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Showing 1 to 20 of 119 for “"protein sequences"”.
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Folding patterns in protein sequences
… fruitful genome projects, a growing number of protein sequences remain uncharacterised. Generally, computational techniques have not been developed to distinguish between regions that are conserved in proteins owing to evolutionary pressures to maintain structure and those that are conserved in …
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Improving Profile Similarity Search and Alignment of Protein Sequences
Protein function prediction is one of the most important problems in the field of computational biology. The most reliable method to predict protein function is to detect homologs. Homologous proteins tend to possess conserved sequence motifs, the same structure folds, and similar functional sites. …
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Modeling protein sequences, structures and functions with deep neural networks
Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2023-12-04 without embargo terms
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Unsupervised inference models for structural and functional properties of protein sequences
L'abstract è presente nell'allegato / the abstract is in the attachment
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Enabling the discovery of novel bioactives and enzymes from billions of protein sequences
… used platforms for the analysis of metagenomic sequences. Since 2018, MGnify has assembled and analysed over 57,000 shotgun metagenomics datasets. From these assemblies, over 2.4 billion non-redundant protein sequences have been identified. This protein database outscales other protein …
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Prediction of parallel in-register amyloidogenic beta-structures In highly beta-rich protein sequences by pairwise propensity analysis
Amyloids and prion proteins are clinically and biologically important beta-structures, whose supersecondary structures are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid …
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ChaperoNet: Distillation of Language Model Semantics to Folded Three-Dimensional Protein Structures
Determining the structure of proteins has been a long-standing goal in biology. Lan- guage models have been recently deployed to capture the evolutionary semantics of protein sequences, and as an emergent property, were found to be structural learn- ers. Enriched with multiple sequence alignments …
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Integrating Functional Knowledge into Protein Design: A Novel Approach to Tokenization and Noise Injection for Function-Aware Protein Language Models
Designing novel proteins with specific biological functions remains a fundamental challenge in computational biology. While recent advances in protein language models have enabled powerful sequence-based representations, most models, including state-of-the-art systems like ESM3, fall short in …
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Calculating the structure-based phylogenetic relationship of distantly related homologous proteins utilizing maximum likelihood structural alignment combinatorics and a novel structural molecular clock hypothesis
… relationships and homology of species, proteins, or genes. Homology modeling, ligand binding, and pharmaceutical testing all depend upon the homology ascertained by dendrograms. Regardless of the specific algorithm, all dendrograms that ascertain protein evolutionary homology are …
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Assessing the Role of Clusters Derived from Large Sequence Similarity Networks for Gene Function Predictions
… utilize various forms of data, such as DNA/RNA/protein sequences, protein structures, interaction networks, literature mining, and a combination of these data sources. However, these methods do not always produce precise results as the underlying data sets used for training or modeling are quite …
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Fast learning optimized prediction methodology for protein secondary structure prediction, relative solvent accessibility prediction and phosphorylation prediction
… and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein sequences and a slower growth in the number of structures. There is therefore an urgent need to develop computed structures and identify …
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Molecular Evolution of Viruses
… of evolution at the scale of DNA, RNA and proteins. Our goal was to study molecular evolution of viruses with special reference to Influenza A Virus.</p> <p>The recent Influenza A/H1N1(2009) outbreak has been the focus of intense research because of its high level of infectivity across the …
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Intrinsically Disordered Protein Polymer Libraries as Tools to Understand Protein Hydrophobicity
<p>Intrinsically disordered protein polymers (IDPPs) are repetitive biopolymers that, when enriched with prolines, glycines, and aliphatic amino acids, have observable lower critical solution temperature (LCST) phase transition behavior at physiologically relevant temperature and concentration …
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Improving the genome assembly and annotation of the white-tailed deer (Odocoileus virginianus borealis)
… the BRAKER annotation pipeline using RNA and protein sequences as extrinsic evidence. The final assembly was highly contiguous, with 90% of the total length represented by 134 contigs. The largest contig was 108 million base pairs. Functional annotation was performed using reciprocal best hits …
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Studies of the structure, evolution, and TonB-dependence of the colicin I receptor of Escherichia coli
The colicin I receptor (Cir) is an outer membrane protein, the expression of which is iron regulated. The DNA downstream of the cloned cir gene, when expressed in a maxicell system, encoded a protein of molecular weight 32,000. The expression of this protein was determined to be directed toward the …
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PASSS: Protein Active Site Structure Search
The Protein Structure Initiative, a project on the scale of the Human Genome Project aimed at protein structure determination, has successfully identified the structure of multiple human proteins. Unfortunately, knowledge of structure alone provides little insight into a protein's function within …
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Structural and functional relationship of photosynthetic bacterial reaction centers
… Rhodopseudomonas viridis. By comparison of the protein sequences and structures of RCs of three species, it was suggested that Cys$\sp{\rm L108}$ in Rb. sphaeroides (Cys$\sp{\rm L109}$ in Rb. capsulatus) is the best candidate for the mercurial reagents to inhibit Q$\sb{\rm B}$ function. And a …
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Predicting the beta-trefoil fold from protein sequence data
… level, to predict the beta-structural motifs in protein sequences. A program called Wrap-and-Pack implements this method, and is shown to recognize β-trefoils, an important class of globular β-structures, in the Protein Data Bank with 92% specificity and 92.3% sensitivity in cross-validation. It …
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Statistics and algorithms for peptide mass fingerprinting
… (PMF). In a PMF experiment, a purified protein sample is digested by a protease using an enzymatic cleavage reaction, the masses of the resulting peptides are measured by mass spectrometry, yielding the mass fingerprint, and compared to predicted mass fingerprints of reference protein …
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