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Towards an intelligent system for the automatic assignment of domains in globular proteins

M J Sternberg, H Hegyi, S A Islam, J Luo, R B Russell
1995 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
The automatic identification of protein domains from coordinates is the first step in the classification of protein folds and hence is required for databases to guide structure prediction.  ...  Our development of an automatic approach to identify reliably domains from protein coordinates is described.  ...  Domain assignment 1 by DAD algorithm Our aim is to develop an automatic algorithm for domain assignment that incorporates the concepts actually used by workers (see Figurel).  ... 
pmid:7584461 fatcat:x5bnnea6a5hm3ap4hwdv2kxjkq

SEALS: a system for easy analysis of lots of sequences

D R Walker, E V Koonin
1997 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
The system is designed to provide modular elements which can be combined, modified, and integrated with other methods in order to quickly design and execute computer experiments for sequence analysis projects  ...  SEALS (System for Easy Analysis of Lots of Sequences) is a logically organized set of flexible, easily modifiable research tools, designed to run on open systems.  ...  Acknowledgements: DRW thanks Colombe Chappey for her generous assistance, and gratefully acknowledges the support of the Foundation for Advanced Education in the Sciences.  ... 
pmid:9322058 fatcat:zkiht3bqhfgb3a5asshi7xjasu

Elementary approach towards Biological Data Mining

Faiz Hashmi
2017 International Journal of Trend in Scientific Research and Development  
towards solving these challenges: with the goal of supporting human intelligence with machine intelligence.  ...  The application of data mining in the domain of bioinformatics is explained. It also highlights some of the current challenges and opportunities of data mining in bioinformatics.  ...  One of the concerns of Proteomics is the prediction of protein properties such as active sites, modification sites, localization, stability, globularity, shape, protein domains, secondary structure and  ... 
doi:10.31142/ijtsrd7198 fatcat:7q7uw6csazc4dolpaz5zenb574

References [chapter]

2012 Protein Bioinformatics  
Siddiqui AS and Barton GJ 1995 continuous and discontinuous domainsan algorithm for the automatic generation of reliable protein domain definitions. Prot. Sci. 4, 872–884.  ...  Pavesi G, Mauni G and Pesole G 2001 An algorithm for finding signals of unknown length in DNA sequences. In Proc. Ninth Int. Conf. on Intelligent Systems for Molecular Biology (ed.  ... 
doi:10.1002/9780470092620.refs fatcat:7655rwkhlnfrldcwb4vky3uqcm

A machine learning strategy for protein analysis

P. Baldi, G. Pollastri
2002 IEEE Intelligent Systems and their Applications  
Here, we offer an overview of the domain and our machine-learning techniques, and describe the software suite we've developed, which is available at Proteins are polymer chains composed of 20 simpler building  ...  the structure and function of all the proteins in a given genome.  ...  Acknowledgements Our work is supported by grants from the NIH, a Laurel Wilkening Faculty Innovation award, and a Sun Microsystems award to Pierre Baldi.  ... 
doi:10.1109/5254.999217 fatcat:6bhfp5i3njhrhemd4kiwgg4je4

Automatic identification of secondary structure in globular proteins

Michael Levitt, Jonathan Greer
1977 Journal of Molecular Biology  
For a few proteins, the mean and standard deviation of the distance between adjacent oc-carbons were abnormal, as the co-ordinates had not been specified in an orthogonal Cartesian co-ordinates system  ...  A computer program is used to analyse automatically and objectively the atomic co-ordinates of a large number of globular proteins in order to identify the regions of a-helix, p-sheet and reverse-turn  ...  We thank Dr Bruce Bush for his suggestion of the molecular representation used in Tables 7 to 10 .  ... 
doi:10.1016/0022-2836(77)90207-8 pmid:909086 fatcat:7cxdl3ux5baljhu6ubwr4xw5nm

Understanding eukaryotic linear motifs and their role in cell signaling and regulation

Francesca Diella
2008 Frontiers in Bioscience  
ACKNOWLEDGEMENTS We thank all contributors to the ELM resource for making our work possible. This work was supported in part by the EU ProteomeBinders and EU EMBRACE (LHSG-CT-2004-512092) grants.  ...  Linear motifs tend to occur towards the unstructured end of this scale. In one example of such a strategy, Kikuchi et al. developed an antibody that recognises an N-glycosylation site (126) .  ...  While the distinctions are clear, in practice a given interaction might employ varying amounts of the three interaction types: For example, an interface between two globular domains might have several  ... 
doi:10.2741/3175 pmid:18508681 fatcat:ccuqk353krgz7ekm36c7udeqvu

