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A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
We investigate the formation of beta-sheet structures in proteins without taking into account specific sequence-dependent hydrophobic interactions. To accomplish this, we introduce a model which explicitly incorporates both solvation…
Identifying protein-protein interactions is crucial for a systems-level understanding of the cell. Recently, algorithms based on inverse statistical physics, e.g. Direct Coupling Analysis (DCA), have allowed to use evolutionarily related…
Understanding the pivotal role of oxygen-containing organic compounds in serving as an energy source for living organisms and contributing to protein formation is crucial in the field of biochemistry. This study addresses the challenge of…
This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details…
In this paper, a new method for PPI (proteinprotein interaction) prediction is proposed. In PPI prediction, a reliable and sufficient number of training samples is not available, but a large number of unlabeled samples is in hand. In the…
The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation.…
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Given native 2D contact map, protein 3D structure could be reconstructed with accuracy of 2A or better, and such reconstruction is a feasible computational approach for protein folding problem. The prediction accuracy from traditional…
One key task in virtual screening is to accurately predict the binding affinity ($\triangle$$G$) of protein-ligand complexes. Recently, deep learning (DL) has significantly increased the predicting accuracy of scoring functions due to the…
In this paper we introduce a novel method of deriving a pairwise potential for protein folding. The potential is obtained by optimization procedure, which simultaneously maximizes the energy gap for {\it all} proteins in the database. To…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
Protein design is the inverse approach of the three-dimensional (3D) structure prediction for elucidating the relationship between the 3D structures and amino acid sequences. In general, the computation of the protein design involves a…
High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…
We formulate statistical-mechanical inverse methods in order to determine optimized interparticle interactions that spontaneously produce target many-particle configurations. Motivated by advances that give experimentalists greater and…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…