AIMC Topic: Sequence Analysis, Protein

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SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition.

Briefings in bioinformatics Mar 27, 2024
Protein sequence design can provide valuable insights into biopharmaceuticals and disease treatments. Currently, most protein sequence design methods based on deep learning focus on network architecture optimization, while ignoring protein-specific p...
Amino Acid Sequence Sequence Alignment Sequence Analysis, Protein Neural Networks, Computer Proteins
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MMSMAPlus: a multi-view multi-scale multi-attention embedding model for protein function prediction.

Briefings in bioinformatics Jul 20, 2023
Protein is the most important component in organisms and plays an indispensable role in life activities. In recent years, a large number of intelligent methods have been proposed to predict protein function. These methods obtain different types of pr...
Proteins Amino Acid Sequence Sequence Analysis, Protein Neural Networks, Computer Software
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Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2023
Homology modeling was long considered a method of choice in tertiary protein structure prediction. However, it used to provide models of acceptable quality only when templates with appreciable sequence identity with a target could be found. The thres...
Databases, Protein Protein Conformation Protein Structure, Tertiary Sequence Analysis, Protein Protein Folding Computational Biology Proteins Machine Learning
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DistilProtBert: a distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts.

Bioinformatics (Oxford, England) Sep 16, 2022
SUMMARY: Recently, deep learning models, initially developed in the field of natural language processing (NLP), were applied successfully to analyze protein sequences. A major drawback of these models is their size in terms of the number of parameter...
Natural Language Processing Amino Acids Amino Acid Sequence Humans Proteome Sequence Analysis, Protein
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LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation.

Nucleic acids research Jul 5, 2022
Deep learning techniques have significantly advanced the field of protein structure prediction. LOMETS3 (https://zhanglab.ccmb.med.umich.edu/LOMETS/) is a new generation meta-server approach to template-based protein structure prediction and function...
Sequence Alignment Sequence Analysis, Protein Models, Chemical Protein Conformation Software Deep Learning Proteins Algorithms
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ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features.

Briefings in bioinformatics Jan 17, 2022
MOTIVATION: The Estimation of Model Accuracy problem is a cornerstone problem in the field of Bioinformatics. As of CASP14, there are 79 global QA methods, and a minority of 39 residue-level QA methods with very few of them working on protein complex...
Protein Structure, Quaternary Protein Structure, Tertiary Sequence Analysis, Protein Caspases Viral Proteins Humans Machine Learning SARS-CoV-2 Models, Molecular COVID-19
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Organism-specific training improves performance of linear B-cell epitope prediction.

Bioinformatics (Oxford, England) Dec 11, 2021
MOTIVATION: In silico identification of linear B-cell epitopes represents an important step in the development of diagnostic tests and vaccine candidates, by providing potential high-probability targets for experimental investigation. Current predict...
Epitopes, B-Lymphocyte Epitope Mapping Humans Species Specificity Animals Machine Learning Sequence Analysis, Protein Datasets as Topic
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Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics.

Bioinformatics (Oxford, England) Dec 7, 2021
MOTIVATION: The investigation of the structure of biological systems at the molecular level gives insights about their functions and dynamics. Shape and surface of biomolecules are fundamental to molecular recognition events. Characterizing their geo...
Computational Biology Databases, Protein Artificial Intelligence Protein Folding Sequence Analysis, Protein Datasets as Topic Protein Conformation
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Applying and improving AlphaFold at CASP14.

Proteins Dec 1, 2021
We describe the operation and improvement of AlphaFold, the system that was entered by the team AlphaFold2 to the "human" category in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The AlphaFold system entered in CASP14 is ent...
Models, Molecular Software Amino Acid Sequence Deep Learning Computational Biology Neural Networks, Computer Sequence Analysis, Protein Proteins Protein Conformation Protein Folding
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Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework.

Bioinformatics (Oxford, England) Nov 5, 2021
MOTIVATION: Over the past 50 years, our ability to model protein sequences with evolutionary information has progressed in leaps and bounds. However, even with the latest deep learning methods, the modelling of a critically important class of protein...
Datasets as Topic Amino Acid Sequence Computational Biology Sequence Analysis, Protein Data Accuracy Supervised Machine Learning
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