Protein identification using public protein sequence database
Identification of interface residues involved in protein-protein and protein-DNA interactions from sequence using machine learning approaches
... The results show that hydrophobic residues and aromatic residues have high propensities for the interfaces; hydrophilic residues, except Arg and His, have negative propensities fo[r] ...
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PROFESS: a PROtein Function, Evolution, Structure and Sequence database
... and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data ...the identification of potential pancreatic cancer ...
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RIDOM: Comprehensive and public sequence database for identification of Mycobacteriumspecies
... National Public Health Institute, Kuopio, Finnland; Christine Turenne, National Reference Center for Mycobacteriology, Winnipeg, Canada; and Veronique Vincent, Laboratoire de Reference des Mycobacteries, Institut ...
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Identification of protein functions using a machine-learning approach based on sequence-derived properties
... of protein function is SVM ...of protein function was per- formed using an SVM statistical learning algorithm, based on features such as amino acid composition, hydropho- bicity, solvent ...
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Protein-protein interface: database, analysis and prediction
... Introduction Protein-protein interactions play a pivotal role in cellular processes such as DNA replication and transcription, RNA splicing, signal transduction and metabolic ...the sequence and ...
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Discover protein sequence signatures from protein-protein interaction data
... example, using a hybrid system of gene ontology, functional domain and pseudo amino acid composition approaches, Chou and Cai obtained 70% of overall success identification rate ...
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MoRFPred-plus: Computational Identification of MoRFs in Protein Sequence using physicochemical properties and HMM profiles
... with protein-peptide interaction from protein data bank (PDB) and identified peptide regions of 5 to 25 residues which were supposed to be MoRF ...840 protein sequences they obtained, further to ...
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Utilization of Protein Tertiary Contacts to Improve Protein Structure Prediction Using Sequence Homology
... the database searching dynamic programming algorithms for finding similar sequences (Nicholas et ...and using a heuristic method for aligning sequences, has the best of both worlds as a sequence ...
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Identification of ATP binding residues of a protein from its primary sequence
... a protein First we analyzed ATP interacting residues and its neighbors, and found that there is a significant difference in interacting and non- interacting ...predicted using any machine leaning ...a ...
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Identification of sequence motifs for the protein components of type IX secretion system
... each protein component of the T9SS have yet to be characterized thus limiting our understanding of the mechanisms associated with the translocation and modification processes of the ...the sequence motifs ...
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Using context to improve protein domain identification
... Pfam using HMMER2, there are other tools available which could be used, including SAM [45] and the new HMMER3 [21], as well as other domain databases, like SMART, Superfamily, and ...other protein ...
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Protein identification using MS/MS data
... 2. Sequence tag searches The first approach to database searching with MS/MS data was the sequence tag, originally described by Mann and Wilm ...short sequence ladder, and read off three or ...
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Protein subfamily assignment using the Conserved Domain Database
... by sequence sim- ilarity, profiles of protein domain families make it possi- ble to quickly classify more distant homologs [23] and can better handle multi-domain ...known protein fam- ilies is ...
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Visualizing the Protein Sequence Universe
... To demonstrate the performance of the method, we apply it to the COG data creating a 3D projection of the prokary- otic PSU. Prokaryotes are one of the four major biologi- cal kingdoms. Despite lack of support, the COG ...
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Improving Protein Sequence Classification Performance Using Adjacent and Overlapped Segments on Existing Protein Descriptors
... ilies using SVM as a ...predicting protein functional ...Quasi Sequence Order, Pseudo Amino Acid Composition, and Descriptors of Composition, Transition, and ...combinations using Pseudo Amino ...
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Protein Function Prediction from Protein Interaction Network Using Clustering and Sequence of Amino Acid
... random protein from the set of proteins of top5 ...its sequence counterpart, the sources for protein structural data are not as diverse as those for ...for Protein Sequences ...
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Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top-Down Mass Spectrometry
... target database sequence and the ...into database sequences to generate a proteoform ...PTM identification in bottom-up MS, but it is inefficient in top-down ...proteoform database may ...
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The Pfam Protein Families Database
... listed protein-identifiers cross-referenced by the UniProtKB accession P51003 ...same sequence region. We resolve such overlaps using the same method as we use when resolving overlapping ...
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The Pfam Protein Families Database
... Using the taxonomy search software we have evaluated how the four major kingdoms (eukaryota, bacteria, archaea and viruses) are represented in the Pfam collection. The results are shown in Table 1. The data ...
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Identification of Candidate Genes related to Bovine Marbling using Protein-Protein Interaction Networks
... the identification of candidate genes related to complex diseases or traits at the system ...obtained using MedScan text-mining tools and linked by protein-protein interaction (PPI) from the ...
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