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Protein remote homology detection and structural alignment using deep learning
Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence...
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Homology Modeling of the G Protein-Coupled Receptors
G protein-coupled receptors (GPCRs) are therapeutically important family of membrane proteins. Despite growing number of experimental structures...
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Homology Modeling of Transporter Proteins
Membrane transporter proteins are divided into channels/pores and carriers and constitute protein families of physiological and pharmacological...
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Optimal Alignment
When we align two sequences, we in fact propose an evolutionary history for them. A history, where we account for three kinds of events, mutation,...
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Protein embedding based alignment
PurposeDespite the many progresses with alignment algorithms, aligning divergent protein sequences with less than 20–35% pairwise identity (so called...
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Fast Alignment
We’ve seen that optimal alignment is slow but accurate while exact matching is fast but cannot account for mutations. In this Chapter we tweak exact...
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Sequence Alignment
New biological sequences do not emerge de novo in nature but rather are derived from pre-existing sequences. This foundational principle underlies...
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Protein Homology Modeling for Effective Drug Design
The effective drug design, especially for combating the multi-drug-resistant bacterial pathogens, requires more and more sophisticated procedures to...
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Deep embedding and alignment of protein sequences
Protein sequence alignment is a key component of most bioinformatics pipelines to study the structures and functions of proteins. Aligning highly...
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Approaches to increase the validity of gene family identification using manual homology search tools
Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species....
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Contact-Assisted Threading in Low-Homology Protein Modeling
The ability to successfully predict the three-dimensional structure of a protein from its amino acid sequence has made considerable progress in the...
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Interpreting Gene Ontology Annotations Derived from Sequence Homology Methods
The Gene Ontology (GO) project describes the functions of the gene products of organisms from all kingdoms of life in a standardized way, enabling...
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TEMPROT: protein function annotation using transformers embeddings and homology search
BackgroundAlthough the development of sequencing technologies has provided a large number of protein sequences, the analysis of functions that each...
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Homology Modeling in the Twilight Zone: Improved Accuracy by Sequence Space Analysis
The analysis of the relationship between sequence and structure similarities during the evolution of a protein family has revealed a limit of...
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Functional Annotation from Structural Homology
With the nexus of super computing and the biotech revolution, it seems an era of predictive biology through systems biology may be at hand. Modern...
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Specificities of Modeling of Membrane Proteins Using Multi-Template Homology Modeling
Structures of membrane proteins are challenging to determine experimentally and currently represent only about 2% of the structures in the Protein...
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Homology Modeling of Antibody Variable Regions: Methods and Applications
Adaptive immunity specifically protects us from antigenic challenges. Antibodies are key effector proteins of adaptive immunity, and they are...
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Omics and Remote Homology Integration to Decipher Protein Functionality
In the recent years, several “omics” technologies based on specific biomolecules (from DNA, RNA, proteins, or metabolites) have won growing...
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Optimal Alignment
We change into the chapter directory and make the directory for this chapter, 2. We change into that directory, make the directory for this section,...
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Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD
Sequence alignments are the foundations of life science research, but most innovation so far focuses on optimal alignments, while information derived...
