bind to human cells, and a thorough understanding of its 3-dimensional structure is therefore critical…

A theory on the conformation transition for SARS-CoV-2 spike protein (S) is proposed. The conformation equilibrium between open (up) and closed (down) conformations of receptor binding domain (RBD) of the spike is studied from the…

Coronaviruses are a class of virus responsible of the recent outbreak of Human Severe Acute Respiratory Syndrome. The molecular machinery behind the viral entry and thus infectivity is based on the formation of the complex of virus spike…

Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D…

Most of the ongoing projects aimed at the development of specific therapies and vaccines against COVID-19 use the SARS-CoV-2 spike (S) protein as the main target [1-3]. The binding of the spike protein with the ACE2 receptor (ACE2) of the…

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…