Related papers: Simulating Protein Conformations through Global Op…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
The computation of the global minimum energy conformation (GMEC) is an important and challenging topic in structure-based computational protein design. In this paper, we propose a new protein design algorithm based on the AND/OR…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Protein folding is a central challenge in computational biology, with important applications in molecular biology, drug discovery and catalyst design. As a hard combinatorial optimisation problem, it has been studied as a potential target…
The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
Aligning partially overlapping point sets where there is no prior information about the value of the transformation is a challenging problem in computer vision. To achieve this goal, we first reduce the objective of the robust point…
Modelling and predicting protein configurations is crucial for advancing drug discovery, enabling the design of treatments for life-threatening diseases. A critical aspect of this challenge is rotamer optimisation - the determination of…
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…
To find the best lattice model representation of a given full atom protein structure is a hard computational problem. Several greedy methods have been suggested where results are usually biased and leave room for improvement. In this paper…
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
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 apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Numerous applications require algorithms that can align partially overlapping point sets while maintaining invariance to geometric transformations (e.g., similarity, affine, rigid). This paper introduces a novel global optimization method…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…