AIMC Topic: Amino Acid Sequence

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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...
Humans Proteins Models, Molecular Bayes Theorem Amino Acid Sequence Neural Networks, Computer Machine Learning Support Vector Machine
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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 Databases, Protein Host Microbial Interactions Bacterial Proteins Type III Secretion Systems Neural Networks, Computer Amino Acid Sequence Deep Learning Computational Biology
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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 ...
Humans Markov Chains Machine Learning Databases, Protein Algorithms ROC Curve Amino Acids DNA-Binding Proteins Computational Biology Amino Acid Sequence Support Vector Machine
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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...
Structural Homology, Protein Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Mapping Protein Multimerization Protein Interaction Domains and Motifs Proteins Humans Benchmarking Thermodynamics Ligands Amino Acid Sequence Molecular Docking Simulation Software Computer Graphics Binding Sites Deep Learning Protein Binding Research Design Peptides
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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 ...
Internet Deep Learning Amino Acid Sequence Computational Biology Intrinsically Disordered Proteins Evolution, Molecular
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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...
Amino Acids Amino Acid Sequence Neural Networks, Computer Computational Biology Proteins
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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...
Proteins Models, Molecular Amino Acid Sequence Software Sequence Homology Protein Conformation Humans Algorithms Neural Networks, Computer Cryoelectron Microscopy Deep Learning
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Sequence-Based Prediction of Fuzzy Protein Interactions.

Journal of molecular biology Feb 27, 2020
It is becoming increasingly recognised that disordered proteins may be fuzzy, in that they can exhibit a wide variety of binding modes. In addition to the well-known process of folding upon binding (disorder-to-order transition), many examples are em...
Protein Conformation Protein Folding Sequence Analysis, Protein Protein Domains Amino Acid Sequence Intrinsically Disordered Proteins Protein Interaction Domains and Motifs Sequence Homology Humans Algorithms Protein Binding Fuzzy Logic Databases, Protein Models, Molecular
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Exploration and Evaluation of Machine Learning-Based Models for Predicting Enzymatic Reactions.

Journal of chemical information and modeling Feb 27, 2020
Unannotated gene sequences in databases are increasing due to sequencing advances. Therefore, computational methods to predict functions of unannotated genes are needed. Moreover, novel enzyme discovery for metabolic engineering applications further ...
Algorithms Databases, Factual Computational Biology Amino Acid Sequence Machine Learning
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Computational Identification and Analysis of Ubiquinone-Binding Proteins.

Cells Feb 24, 2020
Ubiquinone is an important cofactor that plays vital and diverse roles in many biological processes. Ubiquinone-binding proteins (UBPs) are receptor proteins that dock with ubiquinones. Analyzing and identifying UBPs via a computational approach will...
Amino Acid Sequence Computational Biology Humans Ubiquinone Membrane Proteins Machine Learning Gene Ontology Carrier Proteins Protein Binding Protein Interaction Domains and Motifs Binding Sites Position-Specific Scoring Matrices Sequence Analysis, Protein
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