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THE USE OF FUNCTIONAL DOMAINS TO IMPROVE TRANSMEMBRANE PROTEIN TOPOLOGY PREDICTION

EMILY W. XU, DANIEL G. BROWN, PAUL KEARNEY
2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
Computational tools for transmembrane protein topology prediction fill in the gap between the abundance of transmembrane proteins and the scarcity of known membrane protein structures.  ...  As prediction of functional domain improves, our system's prediction accuracy will likely improve as well. † For correspondence.  ...  discussions and Michel Dominguez from Caprion for his opinion on functional domain sidedness.  ... 
doi:10.1142/9781860947322_0011 fatcat:h2g7mrevhzbyjmv3hh4dxcqt5m

THE USE OF FUNCTIONAL DOMAINS TO IMPROVE TRANSMEMBRANE PROTEIN TOPOLOGY PREDICTION

EMILY W. XU, PAUL KEARNEY, DANIEL G. BROWN
2006 Journal of Bioinformatics and Computational Biology  
Computational tools for transmembrane protein topology prediction fill in the gap between the abundance of transmembrane proteins and the scarcity of known membrane protein structures.  ...  As prediction of functional domain improves, our system's prediction accuracy will likely improve as well. † For correspondence.  ...  discussions and Michel Dominguez from Caprion for his opinion on functional domain sidedness.  ... 
doi:10.1142/s0219720006001722 pmid:16568545 fatcat:d3pp2teqbnh3dbqqun7xe5w4ma

TOPDOM: database of domains and motifs with conservative location in transmembrane proteins

G. E. Tusnady, L. Kalmar, H. Hegyi, P. Tompa, I. Simon
2008 Bioinformatics  
The TOPDOM database is a collection of domains and sequence motifs located consistently on the same side of the membrane in -helical transmembrane proteins.  ...  The identified domains or motifs were added to the database if they were uniformly annotated on the same side of the membrane of the various proteins in the UniProt database.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btn202 pmid:18434342 pmcid:PMC2427164 fatcat:qomckmllrfhk5egazn4ecx7nqi

The HMMTOP transmembrane topology prediction server

G. E. Tusnady, I. Simon
2001 Bioinformatics  
The HMMTOP transmembrane topology prediction server predicts both the localization of helical transmembrane segments and the topology of transmembrane proteins.  ...  Recently, several improvements have been introduced to the original method. Now, the user is allowed to submit additional information about segment localization to enhance the prediction power.  ...  The number of proteins, where all transmembrane helices were correctly predicted changed from 128 to 131, while the number of proteins, whose topology was also correctly predicted increased from 100 to  ... 
doi:10.1093/bioinformatics/17.9.849 pmid:11590105 fatcat:h7qo3zlaujddxickn5naf3y5di

SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803

Woo-Yeon Kim, Sungsoo Kang, Byoung-Chul Kim, Jeehyun Oh, Seongwoong Cho, Jong Bhak, Jong-Soon Choi
2008 BMC Bioinformatics  
Furthermore, SynechoNET provides information on transmembrane topology, signal peptide, and domain structure in order to support the analysis of regulatory membrane proteins.  ...  It provides a platform for biologists to extend the genomic data of cyanobacteria by predicting interaction partners, membrane association, and membrane topology of Synechocystis proteins.  ...  SynechoNET can be used for the analysis of regulatory membrane proteins by predicting transmembrane topology and domain structure.  ... 
doi:10.1186/1471-2105-9-s1-s20 pmid:18315852 pmcid:PMC2259421 fatcat:7sggykke6fee7ceedcc23wbyam

Protein annotation and modelling servers at University College London

D. W. A. Buchan, S. M. Ward, A. E. Lobley, T. C. O. Nugent, K. Bryson, D. T. Jones
2010 Nucleic Acids Research  
, DomPred and FFPred for the prediction of secondary structure, protein fold, protein structural domain, transmembrane helix topology, metal binding sites, regions of protein disorder, protein domain boundaries  ...  The UCL Bioinformatics Group web portal offers several high quality protein structure prediction and function annotation algorithms including PSIPRED, pGenTHREADER, pDomTHREADER, MEMSAT, MetSite, DISOPRED2  ...  Both algorithms employ dynamic programming to enumerate all possible transmembrane topologies, but differ in the method used to score the different topologies.  ... 
doi:10.1093/nar/gkq427 pmid:20507913 pmcid:PMC2896093 fatcat:fpytaqlup5fzjkanpwy5lrvov4

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

T. Nugent, D. T. Jones
2012 Proceedings of the National Academy of Sciences of the United States of America  
A new de novo protein structure prediction method for transmembrane proteins (FILM3) is described that is able to accurately predict the structures of large membrane proteins domains using an ensemble  ...  FILM was shown to be able to predict the correct topology and conformation for four out of five small protein domains of up to 79 residues at a reasonable level of accuracy.  ...  This work was supported by the UK Medical Research Council (MRC).  ... 
doi:10.1073/pnas.1120036109 pmid:22645369 pmcid:PMC3386101 fatcat:hpuq6lgaw5gxdbe55ankpwdhsu

