Related papers: Structured Random Binding: a minimal model of prot…
Accurately measuring protein-RNA binding affinity is crucial in many biological processes and drug design. Previous computational methods for protein-RNA binding affinity prediction rely on either sequence or structure features, unable to…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
Robust control theory has been successfully applied to numerous real-world problems using a small set of devices called {\it controllers}. However, the real systems represented by networks contain unreliable components and modern robust…
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein…
Correlations and other collective phenomena in a schematic model of heterogeneous binary agents (individual spin-glass samples) are considered on the complete graph and also on 2d and 3d regular lattices. The system's stochastic dynamics is…
Numerous experiments demonstrate a high level of promiscuity and structural disorder in organismal proteomes. Here we ask the question what makes a protein promiscuous, i.e., prone to non-specific interactions, and structurally disordered.…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
Many biochemical applications such as molecular property prediction require models to generalize beyond their training domains (environments). Moreover, natural environments in these tasks are structured, defined by complex descriptors such…
The theory of transition between $\alpha$-helix, $\beta$-sheet and random coil conformation of a protein is discussed through a simple model, that includes both short and long-range interactions. Besides the bonding parameter and helical…
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…
A structure is called homogeneous if every isomorphism between finite substructures of the structure extends to an automorphism of the structure. Recently, P. J. Cameron and J. Ne\v{s}et\v{r}il introduced a relaxed version of homogeneity:…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
This study proposes an adaptive subsystem-based control (SBC) for systematic and straightforward nonlinear~control of nth-order strict-feedback form (SFF) systems.~By decomposing the SFF system to subsystems, a generic~term (namely…
We investigate protein-protein interactions in solution by small-angle X-ray scattering (SAXS) and theoretical modeling. The structure factor for solutions of bovine pancreatic trypsin inhibitor (BPTI), myoglobin (Mb), and intestinal fatty…
Score-based generative models (SGMs) have proven to be powerful tools for designing new proteins. Designing proteins that bind a pre-specified target is highly relevant to a range of medical and industrial applications. Despite the flurry…
Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…
Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general…
A statistical model of protein families, called profile conditional random fields (CRFs), is proposed. This model may be regarded as an integration of the profile hidden Markov model (HMM) and the Finkelstein-Reva (FR) theory of protein…