Maxent-Stress Optimization of 3D Biomolecular Models
نویسندگان
چکیده
Knowing a biomolecule’s structure is inherently linked to and a prerequisite for any detailed understanding of its function. Significant effort has gone into developing technologies for structural characterization. These technologies do not directly provide 3D structures; instead they typically yield noisy and erroneous distance information between specific entities such as atoms or residues, which have to be translated into consistent 3D models. Here we present an approach for this translation process based on maxent-stress optimization. Our new approach extends the original graph drawing method for the new application’s specifics by introducing additional constraints and confidence values as well as algorithmic components. Extensive experiments demonstrate that our approach infers structural models (i. e., sensible 3D coordinates for the molecule’s atoms) that correspond well to the distance information, can handle noisy and error-prone data, and is considerably faster than established tools. Our results promise to allow domain scientists nearly-interactive structural modeling based on distance constraints.
منابع مشابه
TOPOLOGY OPTIMIZATION OF PRETENSIONED CONCRETE BEAMS CONSIDERING MATERIAL NONLINEARITY
In this paper, the bi-directional evolutionary structural optimization (BESO) method is used to find optimal layouts of 3D prestressed concrete beams. Considering the element sensitivity number as the design variable, the mathematical formulation of topology optimization is developed based on the ABAQUS finite element software package. The surface-to-surface contact with a small sliding between...
متن کاملMaximum entropy model parameterization with TF∗IDF weighted vector space model
Maximum entropy (MaxEnt) models have been used in many spoken language tasks. The training of a MaxEnt model often involves an iterative procedure that starts from an initial parameterization and gradually updates it towards the optimum. Due to the convexity of its objective function (hence a global optimum on a training set), little attention has been paid to model initialization in MaxEnt tra...
متن کاملStress Distribution in Four Restorative Methods in Endodontically Treated Maxillary Premolar: A 3D Finite Element Analysis
Introduction: the Restoration of endodontically treated teeth is critical, and the Awareness of stresses developed by oblique and vertical forces in restorative methods take a great role in treatment plans. Due to the anatomical shape and inherent form of the stress distribution premolars, could be lost by fractures. Some fractures such as vertical fracture which is probable in...
متن کاملA New Entropy Optimization Model for Graduation of Data in Survival Analysis
Graduation of data is of great importance in survival analysis. Smoothness and goodness of fit are two fundamental requirements in graduation. Based on the instinctive defining expression for entropy in terms of a probability distribution, two optimization models based on the Maximum Entropy Principle (MaxEnt) and Minimum Cross Entropy Principle (MinCEnt) to estimate mortality probability distr...
متن کامل