CHOP proteins into structural domain-like fragments

Jinfeng Liu, Burkhard Rost
2004 Proteins: Structure, Function, and Bioinformatics  
This average was similar for eukaryotic and prokaryotic proteins, and it is also valid-although previously not described-for all proteins in the PDB.  ...  Third, single-domain proteins were significant longer than most domains in multidomain proteins. Fourth, three fourths of all domains appeared shorter than 210 residues.  ...  SUPERFAMILY assigned 4794 domains in a subset of 3359 proteins. In contrast, CHOP found 6000 Fig. 4 . Length distribution of CHOP fragments.  ... 
doi:10.1002/prot.20095 pmid:15103630 fatcat:tzo53dimtjdf5bcdsub3loozcu

Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison

E Birney, R Durbin
1997 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
proteins, with the simultaneous assignment of transmembrane helices and (ii) to align protein information to genomic DNA, allowing for introns and sequencing error.  ...  An innovation is a flexible labelling system, which can be used to annotate the original sequences with biological information.  ...  We would like to thank Ian Holmes, Sean Eddy, Mor Amitai and Toby Gibson for their interest, support and discussions during the development of Dynamite.  ... 
pmid:9322016 fatcat:m3nt7jf6hjbpzbaodx72cfhjiy

Structural Principles Analysis of Host-Pathogen Protein-Protein Interactions: A Structural Bioinformatics Survey

Huaming Chen, William Guo, Jun Shen, Lei Wang, Jiangning Song
2018 IEEE Access  
for a cohort of macromolecules underpinning the biological system.  ...  Computational-intelligence methods in bioinformatics and systems biology show promising potential for leveraging abundant, large-scale molecular data.  ...  degree in the University of Wollongong.  ... 
doi:10.1109/access.2018.2807881 fatcat:ar5akdqs4ncydnd35ga5cgjagu

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

Therese Malliavin
2006 Current organic chemistry  
(ordering the spin systems in the sequence), and finally by performing the assignments of the nuclear Overhauser effects (NOEs).  ...  Such an assignment is usually solved in a progressive way, by determining first the spin systems (clustering the chemical shifts according to the residues), then by determining the sequential assignment  ...  Automatic methods for sequential assignment are based on algorithms previously developed in computer science, as artificial intelligence (AUTOASSIGN: Ref 36) [40] is using only the 13 C / 13 C connectivity  ... 
doi:10.2174/138527206776055286 fatcat:42zec6wzbvdx5j2rziaqxrbaeq

Striped sheets and protein contact prediction

R. M. MacCallum
2004 Bioinformatics  
In this study, an observation of "striped" sequence patterns across β-sheets prompted the development of a new type of contact map predictor.  ...  The results suggest that protein architectures impose regularities in local sequence environments.  ...  Acknowledgement The author would like to thank Varun Aggarwal for his analysis of profile SOMs and secondary structure, Arne Elofsson for valuable suggestions and discussion, and the PDC for cluster management  ... 
doi:10.1093/bioinformatics/bth913 pmid:15262803 fatcat:mcdfvegtcvd7zcarqjxkc4yd5m

Constraint satisfaction techniques for modeling large complexes: application to the central domain of 16S ribosomal RNA

R B Altman, B Weiser, H F Noller
1994 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
In this paper, we show that a method based on the constraint satisfaction paradigm produces a three-dimensional topology for the central domain of the 16S ribosomal RNA that is generally consistent with  ...  The system uses a grid search, checks distances in a direction-dependent manner, uses disjunctive distance constraints, and checks for volume overlap violations.  ...  Computing services provided by the CAMIS resource at Stanford, NIH grant no. LM-05305. Work at UCSC was supported by NIH grant no. GM-17129 (to H.F.N.) and a grant from the Lucille P.  ... 
pmid:7584378 fatcat:buiwvzuzb5d2jioiwtibyvqco4

Structural characterization of proteins and complexes using small-angle X-ray solution scattering

Haydyn D.T. Mertens, Dmitri I. Svergun
2010 Journal of Structural Biology  
Small-angle scattering of x-rays (SAXS) is an established method for the low resolution structural characterization of biological macromolecules in solution.  ...  The tools for the analysis of proteins in solution are presented, and the impact that these tools have made in modern structural biology is discussed.  ...  Typically, for a globular protein V p (in nm 3 ) is 1.5 to 2 times the MM (in kDa).  ... 
doi:10.1016/j.jsb.2010.06.012 pmid:20558299 fatcat:ltx74s7mkfch5pylqqibeqmdji

CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins

Alex S. Holehouse, Rahul K. Das, James N. Ahad, Mary O.G. Richardson, Rohit V. Pappu
2017 Biophysical Journal  
In addition to introducing the two packages, we demonstrate the utility of these resources using examples where sequence analysis offers biophysical insights.  ...  Intrinsically disordered proteins and regions (IDPs) represent a large class of proteins that are defined by conformational heterogeneity and lack of persistent tertiary/secondary structure.  ...  SUPPORTING CITATIONS References (37) (38) (39) (40) (41) (42) (43) (44) (45) appear in the Supporting Material.  ... 
doi:10.1016/j.bpj.2016.11.3200 pmid:28076807 pmcid:PMC5232785 fatcat:6bdl6e6mzjbovjfepmmqnohyse
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