AIMC Topic: Sequence Analysis, Protein

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PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool.

Bioinformatics (Oxford, England) Oct 1, 2014
UNLABELLED: Protein function prediction (PFP) is an automated function prediction method that predicts Gene Ontology (GO) annotations for a protein sequence using distantly related sequences and contextual associations of GO terms. Extended similarit...
Gene Ontology Humans Computer Graphics Algorithms Databases, Protein Sequence Analysis, Protein Computational Biology Molecular Sequence Annotation Proteins
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PseDNA-Pro: DNA-Binding Protein Identification by Combining Chou's PseAAC and Physicochemical Distance Transformation.

Molecular informatics Sep 26, 2014
Identification of DNA-binding proteins is an important problem in biomedical research as DNA-binding proteins are crucial for various cellular processes. Currently, the machine learning methods achieve the-state-of-the-art performance with different ...
Support Vector Machine Sequence Analysis, Protein Humans Databases, Protein Animals DNA-Binding Proteins
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SHARK: web server for alignment-free homology assessment for intrinsically disordered and unalignable protein regions.

Nucleic acids research Jul 7, 2025
Whereas alignment has been fundamental to sequence-based assessments of protein homology, it is ineffective for intrinsically disordered regions (IDRs) due to their lowered sequence conservation and unique sequence properties. Here, we present a web ...
Internet Amino Acid Sequence Intrinsically Disordered Proteins Sequence Alignment Sequence Analysis, Protein Sequence Homology, Amino Acid Humans Software Machine Learning Algorithms Animals
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StructMAn 2.0 Web: a web server for structural annotation of protein sequences and mutations.

Nucleic acids research Jul 7, 2025
StructMAn is a method for protein structural annotation. It describes each position of a protein sequence or specific variants in it in terms of their importance for the three-dimensional (3D) structure of the protein and its interactions with other ...
Software Protein Conformation User-Computer Interface Proteins Molecular Sequence Annotation Mutation Models, Molecular Sequence Analysis, Protein Internet Amino Acid Sequence
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MVSF-AB: accurate antibody-antigen binding affinity prediction via multi-view sequence feature learning.

Bioinformatics (Oxford, England) May 6, 2025
MOTIVATION: Predicting the binding affinity between antigens and antibodies accurately is crucial for assessing therapeutic antibody effectiveness and enhancing antibody engineering and vaccine design. Traditional machine learning methods have been w...
Machine Learning Algorithms Protein Binding Humans Antibody Affinity Sequence Analysis, Protein Antigen-Antibody Reactions Computational Biology Antibodies Antigens
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MEGA-GO: functions prediction of diverse protein sequence length using Multi-scalE Graph Adaptive neural network.

Bioinformatics (Oxford, England) Feb 4, 2025
MOTIVATION: The increasing accessibility of large-scale protein sequences through advanced sequencing technologies has necessitated the development of efficient and accurate methods for predicting protein function. Computational prediction models hav...
Sequence Analysis, Protein Computational Biology Proteins Databases, Protein Amino Acid Sequence Gene Ontology Neural Networks, Computer Algorithms
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[AcidBasePred: a protein acid-base tolerance prediction platform based on deep learning].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology Dec 25, 2024
The structures and activities of enzymes are influenced by pH of the environment. Understanding and distinguishing the adaptation mechanisms of enzymes to extreme pH values is of great significance for elucidating the molecular mechanisms and promoti...
Deep Learning Sequence Analysis, Protein Proteins Amino Acid Sequence Bacterial Proteins Enzymes Hydrogen-Ion Concentration
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Deep learning for the PSIPRED Protein Analysis Workbench.

Nucleic acids research Jul 5, 2024
The PSIRED Workbench is a long established and popular bioinformatics web service offering a wide range of machine learning based analyses for characterizing protein structure and function. In this paper we provide an update of the recent additions a...
Protein Conformation Sequence Analysis, Protein Computational Biology Proteins Internet Software Deep Learning
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Effect of tokenization on transformers for biological sequences.

Bioinformatics (Oxford, England) Mar 29, 2024
MOTIVATION: Deep-learning models are transforming biological research, including many bioinformatics and comparative genomics algorithms, such as sequence alignments, phylogenetic tree inference, and automatic classification of protein functions. Amo...
Computational Biology Proteins Algorithms Natural Language Processing Deep Learning Sequence Alignment Sequence Analysis, Protein
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DeepSS2GO: protein function prediction from secondary structure.

Briefings in bioinformatics Mar 27, 2024
Predicting protein function is crucial for understanding biological life processes, preventing diseases and developing new drug targets. In recent years, methods based on sequence, structure and biological networks for protein function annotation hav...
Computational Biology Proteins Databases, Protein Neural Networks, Computer Software Sequence Analysis, Protein Gene Ontology Algorithms Protein Structure, Secondary
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