相关论文: Weak self-interactions of globular proteins studie…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
We present an efficient algorithm to recover the three dimensional structure of a protein from its contact map representation. First we show that when a physically realizable map is used as target, our method generates a structure whose…
Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently,…
A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected…
We study here the small-angle scattering structure factor for deterministic fat fractals in the reciprocal space. It is shown that fat fractals are exact self-similar in the range of iterations having the same values of the scaling factor,…
The prediction of protein interactions (CPIs) is crucial for the in-silico screening step in drug discovery. Recently, many end-to-end representation learning methods using deep neural networks have achieved significantly better performance…
Statistical thermodynamics basis of energy and residue position fluctuations is explained for native proteins. The protein and its surroundings are treated as a canonical system with emphasis on the effects of energy exchange between the…
Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement…
Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the…
The isospin breaking effects due to the Coulomb interaction in weakly-bound nuclei are studied using the Gamow Shell Model, a complex-energy configuration interaction approach which simultaneously takes into account many-body correlations…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
Small molecules play a pivotal role in modern medicine, and scrutinizing their interactions with protein targets is essential for the discovery and development of novel, life-saving therapeutics. The term "bioactivity" encompasses various…
Physically, disordered ensembles of non-homopolymeric polypeptides are expected to be heterogeneous; i.e., they should differ from those homogeneous ensembles of homopolymers that harbor an essentially unique relationship between average…
In this thesis, the ground state properties of nuclear matter, namely the energy per particle and the response to weak probes, are computed, studying the effects of three nucleon interactions. Both the variational approach, based on the…
Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…
Molecular self-assembly on surfaces constitutes a powerful method for creating tailor-made surface structures with dedicated functionalities. Varying the intermolecular interactions allows for tuning the resulting molecular structures in a…
This study is concerned with behaviour of fluid of monoclonal antibodies (mAbs) when trapped in a confinement represented by rigid spherical obstacles that attract proteins. The antibody molecule is depicted as an assembly of seven hard…
We show that the contact map of the native structure of globular proteins can be reconstructed starting from the sole knowledge of the contact map's principal eigenvector, and present an exact algorithm for this purpose. Our algorithm…
Colloid models have frequently been used to successfully describe the influence of protein-protein interactions on antibody solution properties, but they suffer from inherent problems due to the anisotropic shape of the particles. The net…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…