Related papers: Protein structure prediction by an iterative searc…
Motivation: Human cancer is caused by the accumulation of somatic mutations in tumor suppressors and oncogenes within the genome. In the case of oncogenes, recent theory suggests that there are only a few key "driver" mutations responsible…
Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in {\em in silico} materials design and drug discovery. In this paper, we propose a variable neighbourhood search…
Predicting the physical interaction of proteins is a cornerstone problem in computational biology. New classes of learning-based algorithms are actively being developed, and are typically trained end-to-end on protein complex structures…
We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition…
In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to…
Point matching refers to the process of finding spatial transformation and correspondences between two sets of points. In this paper, we focus on the case that there is only partial overlap between two point sets. Following the approach of…
An important problem in shape analysis is to match configurations of points in space filtering out some geometrical transformation. In this paper we introduce hierarchical models for such tasks, in which the points in the configurations are…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
This paper presents efficient algorithms for solving the problem of aligning a protein structure template to a query amino-acid sequence, known as protein threading problem. We consider the problem as a special case of graph matching…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
Energy minimization algorithms, such as graph cuts, enable the computation of the MAP solution under certain probabilistic models such as Markov random fields. However, for many computer vision problems, the MAP solution under the model is…
The advent of advanced crystallographic techniques has shifted structural biology from static, single-conformer models toward probing protein dynamics. Extracting cooperative motions from temporally and spatially averaged electron density…
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
Physical systems ranging from elastic bodies to kinematic linkages are defined on high-dimensional configuration spaces, yet their typical low-energy configurations are concentrated on much lower-dimensional subspaces. This work addresses…
Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interacting patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number…
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…