294,715 Hits in 8.2 sec

Prediction of enzyme function by combining sequence similarity and protein interactions

Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X Avilés, Andrej Sali, Marc A Marti-Renom, Baldomero Oliva
2008 BMC Bioinformatics  
Abstract Background A number of studies have used protein interaction data alone for protein function prediction.  ...  Therefore, CYP7 and TLP20, which belong to different organisms, can be related by sequence similarity and protein interactions by means of homologous proteins in a third organism that have a common interacting  ... 
doi:10.1186/1471-2105-9-249 pmid:18505562 pmcid:PMC2430716 fatcat:itvxfzba4zcojb5dq3jpmildwa

Computational Approaches for Automated Classification of Enzyme Sequences

Akram Mohammed
2011 Journal of Proteomics & Bioinformatics  
Similarly, by combining sequence similarity with other functional features such as interacting partners, Espadaler et al.  ...  [61] developed enzyme prediction methods by combining predictions from independent components to infer the enzyme function.  ...  Funding This work was supported by National Institutes of Health [1R01GM086533-01A1 to CG]; and startup funds to CG from University of Nebraska Medical Center.  ... 
doi:10.4172/jpb.1000183 pmid:22114367 pmcid:PMC3221388 fatcat:jlmaj467obelvnrdcicn3kjkey

Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study

Swati Sinha, Andrew M. Lynn, Dhwani K. Desai
2020 BMC Bioinformatics  
The non-homology methods based on the context and the interactions of a protein are very useful for identifying missing metabolic activities and functional annotation in the absence of significant sequence  ...  A major limitation of these methods is the absence of well-characterized sequences for certain functions.  ...  inferred by analyzing its sequence similarity with other proteins of well-characterized functions.  ... 
doi:10.1186/s12859-020-03794-x pmid:33076816 fatcat:i6uxvaj2mjgi5eqljd7bwemufa

Prediction of Human Protein Function from Post-translational Modifications and Localization Features

L.J. Jensen, R. Gupta, N. Blom, D. Devos, J. Tamames, C. Kesmir, H. Nielsen, H.H. Stærfeldt, K. Rapacki, C. Workman, C.A.F. Andersen, S. Knudsen (+3 others)
2002 Journal of Molecular Biology  
We have developed an entirely sequence-based method that identifies and integrates relevant features that can be used to assign proteins of unknown function to functional classes, and enzyme categories  ...  We show that strategies for the elucidation of protein function may benefit from a number of functional attributes that are more directly related to the linear sequence of amino acids, and hence easier  ...  We did, as an example, predict the function of both sequences in all interaction partners found in the database of interacting proteins (DIP). 31 If the functional categories of the interacting proteins  ... 
doi:10.1016/s0022-2836(02)00379-0 pmid:12079362 fatcat:sxc66jdxnrcxxi7sldeqqqvi4q

Exploring Mouse Protein Function via Multiple Approaches

Guohua Huang, Chen Chu, Tao Huang, Xiangyin Kong, Yunhua Zhang, Ning Zhang, Yu-Dong Cai, Alexey Porollo
2016 PLoS ONE  
The approach was a sequential combination of a similarity-based approach, an interaction-based approach and a pseudo amino acid composition-based approach.  ...  For the results yielded by the leave-one-out cross-validation, although the similarity-based approach alone achieved an accuracy of 0.8756, it was unable to predict the functions of proteins with no homologues  ...  Prediction by the Combined Approach We combined the three approaches to predict the functions of proteins to make use of their respective advantages and disadvantages.  ... 
doi:10.1371/journal.pone.0166580 pmid:27846315 pmcid:PMC5112993 fatcat:uf5r6zlw4vb5dhcuxl5qx3bugu

A Survey of Computational Intelligence Techniques in Protein Function Prediction

Arvind Kumar Tiwari, Rajeev Srivastava
2014 International Journal of Proteomics  
This paper presents a state-of-the-art comprehensive review of various computational intelligence techniques for protein function predictions using sequence, structure, protein-protein interaction network  ...  , and gene expression data used in wide areas of applications such as prediction of DNA and RNA binding sites, subcellular localization, enzyme functions, signal peptides, catalytic residues, nuclear/G-protein  ...  Conflict of Interests The authors declare that there is no conflict of interests regarding the publication of this paper.  ... 
doi:10.1155/2014/845479 pmid:25574395 pmcid:PMC4276698 fatcat:p3vwanr2nran7arwzotirhgyte


2007 Journal of Bioinformatics and Computational Biology  
Function prediction of uncharacterized protein sequences generated by genome projects has emerged as an important focus for computational biology.  ...  Because they incorporate structural and experimental data that is not used in sequence-based methods, they can provide additional accuracy and reliability to protein function prediction.  ...  Acknowledgments This work is partially supported by National Institutes of Health (R01 GM075004 and U24 GM077905) and National Science Foundation (DMS 0604776).  ... 
doi:10.1142/s0219720007002503 pmid:17477489 fatcat:n7a5cf3hkbaivbyv6yyjm45wdq

