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ITHEA Classification Structure > J. Computer Applications  > J.2 PHYSICAL SCIENCES AND ENGINEERING 
ITHEA Classification Structure > J. Computer Applications  > J.3 LIFE AND MEDICAL SCIENCES 
SYMMETRIZATION: RANKING AND CLUSTERING IN PROTEIN INTERFACES
By: Giovanni Feverati, Claire Lesieur, Laurent Vuillon (4122 reads)
Rating: (1.00/10)

Abstract: Purely geometric arguments are used to extract information from three-dimensional structures of oligomeric proteins, that are very common biological entities stably made of several polypeptidic chains. They are characterized by the presence of an interface between adjacent amino acid chains and can be investigated with the approach proposed here. We introduce a method, called symmetrization, that allows one to rank interface interactions on the basis of inter-atomic distances and of the local geometry. The lowest level of the ranking has been used previously with interesting results. Now, we need to complete this picture with a careful analysis of the higher ranks, that are for the first time introduced here, in a proper mathematical set up. The interface finds a very nice mathematical abstraction by the notion of weighted bipartite graph, where the inter-atomic distance provides the weight. Thus, our approach is partially inspired to graph theory decomposition methods but with an emphasis to “locality”, namely the idea that structures constructed by the symmetrization adapt to the local scales of the problem. This is an important issue as the known interfaces may present major differences in relation to their size, their composition and the local geometry. Thus, we looked for a local method, that can autonomously detect the local structure. The physical neighborhood is introduced by the concept of cluster of interactions. We discuss the biological applications of this ranking and our previous fruitful experience with the lowest symmetrized level. An example is given, using the prototypical cholera toxin.

Keywords: symmetrization, protein interfaces, oligomeric proteins, graphs, bonds ranking, interaction clusters.

ACM Classification Keywords: J.2 Physical sciences - Mathematics and statistics J.3 Life and medical sciences - Biology and genetics

Link:

SYMMETRIZATION: RANKING AND CLUSTERING IN PROTEIN INTERFACES

Giovanni Feverati, Claire Lesieur, Laurent Vuillon

http://www.foibg.com/ibs_isc/ibs-25/ibs-25-p12.pdf

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J.2 PHYSICAL SCIENCES AND ENGINEERING
article: DIDACTIC DESIGNING OF RESOURCE SUPPORT FOR TRAINING ENVIRONMENT · PREDICTIVE MODELING OF SPATIAL REDISTRIBUTION IN DYNAMICAL MODELS OF GLOBAL ... · WIRELESS DATA TRANSMISSION OPTIONS IN ROTARY IN-DRILLING ALIGNMENT(R-IDA) ... · BIOLOGICAL PROCESSES STUDIES THROUGH SOFTWARE TOOLS:... · ENERGY HARVESTING IN HORIZONTAL DRILLING PROCESSES FOR THE PURPOSE OF INFORMATIO · METHODS OF RECONSTRUCTION OF SURFACE PROFILES MEASURED BY STYLUS METHOD · USING REAL-TIME SYSTEM TO MANAGE PRODUCTION DATA IN A DISTRIBUTED SYSTEM · SYMMETRIZATION: RANKING AND CLUSTERING IN PROTEIN INTERFACES · GOD-ICS. ON FUNDAMENTAL INFORMATION FIELD QUEST · PREDICTION OF STYLUS TIP RADIUS · SIMULATION OF THE EFFECT OF STYLUS TIP RADIUS ON THE RESULTS OF SURFACE ... · ON A DIRECT APPROACH TO THE SOLUTION OF INVERSE OPTICAL PROBLEMS · PREDICTION OF STYLUS TIP RADIUS · MODELING OPTICAL RESPONSE OF THIN FILMS: CHOICE OF THE REFRACTIVE INDEX ... · DEVICE FOR COUNTING OF THE GLASS BOTTLES ON THE CONVEYOR BELT ·
J.3 LIFE AND MEDICAL SCIENCES
article: About estimate of fuzzy differential equations distribution · APPLICATION OF FIBER-OPTICAL MODULATORS AS MEASURING DEVICES IN ... · IT-COMMUNICATORS FOR MEDICINE · MULTILEVEL SENSOR NETWORKS FOR PRECISION FARMING AND ENVIRONMENTAL MONITORING · CHARACTERIZATION OF A CUFF-BASED SHAPE MEMORY ALLOY (SMA) ACTUATOR · PORTABLE BIOSENSOR: FROM IDEA TO MARKET · GEOMETRIC APPROACH FOR GAUSSIAN-KERNEL BOLSTERED ERROR ESTIMATION... · SIMULATION OF BIOLOGICAL MODELS USING CAD TOOLS: NEEDS AND FUTURE · BIOLOGICAL PROCESSES STUDIES THROUGH SOFTWARE TOOLS:... · REMOTE SMART BIOSENSORS FOR PRECISION FARMING AND ENVIRONMENT PROTECTION · AUTOMATED SYSTEM FOR QUANTIFYING THE LEVEL OF PREPARATION IN COLONOSCOPY · АНАЛИЗ АЛГОРИТМОВ ПРОГНОЗИРОВАНИЯ ТРЕТИЧН� · ON THE DISCRETIZATION OF DISTANCE GEOMETRY PROBLEMS · SYMMETRIZATION: RANKING AND CLUSTERING IN PROTEIN INTERFACES · DATA ACQISITION SYSTEMS FOR PRECISION FARMING · HISTOLOGY IMAGE SEGMENTATION · ВЫЯВЛЕНИЕ ФРАКТАЛОПОДОБНЫХ СТРУКТУР В ДНК- · PORTABLE DEVICE "FLORATEST" AS TOOL FOR ESTIMATING OF MEGALOPOLIS ECOLOGY STATE · KIRLIAN IMAGE PREPROCESSING DIAGNOSTIC SYSTEM · WIRELESS COMMUNICATION AND CONTROL SYSTEM FOR PORTABLE ... · ON THE FEASIBILITY OF STEERING SWALLOWABLE MICROSYSTEM CAPSULES USING ... · ANALYSIS OF DERMATOGLYPHIC SIGNS FOR DEFINITION PSYCHIC FUNCTIONAL ... · PORTABLE DEVICE "FLORATEST" AS TOOL FOR ESTIMATING OF MEGALOPOLIS ECOLOGY STATE · SMART PORTABLE FLUOROMETER FOR EXPRESS-DIAGNOSTICS OF PHOTOSYNTHESIS: ... · APPLICATION OF THE ARTIFICIAL INTELLIGENCE ALGORITHMS FOR SYSTEM ANALYSIS ... · APPLICATION OF NETWORK TECHNOLOGIES FOR DEVELOPMENT ... · ANALYSIS AND OPTIMIZATION OF SYNTHETIC APERTURE ULTRASOUND ... · EXPLORATION BY MEANS OF COMPUTER SIMULATION OF NONLINEAR HIERARCHICAL ... · MODEL CONSTRUCTION AND RESEARCH USING SYSTEM COMPOSITIONAL ... · GROUND OF MODEL FOR THE GENERALIZED CRITERION FORMING AT ... ·
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