Many areas of chemical biology, such as drug discovery, rely heavily on chemical libraries offeri... more Many areas of chemical biology, such as drug discovery, rely heavily on chemical libraries offering compounds usable in the industrial processes. However, the ”universe” containing all possible compounds, the so-called chemical space, is vast, and therefore, the libraries store only its representative parts. Thus, to explore the whole chemical space and to identify all its promising parts containing e.g., drug-like molecules computational methods have to be developed and employed.
In this paper, we propose a method for traveling in the chemical space called Molpher. Given two molecules, Molpher is intended to find a sequence of related compounds, called path in the chemical space, leading from the starting molecule to the target one. The path is generated by iterative application of the so-called morphing operators corresponding to simple chemical operations such as adding or removing an atom or a bond. The molecules on the resulting path represent a focused library that can be used as a starting point for other experiments. We also propose a testbed for examining qualities of algorithms such as Molpher. The testbed is used to describe Molpher’s qualities in terms of ability of finding a path in the space in the given time.
The recent interest in function of various RNA structures, reflected in the growth of solved RNA ... more The recent interest in function of various RNA structures, reflected in the growth of solved RNA structures in PDB, calls for methods for effective and effient similarity search in RNA structural databases. Here, we propose a method called SETTER (RNA SEcondary sTructure-based TERtiary structure similarity) based on partitioning of RNA structures into so-called generalized secondary structure units (GSSU). We introduce a fast similarity method exploiting RMSD-based algorithm allowing to assess distance to a pair of GSSU, and a method for aggregating these partial distances into a final distance corresponding to structural similarity of the examined RNA structures. Our algorithm yields not only the distance but also a superposition allowing to visualize the structural similarity. Comparative experiments show that our proposed method is competitive with the best existing solutions, both in terms of effectiveness and efficiency.
AbstractFinding similarity between a pair of protein structures is one of the fundamental tasks ... more AbstractFinding similarity between a pair of protein structures is one of the fundamental tasks in many areas of bioinformatical research such as protein structure prediction, function mapping, etc. We propose a method for finding pairing of amino acids based on densities ...
Many areas of chemical biology, such as drug discovery, rely heavily on chemical libraries offeri... more Many areas of chemical biology, such as drug discovery, rely heavily on chemical libraries offering compounds usable in the industrial processes. However, the ”universe” containing all possible compounds, the so-called chemical space, is vast, and therefore, the libraries store only its representative parts. Thus, to explore the whole chemical space and to identify all its promising parts containing e.g., drug-like molecules computational methods have to be developed and employed.
In this paper, we propose a method for traveling in the chemical space called Molpher. Given two molecules, Molpher is intended to find a sequence of related compounds, called path in the chemical space, leading from the starting molecule to the target one. The path is generated by iterative application of the so-called morphing operators corresponding to simple chemical operations such as adding or removing an atom or a bond. The molecules on the resulting path represent a focused library that can be used as a starting point for other experiments. We also propose a testbed for examining qualities of algorithms such as Molpher. The testbed is used to describe Molpher’s qualities in terms of ability of finding a path in the space in the given time.
The recent interest in function of various RNA structures, reflected in the growth of solved RNA ... more The recent interest in function of various RNA structures, reflected in the growth of solved RNA structures in PDB, calls for methods for effective and effient similarity search in RNA structural databases. Here, we propose a method called SETTER (RNA SEcondary sTructure-based TERtiary structure similarity) based on partitioning of RNA structures into so-called generalized secondary structure units (GSSU). We introduce a fast similarity method exploiting RMSD-based algorithm allowing to assess distance to a pair of GSSU, and a method for aggregating these partial distances into a final distance corresponding to structural similarity of the examined RNA structures. Our algorithm yields not only the distance but also a superposition allowing to visualize the structural similarity. Comparative experiments show that our proposed method is competitive with the best existing solutions, both in terms of effectiveness and efficiency.
AbstractFinding similarity between a pair of protein structures is one of the fundamental tasks ... more AbstractFinding similarity between a pair of protein structures is one of the fundamental tasks in many areas of bioinformatical research such as protein structure prediction, function mapping, etc. We propose a method for finding pairing of amino acids based on densities ...
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Papers by David Hoksza
In this paper, we propose a method for traveling in the chemical space called Molpher. Given two molecules, Molpher is intended to find a sequence of related compounds, called path in the chemical space, leading from the starting molecule to the target one. The path is generated by iterative application of the so-called morphing operators corresponding to simple chemical operations such as adding or removing an atom or a bond. The
molecules on the resulting path represent a focused library that can be used as a starting point for other experiments. We also propose a testbed for examining qualities of algorithms such as Molpher. The testbed is used to describe Molpher’s qualities in terms of ability of finding a path in the space in the given time.
In this paper, we propose a method for traveling in the chemical space called Molpher. Given two molecules, Molpher is intended to find a sequence of related compounds, called path in the chemical space, leading from the starting molecule to the target one. The path is generated by iterative application of the so-called morphing operators corresponding to simple chemical operations such as adding or removing an atom or a bond. The
molecules on the resulting path represent a focused library that can be used as a starting point for other experiments. We also propose a testbed for examining qualities of algorithms such as Molpher. The testbed is used to describe Molpher’s qualities in terms of ability of finding a path in the space in the given time.