Related papers: Soliton concepts and the protein structure
Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain.…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
A model for soliton dynamics on a hydrogen-bond network in helical proteins is proposed. It employs in three dimensions the formalism of fully integrable Toda lattices which admits phonons as well as solitons along the hydrogen-bonds of the…
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins.…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence.…
Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
Small-molecule foundation models are typically pretrained on standalone molecular data, unlike vision and language models that often benefit from cross-modal or relational supervision. Protein-ligand co-folding provides a molecular analogue…
Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to…
The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein design. In so-called inverse protein…
We explore stability regions for solitons in the nonlinear Schrodinger equation with a spatially confined region carrying a combination of self-focusing cubic and septimal terms, with a quintic one of either focusing or defocusing sign.…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Protein tertiary structure prediction has improved dramatically in recent years. A considerable fraction of various proteomes can be modelled in the absence of structural templates. We ask whether our DMPfold method can model all the…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a…