Related papers: Unfolding designable structures
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
We study the problem of deciding whether a crease pattern can be folded by simple folds (folding along one line at a time) under the infinite all-layers model introduced by [Akitaya et al., 2017], in which each simple fold is defined by an…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
The aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment. Using an exactly solvable lattice model, we design…
The discovery of new functional and stable materials is a big challenge due to its complexity. This work aims at the generation of new crystal structures with desired properties, such as chemical stability and specified chemical…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
Inspired by protein folding, we explored the construction of three-dimensional structures and machines from one-dimensional chains of simple building blocks. This approach not only allows us to recreate the self-replication mechanism…
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…
Metamorphic proteins like Lymphotactin are a notable exception of the empirical principle that structured natural proteins possess a unique three dimensional structure. In particular, the human chemokine lymphotactin protein (Ltn) exists in…
De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables…
We use a tensor unfolding technique to prove a new identifiability result for discrete bipartite graphical models, which have a bipartite graph between an observed and a latent layer. This model family includes popular models such as…
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…
The potential energy surface of an off-lattice model protein is characterized in detail by constructing a disconnectivity graph and by examining the organisation of pathways on the surface. The results clearly reveal the frustration…
A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past…
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…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
We consider the problem of counting the number of possible sets of rankings (called ranking patterns) generated by unfolding models of codimension one. We express the ranking patterns as slices of the braid arrangement and show that all…