Modulator of Diabetes and Metabolic Syndrome: Silent Proteins, newer Insights

Sridhar GR
2015 Journal of Diabetes Research and Therapy  
In this review the enzyme butyrylcholinesterase, involved in the expression of metabolic syndrome is presented, and recently available methods to predict protein structure, function and active sites are  ...  From methods using amino acid and nucleotide sequences evidence is available that residues in the enzyme core are selected for stability while those at the surface, which are sites of protein interaction  ...  Acknowledgement I thank Dr G Lakshmi MD for her help in the preparation of the revised manuscript.  ... 
doi:10.16966/2380-5544.107 fatcat:ownbrwoemzbsfdcv6lygjqq7r4

Network Analysis of Protein Structures Identifies Functional Residues

Gil Amitai, Arye Shemesh, Einat Sitbon, Maxim Shklar, Dvir Netanely, Ilya Venger, Shmuel Pietrokovski
2004 Journal of Molecular Biology  
Detailed structural analysis of specific enzymes also located other types of functional residues.  ...  Residues with high closeness values interact directly or by a few intermediates with all other residues of the protein.  ...  consulting, Vladimir Sobolev for developing and providing the CSU software, and Gail Bartlett for providing active site data.  ... 
doi:10.1016/j.jmb.2004.10.055 pmid:15544817 fatcat:pckcfdxxm5enjieuo2xnffa2hy

Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus

Peter Gaudermann, Ina Vogl, Evelyn Zientz, Francisco J Silva, Andres Moya, Roy Gross, Thomas Dandekar
2006 BMC Microbiology  
To extend and re-test predictions and links to experimentally verified protein functions, functional clusters and interactions were assembled.  ...  Improved sequence analysis algorithms, databanks and gene and pathway context methods allowed us to reveal new information on various enzyme and pathways from the Blochmannia floridanus genome sequence  ...  Acknowledgements We thank Biju Joseph for stylistic corrections and DFG (grant Bo-1099/5-3; Germany), BMBF (AZ 03 130 74A; Germany), Government of Valencià (Grupos03/204; Spain) and MCyT (BFM2003-00305  ... 
doi:10.1186/1471-2180-6-1 pmid:16401340 pmcid:PMC1360075 fatcat:napw77wecjc6fgy5zheam2nuem

Toward a systematic definition of protein function that scales to the genome level: defining function in terms of interactions

Ning Lan, R. Jansen, M. Gerstein
2002 Proceedings of the IEEE  
To illustrate how our function grid can be used in genome-wide prediction of function, we construct a grid of yeast genes; combine it with other genomic information, including sequence features, structure  ...  The ultimate goal of functional genomics is to elucidate the function of all the genes in the genome. However, the current notions of function are crafted for individual proteins.  ...  The interaction grid is combined with sequence features, expression data, and localization information to predict DNA binding.  ... 
doi:10.1109/jproc.2002.805302 fatcat:wekrlbbpb5bureswf37a2wjrp4

Leveraging structure for enzyme function prediction: methods, opportunities, and challenges

Matthew P. Jacobson, Chakrapani Kalyanaraman, Suwen Zhao, Boxue Tian
2014 TIBS -Trends in Biochemical Sciences. Regular ed  
Bioinformatics tools are commonly used to predict functions of uncharacterized proteins.  ...  We discuss opportunities to systematically elucidate protein domains of unknown function, orphan enzyme activities, deadend metabolites, and pathways in secondary metabolism.  ...  Acknowledgments This work was part of the Enzyme Function Initiative supported by the National Institutes of Health Grant U54 GM093342. We thank John Gerlt (U. Illinois) for helpful discussions.  ... 
doi:10.1016/j.tibs.2014.05.006 pmid:24998033 pmcid:PMC4117707 fatcat:m7rk4bs2p5b5plq2qpxq4a547a

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

Noah Ollikainen, René M. de Jong, Tanja Kortemme, Robert L Jernigan
2015 PLoS Computational Biology  
Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii)  ...  We assess these improvements in two important tests: the first predicts mutations that change ligand-binding preferences in enzymes, and the second predicts protein sequences that bind a given ligand.  ...  Nir London for testing the described protocols, and the Kortemme lab for insightful discussion. We also thank Dr. Jan-Metske van der Laan and Dr.  ... 
doi:10.1371/journal.pcbi.1004335 pmid:26397464 pmcid:PMC4580623 fatcat:ljxflafnhrekhe2yxvivialvhe

Searchlight on Domains

Monica Riley
2007 Structure  
A valuable type of information in this context is identification of domains in a protein by sequence and knowledge of domain function to help predict the protein function.  ...  the practice of the prediction of protein function from sequence.  ... 
doi:10.1016/j.str.2006.12.003 pmid:17223525 fatcat:uwxp3d436bg53jiu6wdatgxd4i

Modeling enzyme-ligand binding in drug discovery

Janez Konc, Samo Lešnik, Dušanka Janežič
2015 Journal of Cheminformatics  
Enzymes are one of the most important groups of drug targets, and identifying possible ligand-enzyme interactions is of major importance in many drug discovery processes.  ...  contribute to answer open questions in the field of drug discovery like the identification of unknown protein functions, off-target binding, ligand 3D homology modeling and induced-fit simulations.  ...  Acknowledgements Financial support through Grants P1-0002, J1-6743 and L1-6745 of the Ministry of Higher Education, Science and Technology of Slovenia and Slovenian Research Agency is acknowledged.  ... 
doi:10.1186/s13321-015-0096-0 pmid:26457119 pmcid:PMC4594084 fatcat:5d3uvgzwkfbzthuhvic3kfdcxm
« Previous Showing results 1 — 15 out of 294,715 results