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On the relationship between sequence and structure similarities in proteomics

E. Krissinel
2007 Bioinformatics  
This holds true if sequence similarity is sufficiently high, but in general the relationship between protein sequence and structure appears complex and is not well understood.  ...  The results indicate that multiple conservation of residue identity is not common and that relationship between sequence and structure may be explained by a model based on the assumption that protein structure  ...  The author would like to thank Dr Melford John for reading the manuscript and helpful discussion. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btm006 pmid:17242029 fatcat:2zu5tax2xbc7fdjmhjfig52zzu

Bioinformatics Resources for In Silico Proteome Analysis

Manuela Pruess, Rolf Apweiler
2003 Journal of Biomedicine and Biotechnology  
Different from most proteomics tools focusing on similarity searches, structure analysis and prediction, detection of specific regions, alignments, data mining, 2D PAGE analysis, or protein modelling,  ...  In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data.  ...  In addition, there are also a number of derived databases, which enable comparative studies of 3D structures as well as to gain insight on the relationships between sequence, secondary structure elements  ... 
doi:10.1155/s1110724303209219 pmid:14615630 pmcid:PMC514268 fatcat:po7dyx3pafc6rpwy56lm63pki4

The Pfam protein families database: towards a more sustainable future

Robert D. Finn, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Jaina Mistry, Alex L. Mitchell, Simon C. Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, Gustavo A. Salazar, John Tate (+1 others)
2015 Nucleic Acids Research  
Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted  ...  The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.  ...  Example of the improved representation of relationships graph, indicating the similarity between the Pfam entries within a clan.  ... 
doi:10.1093/nar/gkv1344 pmid:26673716 pmcid:PMC4702930 fatcat:o7rimhdmlrawdjm6ahqj3yfyhe

A sweep of earth's virome reveals host-guided viral protein structural mimicry; with implications for human disease [article]

Gorka Lasso, Barry Honig, Sagi Shapira
2020 bioRxiv   pre-print
Molecular mimicry, manifested by structural similarity between viral and endogenous host proteins, allow viruses to harness or disrupt cellular functions including nucleic acid metabolism and modulation  ...  The results point to molecular mimicry as a pervasive strategy employed by viruses and indicate that the protein structure space used by a given virus is dictated by the host proteome.  ...  The vast majority of these mimicry relationships 98 (72.2%) could not be retrieved through sequence similarity alone based on the requirement that no e-value 99 obtained from any one or three sequence-based  ... 
doi:10.1101/2020.06.18.159467 fatcat:trda4ppmkzei3d7zehpokzgq6a

Prokaryotic phylogenies inferred from protein structural domains

E. J. Deeds
2005 Genome Research  
Article and publication are at Deeds et al.  ...  Giribet and S. Baldauf for their comments on the manuscript. We are deeply indebted to Dr. Eugene Koonin for all of his advice.  ...  This work was supported by an HHMI predoctoral fellowship (to E.J.D.) and by the NIH.  ... 
doi:10.1101/gr.3033805 pmid:15741510 pmcid:PMC551566 fatcat:xckdasf7cbguhgz3andayeljqa

Recognition of HIV-1 Peptides by Host CTL Is Related to HIV-1 Similarity to Human Proteins

Morgane Rolland, David C. Nickle, Wenjie Deng, Nicole Frahm, Christian Brander, Gerald H. Learn, David Heckerman, Nebosja Jojic, Vladimir Jojic, Bruce D. Walker, James I. Mullins, Douglas Nixon
2007 PLoS ONE  
We tested the relationship between HIV-1 similarity to host encoded peptides and immune recognition in HIV-infected individuals, and found that HIV immunogenicity could be partially modulated by the sequence  ...  ELISpot responses to peptides spanning the entire viral proteome evaluated in 314 individuals showed a trend indicating an inverse relationship between the similarity to the host proteome and the frequency  ...  By showing a relationship between peptide similarity and immunodominance we validated low similarity to the host proteome as a concurring factor in the modulation of the pool of epitopic sequences, with  ... 
doi:10.1371/journal.pone.0000823 pmid:17786195 pmcid:PMC1952107 fatcat:gkuzxndz4jferayxeurm6evhku

From The Cover: Global analysis of predicted proteomes: Functional adaptation of physical properties

C. G. Knight, R. Kassen, H. Hebestreit, P. B. Rainey
2004 Proceedings of the National Academy of Sciences of the United States of America  
This relationship is not adequately explained by AT bias at the DNA sequence level. Together, these data provide evidence of functional adaptation in the properties of complete proteomes.  ...  Finally, we show that, for the smallest and most alkaline proteomes, there is a negative relationship between proteome size and basicity.  ...  To explore the effect of phylogenetic relatedness on proteome complement in more detail, we considered the relationship of genetic distance between strains to the similarity of their theoretical 2D gels  ... 
doi:10.1073/pnas.0307270101 pmid:15150418 pmcid:PMC420404 fatcat:wnuopokl5nazxmxikr7huzgmrq

