Related papers: Knowledge-based energy functions for computational…
We have considered the problem of protein design based on a model where the contact energy between amino acid residues is fitted phenomenologically using the Miyazawa--Jernigan matrix. Due to the simple form of the contact energy function,…
Knowledge-based potentials were developed to investigate the differentiation of native structures from their decoy sets. This work presents the construction of two different distance-dependent potential energy functions based on two…
An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only $C_\alpha$ atoms need to be specified, an accurate potential function is…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
We discuss probabilistic methods for predicting protein functions from protein-protein interaction networks. Previous work based on Markov Randon Fields is extended and compared to a general machine-learning theoretic approach. Using actual…
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of…
In this study, we propose a Kernel-PCA model designed to capture structure-function relationships in a protein. This model also enables ranking of reaction coordinates according to their impact on protein properties. By leveraging machine…
We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting…
Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most…
Computational protein design facilitates discovery of novel proteins with prescribed structure and functionality. Exciting designs were recently reported using novel data-driven methodologies that can be roughly divided into two categories:…
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. However, many of the current PPI extraction methods need extensive feature engineering and cannot…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
Predicting the 3D structure of a macromolecule, such as a protein or an RNA molecule, is ranked top among the most difficult and attractive problems in bioinformatics and computational biology. Its importance comes from the relationship…
Potential functions are critical for computational studies of protein structure prediction, folding, and sequence design. A class of widely used potentials for coarse grained models of proteins are contact potentials in the form of weighted…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…
Existing data-centric methods for protein science generally cannot sufficiently capture and leverage biology knowledge, which may be crucial for many protein tasks. To facilitate research in this field, we create ProteinKG65, a knowledge…
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…