AIMC Topic: Computational Biology

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EvoStruct-Sub: An accurate Gram-positive protein subcellular localization predictor using evolutionary and structural features.

Journal of theoretical biology
Determining subcellular localization of proteins is considered as an important step towards understanding their functions. Previous studies have mainly focused solely on Gene Ontology (GO) as the main feature to tackle this problem. However, it was s...

Efficient computational model for classification of protein localization images using Extended Threshold Adjacency Statistics and Support Vector Machines.

Computer methods and programs in biomedicine
BACKGROUND AND OBJECTIVE: Discriminative and informative feature extraction is the core requirement for accurate and efficient classification of protein subcellular localization images so that drug development could be more effective. The objective o...

Functional Categorization of Disease Genes Based on Spectral Graph Theory and Integrated Biological Knowledge.

Interdisciplinary sciences, computational life sciences
Interaction of multiple genetic variants is a major challenge in the development of effective treatment strategies for complex disorders. Identifying the most promising genes enhances the understanding of the underlying mechanisms of the disease, whi...

K: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks.

Journal of chemical information and modeling
Accurately predicting protein-ligand binding affinities is an important problem in computational chemistry since it can substantially accelerate drug discovery for virtual screening and lead optimization. We propose here a fast machine-learning appro...

InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk.

BMC genomics
BACKGROUND: Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively used Disease Ontology (DO) and H...

iMem-2LSAAC: A two-level model for discrimination of membrane proteins and their types by extending the notion of SAAC into chou's pseudo amino acid composition.

Journal of theoretical biology
Membrane proteins execute significant roles in cellular processes of living organisms, ranging from cell signaling to cell adhesion. As a major part of a cell, the identification of membrane proteins and their functional types become a challenging jo...

Multi-label Deep Learning for Gene Function Annotation in Cancer Pathways.

Scientific reports
The war on cancer is progressing globally but slowly as researchers around the world continue to seek and discover more innovative and effective ways of curing this catastrophic disease. Organizing biological information, representing it, and making ...

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening.

PLoS computational biology
This work introduces a number of algebraic topology approaches, including multi-component persistent homology, multi-level persistent homology, and electrostatic persistence for the representation, characterization, and description of small molecules...

ProtDet-CCH: Protein Remote Homology Detection by Combining Long Short-Term Memory and Ranking Methods.

IEEE/ACM transactions on computational biology and bioinformatics
As one of the most challenging tasks in sequence analysis, protein remote homology detection has been extensively studied. Methods based on discriminative models and ranking approaches have achieved the state-of-the-art performance, and these two kin...