AIMC Topic: Databases, Protein

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THPep: A machine learning-based approach for predicting tumor homing peptides.

Computational biology and chemistry
In the present era, a major drawback of current anti-cancer drugs is the lack of satisfactory specificity towards tumor cells. Despite the presence of several therapies against cancer, tumor homing peptides are gaining importance as therapeutic agent...

DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information.

Journal of computer-aided molecular design
DNA-binding proteins (DBPs) participate in various biological processes including DNA replication, recombination, and repair. In the human genome, about 6-7% of these proteins are utilized for genes encoding. DBPs shape the DNA into a compact structu...

Prediction of zinc-binding sites using multiple sequence profiles and machine learning methods.

Molecular omics
The zinc (Zn) cofactor has been proven to be involved in numerous biological mechanisms and the zinc-binding site is recognized as one of the most important post-translation modifications in proteins. Therefore, accurate knowledge of zinc ions in pro...

Exploring the Potential of Spherical Harmonics and PCVM for Compounds Activity Prediction.

International journal of molecular sciences
Biologically active chemical compounds may provide remedies for several diseases. Meanwhile, Machine Learning techniques applied to Drug Discovery, which are cheaper and faster than wet-lab experiments, have the capability to more effectively identif...

Extracting chemical-protein interactions from biomedical literature via granular attention based recurrent neural networks.

Computer methods and programs in biomedicine
BACKGROUND AND OBJECTIVE: The extraction of interactions between chemicals and proteins from biomedical literature is important for many biomedical tasks such as drug discovery and precision medicine. In the existing systems, the methods achieving co...

Machine-Learning-Based Predictor of Human-Bacteria Protein-Protein Interactions by Incorporating Comprehensive Host-Network Properties.

Journal of proteome research
The large-scale identification of protein-protein interactions (PPIs) between humans and bacteria remains a crucial step in systematically understanding the underlying molecular mechanisms of bacterial infection. Computational prediction approaches a...

NeuroPIpred: a tool to predict, design and scan insect neuropeptides.

Scientific reports
Insect neuropeptides and their associated receptors have been one of the potential targets for the pest control. The present study describes in silico models developed using natural and modified insect neuropeptides for predicting and designing new n...

Predicting drug-target interaction network using deep learning model.

Computational biology and chemistry
BACKGROUND: Traditional methods for drug discovery are time-consuming and expensive, so efforts are being made to repurpose existing drugs. To find new ways for drug repurposing, many computational approaches have been proposed to predict drug-target...

CiRCus: A Framework to Enable Classification of Complex High-Throughput Experiments.

Journal of proteome research
Despite the increasing use of high-throughput experiments in molecular biology, methods for evaluating and classifying the acquired results have not kept pace, requiring significant manual efforts to do so. Here, we present CiRCus, a framework to gen...

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning.

Proteins
The ability to predict local structural features of a protein from the primary sequence is of paramount importance for unraveling its function in absence of experimental structural information. Two main factors affect the utility of potential predict...