TOPDOM: database of conservatively located domains and motifs in proteins

Julia Varga, László Dobson, Gábor E. Tusnády
2016 Bioinformatics  
By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and  ...  The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in a-helical transmembrane proteins-has been updated and extended by  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btw193 pmid:27153630 pmcid:PMC5013901 fatcat:s4ke4wuv7bcs5pwwk3regnoie4

Structure and function predictions of the Msa protein in Staphylococcus aureus

Vijayaraj Nagarajan, Mohamed O Elasri
2007 BMC Bioinformatics  
We have used several computational tools to predict the physico-chemical properties, secondary structural features, topology, 3D tertiary structure, binding sites, motifs/ patterns/domains and cellular  ...  Function predictions of Msa are complicated by the fact that it does not have a homologous partner in any other organism. This work aims at predicting the structure and function of the Msa protein.  ...  Acknowledgements This study was supported by a grant (1R15AI062727-01A1) from the National Institute of Allergy and Infectious Diseases (NIAID) to MOE and by The Mississippi Functional Genomics Network  ... 
doi:10.1186/1471-2105-8-s7-s5 pmid:18047728 pmcid:PMC2099497 fatcat:feas4xvvdjakplntb7gshrhk5u

Membrane topology of human ABC proteins

Gábor E. Tusnády, Balázs Sarkadi, István Simon, András Váradi
2005 FEBS Letters  
In this review, we summarize the currently available information on the membrane topology of some key members of the human ABC protein subfamilies, and present the predicted domain arrangements.  ...  We suggest that topology models generated by the available prediction methods should only be used as guidelines to provide a basis of experimental strategies for the elucidation of the membrane topology  ...  Acknowledgments: This work has been supported by the following grants: OTKA T049073, AT048729, D42207, and NKFP MediChem2.  ... 
doi:10.1016/j.febslet.2005.11.040 pmid:16337630 fatcat:4uc3hp332jcq7ny6rze2fi4hyi

Membrane topology of the human multidrug resistance-associated protein (MRP) and its homologs

A Váradi, G E Tusnády, E Bakos, B Sarkadi
1998 Cytotechnology (Dordrecht)  
transmembrane helices predicted for both proteins.  ...  Thus empirical prediction methods have been used to obtain molecular models of their structure, especially to predict the locations, the numbers and orientations of the membrane-spanning helices.  ... 
doi:10.1023/a:1008031914247 pmid:19002784 pmcid:PMC3449575 fatcat:dbphuxdvk5bdnk7feilhn3g7sa

Lipids and Topological "rules" of Membrane Protein Assembly: Testing the Generality of Net Charge Balance Rule

Heidi Vitrac, Mikhail Bogdanov, Philip Heacock, William Dowhan
2011 Biophysical Journal  
Based on predicted strand registrations, we are now able to predict the three dimensional structure of the transmembrane region of beta-barrel membrane proteins from sequences alone.  ...  a transmembrane conformation in bilayer-inserted state of the T-domain. 1125-Pos Board B35 Lipids and Topological "rules" of Membrane Protein Assembly: Testing the Generality of Net Charge Balance Rule  ...  Based on predicted strand registrations, we are now able to predict the three dimensional structure of the transmembrane region of beta-barrel membrane proteins from sequences alone.  ... 
doi:10.1016/j.bpj.2010.12.1337 fatcat:kg2umfwoebf7xhvs3mglmsduwe

Towards genome-scale structure prediction for transmembrane proteins

N. Hurwitz, M. Pellegrini-Calace, D. T. Jones
2006 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Our eventual aim is to apply these methods in tandem so that useful three-dimensional models can be built for a large fraction of the transmembrane protein domains in whole proteomes.  ...  The methods we discuss range from methods for transmembrane topology prediction to new methods for low resolution folding simulations in a knowledge-based force field.  ...  As a first step, the MEMSAT method ) was used to predict the topology of each protein along with the transmembrane segment locations and lengths.  ... 
doi:10.1098/rstb.2005.1804 pmid:16524835 pmcid:PMC1609336 fatcat:wmq3sds2v5a5vmilegyw7yd6bi

Predicting protein conformation by statistical methods

István Simon, András Fiser, Gábor E Tusnády
2001 Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology  
Besides this goal, the development of accurate prediction methods helps to reveal principles of protein folding.  ...  The unique folded structure makes a polypeptide a functional protein.  ...  Acknowledgements We thank Dr Mö nika Fuxreiter for helpful discussion on the manuscript. This work was supported by grants T 30566 and T34131 from the Hungarian Sci  ... 
doi:10.1016/s0167-4838(01)00253-9 pmid:11690649 fatcat:6fvdggeojzgx5a6gsz6vsofsxa

Integral membrane protein biosynthesis: why topology is hard to predict

Carolyn M Ott, Vishwanath R Lingappa
2002 Journal of Cell Science  
Integral membrane protein biogenesis requires the coordination of several events: accurate targeting of the nascent chain to the membrane; recognition, orientation and integration of transmembrane (TM)  ...  The importance of these regulated interactions is illustrated by analysis of topology prediction algorithm failures.  ...  We would like to thank D. T. Rutkowski, S. Saghafi, V. Denick, F. Moore, C. Adler, and P. Walter for useful discussion and critical reading of the manuscript.  ... 
pmid:11973342 fatcat:77q5hubn4fay3hk2evizzyc3ti
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