Structural properties and interaction energies affecting drug design. An approach combining molecular simulations, statistics, interaction energies and neural networks

2015 ◽  
Vol 56 ◽  
pp. 7-12
Author(s):  
Dimitris Ioannidis ◽  
Georgios E. Papadopoulos ◽  
Georgios Anastassopoulos ◽  
Alexandros Kortsaris ◽  
Konstantinos Anagnostopoulos
Keyword(s):  
Neural Networks ◽  
Drug Design ◽  
Structural Properties ◽  
Molecular Simulations ◽  
Interaction Energies

AutoLinker: Automatic Fragment Linking with Deep Conditional Transformer Neural Networks

2020 ◽  
Author(s):  
Yuyao Yang ◽  
Shuangjia Zheng ◽  
Shimin Su ◽  
Jun Xu ◽  
Hongming Chen
Keyword(s):  
Neural Networks ◽  
Drug Discovery ◽  
Drug Design ◽  
State Of The Art ◽  
The State ◽  
Generative Model ◽  
Lead Optimization ◽  
Scaffold Hopping ◽  
Reference Models ◽  
Lead Generation

Fragment based drug design represents a promising drug discovery paradigm complimentary to the traditional HTS based lead generation strategy. How to link fragment structures to increase compound affinity is remaining a challenge task in this paradigm. Hereby a novel deep generative model (AutoLinker) for linking fragments is developed with the potential for applying in the fragment-based lead generation scenario. The state-of-the-art transformer architecture was employed to learn the linker grammar and generate novel linker. Our results show that, given starting fragments and user customized linker constraints, our AutoLinker model can design abundant drug-like molecules fulfilling these constraints and its performance was superior to other reference models. Moreover, several examples were showcased that AutoLinker can be useful tools for carrying out drug design tasks such as fragment linking, lead optimization and scaffold hopping.

Artificial Neural Networks (ANNs) and Solution of Civil Engineering Problems

2020 ◽  
pp. 13-38
Author(s):  
Melda Yucel ◽  
Sinan Melih Nigdeli ◽  
Gebrail Bekdaş
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Structural Properties ◽  
Structural Design ◽  
Civil Engineering ◽  
Back Propagation ◽  
Training Algorithm ◽  
Design Problems ◽  
Engineering Problems ◽  
Artificial Neural

This chapter reveals the advantages of artificial neural networks (ANNs) by means of prediction success and effects on solutions for various problems. With this aim, initially, multilayer ANNs and their structural properties are explained. Then, feed-forward ANNs and a type of training algorithm called back-propagation, which was benefited for these type networks, are presented. Different structural design problems from civil engineering are optimized, and handled intended for obtaining prediction results thanks to usage of ANNs.

scholarly journals Zagreb Connection Numbers for Cellular Neural Networks

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Jia-Bao Liu ◽  
Zahid Raza ◽  
Muhammad Javaid
Keyword(s):  
Neural Networks ◽  
Image Processing ◽  
Mathematical Models ◽  
Structural Properties ◽  
Cellular Neural Networks ◽  
Molecular Networks ◽  
Graph Invariants ◽  
Connection Number ◽  
Sensory Motor ◽  
3D Surfaces

Neural networks in which communication works only among the neighboring units are called cellular neural networks (CNNs). These are used in analyzing 3D surfaces, image processing, modeling biological vision, and reducing nonvisual problems of geometric maps and sensory-motor organs. Topological indices (TIs) are mathematical models of the (molecular) networks or structures which are presented in the form of numerical values, constitutional formulas, or numerical functions. These models predict the various chemical or structural properties of the under-study networks. We now consider analogous graph invariants, based on the second connection number of vertices, called Zagreb connection indices. The main objective of this paper is to compute these connection indices for the cellular neural networks (CNNs). In order to find their efficiency, a comparison among the obtained indices of CNN is also performed in the form of numerical tables and 3D plots.

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