Related papers: Algorithm engineering for optimal alignment of pro…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
A goal of computational studies of protein-protein interfaces (PPIs) is to predict the binding site between two monomers that form a heterodimer. The simplest version of this problem is to rigidly re-dock the bound forms of the monomers,…
Motivation: Assessing the match between two biomolecular structures is at the heart of structural analyses such as superposition, alignment and docking. These tasks are typically solved with specialized structure-matching techniques…
We settle the computational complexity of fundamental questions related to multicriteria integer linear programs, when the dimensions of the strategy space and of the outcome space are considered fixed constants. In particular we construct:…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
Crystal structure prediction (CSP) for inorganic materials is one of the central and most challenging problems in materials science and computational chemistry. This problem can be formulated as a global optimization problem in which global…
The task of establishing correspondences between two 3D shapes is a long-standing challenge in computer vision. While numerous studies address full-full and partial-full 3D shape matching, only a limited number of works have explored the…
Protein-ligand scoring is a central component of structure-based drug design, underpinning molecular docking, virtual screening, and pose optimization. Conventional physics-based energy functions are often computationally expensive,…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
Low rank matrix approximation is a popular topic in machine learning. In this paper, we propose a new algorithm for this topic by minimizing the least-squares estimation over the Riemannian manifold of fixed-rank matrices. The algorithm is…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
The paper investigates the problem of fitting protein complexes into electron density maps. They are represented by high-resolution cryoEM density maps converted into overlapping matrices and partly show a structure of a complex. The…
Resonance assignment is a critical first step in the investigation of protein structures using NMR spectroscopy. The development of assignment methods that require less experimental data is possible with prior knowledge of the…
In science and engineering, intelligent processing of complex signals such as images, sound or language is often performed by a parameterized hierarchy of nonlinear processing layers, sometimes biologically inspired. Hierarchical systems…
Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the interrelationships between proteins. This task entails--but is…
In this paper, we consider the optimal coordination of automated vehicles at intersections under fixed crossing orders. We formulate the problem using direct optimal control and exploit the structure to construct a semi-distributed…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution…
Solving linear programs is often a challenging task in distributed settings. While there are good algorithms for solving packing and covering linear programs in a distributed manner (Kuhn et al.~2006), this is essentially the only class of…
Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…