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Amino Acid Sequence

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Deep Dive into Machine Learning Models for Protein Engineering.

Journal of chemical information and modeling May 5, 2020
Protein redesign and engineering has become an important task in pharmaceutical research and development. Recent advances in technology have enabled efficient protein redesign by mimicking natural evolutionary mutation, selection, and amplification s...
Algorithms Amino Acid Sequence Protein Engineering Neural Networks, Computer Machine Learning
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AFP-LSE: Antifreeze Proteins Prediction Using Latent Space Encoding of Composition of k-Spaced Amino Acid Pairs.

Scientific reports Apr 28, 2020
Species living in extremely cold environments resist the freezing conditions through antifreeze proteins (AFPs). Apart from being essential proteins for various organisms living in sub-zero temperatures, AFPs have numerous applications in different i...
Machine Learning Animals Computational Biology Fish Proteins Antifreeze Proteins Amino Acid Sequence Fishes
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TooT-T: discrimination of transport proteins from non-transport proteins.

BMC bioinformatics Apr 23, 2020
BACKGROUND: Membrane transport proteins (transporters) play an essential role in every living cell by transporting hydrophilic molecules across the hydrophobic membranes. While the sequences of many membrane proteins are known, their structure and fu...
Computational Biology Support Vector Machine Machine Learning Amino Acid Sequence Membrane Transport Proteins
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Machine Learning Approaches for Quality Assessment of Protein Structures.

Biomolecules Apr 17, 2020
Protein structures play a very important role in biomedical research, especially in drug discovery and design, which require accurate protein structures in advance. However, experimental determinations of protein structure are prohibitively costly an...
Proteins Models, Molecular Bayes Theorem Machine Learning Support Vector Machine Humans Amino Acid Sequence Neural Networks, Computer
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ACNNT3: Attention-CNN Framework for Prediction of Sequence-Based Bacterial Type III Secreted Effectors.

Computational and mathematical methods in medicine Apr 3, 2020
The type III secretion system (T3SS) is a special protein delivery system in Gram-negative bacteria which delivers T3SS-secreted effectors (T3SEs) to host cells causing pathological changes. Numerous experiments have verified that T3SEs play importan...
Gram-Negative Bacteria Neural Networks, Computer Host Microbial Interactions Bacterial Proteins Deep Learning Type III Secretion Systems Amino Acid Sequence Computational Biology Databases, Protein
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HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection.

Computational and mathematical methods in medicine Mar 28, 2020
Prediction of DNA-binding proteins (DBPs) has become a popular research topic in protein science due to its crucial role in all aspects of biological activities. Even though considerable efforts have been devoted to developing powerful computational ...
DNA-Binding Proteins Amino Acid Sequence ROC Curve Markov Chains Databases, Protein Computational Biology Support Vector Machine Amino Acids Humans Machine Learning Algorithms
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Energy-based graph convolutional networks for scoring protein docking models.

Proteins Mar 16, 2020
Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational alternative for su...
Protein Conformation, beta-Strand Structural Homology, Protein Protein Conformation, alpha-Helical Benchmarking Binding Sites Amino Acid Sequence Humans Ligands Thermodynamics Software Protein Binding Computer Graphics Research Design Proteins Protein Interaction Mapping Peptides Protein Multimerization Molecular Docking Simulation Protein Interaction Domains and Motifs Deep Learning
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SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning.

Genomics, proteomics & bioinformatics Mar 13, 2020
Intrinsically disordered or unstructured proteins (or regions in proteins) have been found to be important in a wide range of biological functions and implicated in many diseases. Due to the high cost and low efficiency of experimental determination ...
Intrinsically Disordered Proteins Deep Learning Computational Biology Evolution, Molecular Internet Amino Acid Sequence
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DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet.

Journal of chemical information and modeling Mar 9, 2020
Computational protein design remains a challenging task despite its remarkable success in the past few decades. With the rapid progress of deep-learning techniques and the accumulation of three-dimensional protein structures, the use of deep neural n...
Neural Networks, Computer Computational Biology Proteins Amino Acids Amino Acid Sequence
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Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps.

Scientific reports Mar 9, 2020
Cryo-electron microscopy (cryo-EM) has become a leading technology for determining protein structures. Recent advances in this field have allowed for atomic resolution. However, predicting the backbone trace of a protein has remained a challenge on a...
Humans Neural Networks, Computer Software Algorithms Deep Learning Proteins Protein Conformation Cryoelectron Microscopy Sequence Homology Models, Molecular Amino Acid Sequence
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