Comparison of biomolecules on the basis of Molecular Interaction Potentials

Rodrigo, Jordi; Barbany, Montserrat; Gutiérrez‐de‐Terán, Hugo; Centeno, Nuría B.; de-Càceres, Miquel; Dezi, Cristina; Fontaine, Fabien; Lozano, Juan José; Pastor, Manuel; Villà, Jordi; Sanz, Ferrán

doi:10.1590/s0103-50532002000600010

Cited by 10 publications

(4 citation statements)

References 11 publications

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“…This allows us to concentrate on stronger regional similarity of protein substructures, oppositely to rough methods, like VAST [12], DALI [13], CE [14] or other [15], [16], [17] that focus on fold similarity. In the view of the structure representation form, our method is more similar to techniques that base on Molecular Interaction Potentials (MIPs) or Mole- cular Interaction Fields (MIFs) [18], [19], [20]. This group of very precise algorithms is usually used in the process of drug design.…”

Section: Introductionmentioning

confidence: 99%

Alignment of protein structure energy patterns represented as sequences of Fuzzy Numbers

Mrozek

Kozielski

2009

NAFIPS 2009 - 2009 Annual Meeting of the North American Fuzzy Information Processing Society

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The comparative analysis of structural and energy features of proteins can be a key to understand how proteins work and interact to each other in cellular reactions. Potential energy, which is a function of atomic positions in a protein structure, can be used to describe molecule's abilities to interact with other biological molecules. Potential energy characteristics are supportive in searching similar, biologically important molecular regions that have similar functions in different organisms or organs. In the paper, we present the similarity searching method, which base on the alignment of energy patterns. In the alignment phase energy patterns are represented as sequences of fuzzy numbers. This increases the fault-tolerance of the alignment and ensures the approximate character of the method. The alignment of fuzzy sequences is one of the main steps in the new FN-EAST method (Fuzzy Numbers -Energy Alignment Search Tool). The FN-EAST allows to seek similar structural regions represented as energy patterns. The new alignment incorporated in the similarity searching eliminates some weaknesses of the FN-EAST predecessors.

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Section: Introductionmentioning

confidence: 99%

Alignment of protein structure energy patterns represented as sequences of Fuzzy Numbers

Mrozek

Kozielski

2009

NAFIPS 2009 - 2009 Annual Meeting of the North American Fuzzy Information Processing Society

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“…30 Several methods to compare MEPs and correlate them with some properties or activities, that avoid the problems related to visual comparisons, have been developed. 4,[30][31][32][33][34][35][36][37][38][39] When examining the wide variety of them, two classes can be clearly identified: those methods requiring the superposition of the corresponding molecular skeletons, i.e., alignment dependent (AD) approaches and those that are alignment independent (AI). While AD methods compare directly the MEP values on a set of points in the 3D ordinary space, AI approaches usually represent molecules by n-tuples whose components correspond to some descriptors that characterize the MEP field.…”

Section: Introductionmentioning

confidence: 99%

Graph Theoretical Similarity Approach To Compare Molecular Electrostatic Potentials

Marín

Aguirre

Daza

2008

J. Chem. Inf. Model.

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In this work we introduce a graph theoretical method to compare MEPs, which is independent of molecular alignment. It is based on the edit distance of weighted rooted trees, which encode the geometrical and topological information of Negative Molecular Isopotential Surfaces. A meaningful chemical classification of a set of 46 molecules with different functional groups was achieved. Structure--activity relationships for the corticosteroid binding affinity (CBG) of 31 steroids by means of hierarchical clustering resulted in a clear partitioning in high, intermediate, and low activity groups, whereas the results from quantitative structure--activity relationships, obtained from a partial least-squares analysis, showed comparable or better cross-validated correlation coefficients than the ones reported for previous methods based solely in the MEP.

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“…They use Molecular Interaction Potentials (MIPs) or Molecular Interaction Fields (MIFs), e.g. [12], [13], [14], [15], [16]. MIPs/ MIFs are results of interaction energies between the considered compounds and relevant probes.…”

Section: Introductionmentioning

confidence: 99%

An optimal alignment of proteins energy characteristics with crisp and fuzzy similarity awards

Mrozek

Małysiak

Kozielski

2007

2007 IEEE International Fuzzy Systems Conference

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In the paper, we discuss the usage of constant and fuzzy similarity awards while establishing an optimal alignment between energy characteristics of two compared protein energy profiles. Single protein energy profile is a set of energy characteristics of various types of energy. The energy profile is determined for a given protein structure. We use these profiles to find protein molecules of the same structural protein family and inspect conformational modifications in their molecular structures as an effect of biochemical reactions or environmental influences. Energy profiles are received in the computational process based on the molecular mechanics theory. Afterwards, these profiles can be stored in the special purpose database (EDB) and used by the search engine to find similar fragments of protein structures on the energy level. To optimize the alignment path we use modified, energy-adapted Smith-Waterman method with one of the tested similarity awards.

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Comparison of biomolecules on the basis of Molecular Interaction Potentials

Cited by 10 publications

References 11 publications

Alignment of protein structure energy patterns represented as sequences of Fuzzy Numbers

Alignment of protein structure energy patterns represented as sequences of Fuzzy Numbers

Graph Theoretical Similarity Approach To Compare Molecular Electrostatic Potentials

An optimal alignment of proteins energy characteristics with crisp and fuzzy similarity awards

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