AIMC Topic: Proteins

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CoRNeA: A Pipeline to Decrypt the Inter-Protein Interfaces from Amino Acid Sequence Information.

Biomolecules Jun 22, 2020
Decrypting the interface residues of the protein complexes provides insight into the functions of the proteins and, hence, the overall cellular machinery. Computational methods have been devised in the past to predict the interface residues using ami...
Amino Acid Sequence Proteins Databases, Protein Humans Protein Binding Computational Biology Machine Learning
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MealTime-MS: A Machine Learning-Guided Real-Time Mass Spectrometry Analysis for Protein Identification and Efficient Dynamic Exclusion.

Journal of the American Society for Mass Spectrometry Jun 17, 2020
Mass spectrometry-based proteomics technologies are prime methods for the high-throughput identification of proteins in complex biological samples. Nevertheless, there are still technical limitations that hinder the ability of mass spectrometry to id...
Humans Algorithms Supervised Machine Learning Tandem Mass Spectrometry HEK293 Cells Proteomics Proteins
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Prediction of Protein-Protein Interactions with Local Weight-Sharing Mechanism in Deep Learning.

BioMed research international Jun 13, 2020
Protein-protein interactions (PPIs) are important for almost all cellular processes, including metabolic cycles, DNA transcription and replication, and signaling cascades. The experimental methods for identifying PPIs are always time-consuming and ex...
Protein Interaction Mapping Mice Computational Biology Saccharomyces cerevisiae Proteins Deep Learning Caenorhabditis elegans Databases, Protein Protein Interaction Maps Humans Escherichia coli Animals
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Rosetta custom score functions accurately predict ΔΔG of mutations at protein-protein interfaces using machine learning.

Chemical communications (Cambridge, England) May 22, 2020
Protein-protein interfaces play essential roles in a variety of biological processes and many therapeutic molecules are targeted at these interfaces. However, accurate predictions of the effects of interfacial mutations to identify "hotspots" have re...
Machine Learning Proteins Protein Interaction Domains and Motifs Mutation
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Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring.

Journal of chemical information and modeling May 11, 2020
Virtual Screening (VS) based on molecular docking is an efficient method used for retrieving novel hit compounds in drug discovery. However, the accuracy of the current docking scoring function (SF) is usually insufficient. In this study, in order to...
Ligands Molecular Docking Simulation Machine Learning Protein Binding Proteins
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Sparsity-Penalized Stacked Denoising Autoencoders for Imputing Single-Cell RNA-Seq Data.

Genes May 11, 2020
Single-cell RNA-seq (scRNA-seq) is quite prevalent in studying transcriptomes, but it suffers from excessive zeros, some of which are true, but others are false. False zeros, which can be seen as missing data, obstruct the downstream analysis of sing...
Transcriptome Deep Learning Single-Cell Analysis Computer Simulation Leukocytes, Mononuclear RNA Datasets as Topic Fetal Blood RNA-Seq Proteins Humans Data Compression
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Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction.

PloS one May 6, 2020
Protein secondary structure prediction remains a vital topic with broad applications. Due to lack of a widely accepted standard in secondary structure predictor evaluation, a fair comparison of predictors is challenging. A detailed examination of fac...
Amino Acid Sequence Protein Structure, Secondary Neural Networks, Computer Software Proteins Databases, Protein Algorithms Amino Acids Deep Learning
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QUATgo: Protein quaternary structural attributes predicted by two-stage machine learning approaches with heterogeneous feature encoding.

PloS one Apr 29, 2020
Many proteins exist in natures as oligomers with various quaternary structural attributes rather than as single chains. Predicting these attributes is an essential task in computational biology for the advancement of proteomics. However, the existing...
Algorithms Animals Support Vector Machine Proteins Computational Biology Humans Viral Proteins Databases, Protein Machine Learning Sequence Analysis, Protein Protein Domains Software Protein Structure, Quaternary
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Anomaly Detection-Based Recognition of Near-Native Protein Structures.

IEEE transactions on nanobioscience Apr 27, 2020
The three-dimensional structures populated by a protein molecule determine to a great extent its biological activities. The rich information encoded by protein structure on protein function continues to motivate the development of computational appro...
Protein Conformation Machine Learning Algorithms Proteins Databases, Protein Computational Biology
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LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening.

Journal of chemical information and modeling Apr 23, 2020
Comparative evaluation of virtual screening methods requires a rigorous benchmarking procedure on diverse, realistic, and unbiased data sets. Recent investigations from numerous research groups unambiguously demonstrate that artificially constructed ...
Molecular Docking Simulation Machine Learning Proteins Ligands
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