Structure-based systems biology for analyzing off-target binding

Lei Xie, Li Xie, Philip E Bourne
2011 Current Opinion in Structural Biology  
Not surprisingly, there is significant interest in determining a priori what offtargets exist on a proteome-wide scale.  ...  Beyond determining putative off-targets is the need to understand the impact of such binding on the complete biological system, with the ultimate goal of being able to predict the phenotypic outcome.  ...  Acknowledgments We appreciate constructive suggestions from the editor and anonymous reviewer on improving the manuscript. This work was supported by the National Institutes of Health Grant GM078596.  ... 
doi:10.1016/j.sbi.2011.01.004 pmid:21292475 pmcid:PMC3070778 fatcat:lx4fzdxptfeohjzbcdwklfgzqa

Simple sequence proteins in prokaryotic proteomes

Mekapati Bala Subramanyam, Muthiah Gnanamani, Srinivasan Ramachandran
2006 BMC Genomics  
Mesophiles and Thermophiles are similar with respect to the content of SSPs. Our analysis serves to expand the commonly held views on SSPs.  ...  Mesophiles and Thermophiles display similar ranges in the content of SSPs.  ...  Acknowledgements SR, MBS and MG thank CSIR for funding support in the form of a grant "Task Force on In Silico Biology for Drug target identification" (CMM0017) and HP Centre for Excellence.  ... 
doi:10.1186/1471-2164-7-141 pmid:16762057 pmcid:PMC1524752 fatcat:wvthdqk4n5bfphxih6ord7gmme

Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: Insights into structure and function

Gayatri Ramakrishnan, Bernardo Ochoa-Montaño, Upadhyayula S. Raghavender, Richa Mudgal, Adwait G. Joshi, Nagasuma R. Chandra, Ramanathan Sowdhamini, Tom L. Blundell, Narayanaswamy Srinivasan
2015 Tuberculosis  
Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures  ...  algorithms resulting in an enhanced annotation of the proteome where 95% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function.  ...  Funding This research was supported primarily by OSDD programme of CSIR and also by Mathematical Biology programme, Department of Science and Technology, Department of Biotechnology, India, and by the  ... 
doi:10.1016/j.tube.2014.10.009 pmid:25467293 fatcat:2expl7qqx5h35o4srlzhnc7wxe

Accomplishments and Challenges of Protein Ontology

Amandeep Sidhu, Tharam Dillon, Farookh Hussain
2006 30th Annual International Computer Software and Applications Conference (COMPSAC'06)  
We report here our development of PO; a semantic heterogeneity framework based on relationships between PO concepts; and analysis of resultant PO Data of Human Proteins.  ...  Protein Ontology is a standard for representing protein data in a way that helps in defining data integration and data mining models for Protein Structure and Function.  ...  An alternative protein annotation approach is to rely on sequence identity, or structural similarity, or functional identification.  ... 
doi:10.1109/compsac.2006.18 dblp:conf/compsac/SidhuDH06 fatcat:j56r6czab5a3vng4f3hnjsstxi

SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison

J. Ren, L. Xie, W. W. Li, P. E. Bourne
2010 Nucleic Acids Research  
The SMAP web service (SMAP-WS) meets this need through parallel computations designed for 3D ligand-binding site comparison and similarity searching on a structural proteome scale.  ...  The proteome-wide characterization and analysis of protein ligand-binding sites and their interactions with ligands can provide pivotal information in understanding the structure, function and evolution  ...  The authors appreciate the constructive suggestions of the anonymous reviewers and the editor in improving the manuscript.  ... 
doi:10.1093/nar/gkq400 pmid:20484373 pmcid:PMC2896174 fatcat:jcvmyzgu7rfgdckrzxpg6wud3a

Objects and processes: Two notions for understanding biological information

Agustín Mercado-Reyes, Pablo Padilla-Longoria, Alfonso Arroyo-Santos
2015 Journal of Theoretical Biology  
also for the relationship between them.  ...  Our results show that semantic sequences do not have unique complexity values different from the value of meaningless sequences.  ...  The authors wish to thank Carlos Rodríguez Silva for designing the figures of the paper; Fabrizzio Guerrero McManus and Mark Olson for reading and commenting on earlier drafts of the manuscript, and two  ... 
doi:10.1016/j.jtbi.2015.05.021 pmid:26026831 fatcat:cwf4zlwjsvdmvkxf5cuzweustq

Language engineering and information theoretic methods in protein sequence similarity studies [chapter]

A. Bogan-Marta, A. Hategan, I. Pitas
2008 Studies in Computational Intelligence  
These terms should have definitions and be placed within a structure of relationships, the most important being the "is-a" relationship between parent and child and the "part-of" relationship between part  ...  The first step in building the tree is to compute the similarity between all the proteomes and the results are presented in Table 3 .  ... 
doi:10.1007/978-3-540-75767-2_8 fatcat:kggzayaoyvg7peckkpdb7xvgn4

Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera

Brett Trost, Monique Haakensen, Vanessa Pittet, Barry Ziola, Anthony Kusalik
2010 BMC Microbiology  
We also analyzed the relationship between protein content similarity and the percent identity of the 16S rRNA gene in pairs of bacterial isolates from the same genus, and found that the strength of this  ...  Results: A variation on reciprocal BLAST hits was used to infer relationships among proteins in several groups of bacteria, and data regarding protein conservation and uniqueness in different bacterial  ...  BZ and AK participated in the design and coordination of the study, helped to draft the manuscript, supervised the research, and are holders of research grants used to fund the study.  ... 
doi:10.1186/1471-2180-10-258 pmid:20942950 pmcid:PMC3020658 fatcat:6hm3vbzbs5dsdgpshncywtcvcm
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