AIMC Topic: Proteins

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The PSIPRED Protein Analysis Workbench: 20 years on.

Nucleic acids research
The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 year...

mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Nucleic acids research
Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predic...

PrankWeb: a web server for ligand binding site prediction and visualization.

Nucleic acids research
PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability cent...

NetGO: improving large-scale protein function prediction with massive network information.

Nucleic acids research
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated with multiple gene ontology terms as its labels. Bas...

An equivariant Bayesian convolutional network predicts recombination hotspots and accurately resolves binding motifs.

Bioinformatics (Oxford, England)
MOTIVATION: Convolutional neural networks (CNNs) have been tremendously successful in many contexts, particularly where training data are abundant and signal-to-noise ratios are large. However, when predicting noisily observed phenotypes from DNA seq...

DeepCrystal: a deep learning framework for sequence-based protein crystallization prediction.

Bioinformatics (Oxford, England)
MOTIVATION: Protein structure determination has primarily been performed using X-ray crystallography. To overcome the expensive cost, high attrition rate and series of trial-and-error settings, many in-silico methods have been developed to predict cr...

Antibody interface prediction with 3D Zernike descriptors and SVM.

Bioinformatics (Oxford, England)
MOTIVATION: Antibodies are a class of proteins capable of specifically recognizing and binding to a virtually infinite number of antigens. This binding malleability makes them the most valuable category of biopharmaceuticals for both diagnostic and t...

Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction.

Bioinformatics (Oxford, England)
MOTIVATION: With the accumulation of DNA sequencing data, convolution neural network (CNN) based methods such as DeepBind and DeepSEA have achieved great success for predicting the function of primary DNA sequences. Previous studies confirm the impor...

High precision protein functional site detection using 3D convolutional neural networks.

Bioinformatics (Oxford, England)
MOTIVATION: Accurate annotation of protein functions is fundamental for understanding molecular and cellular physiology. Data-driven methods hold promise for systematically deriving rules underlying the relationship between protein structure and func...

[Prediction of protein subcellular localization based on multilayer sparse coding].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
In order to provide a theoretical basis for better understanding the function and properties of proteins, we proposed a simple and effective feature extraction method for protein sequences to determine the subcellular localization of proteins. First,...