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Boosting Protein Threading Accuracy [chapter]

Jian Peng, Jinbo Xu
2009 Lecture Notes in Computer Science  
Protein threading is one of the most successful protein structure prediction methods.  ...  We achieve this by modeling the threading problem using a probabilistic graphical model Conditional Random Fields (CRF) and training the model using the gradient tree boosting algorithm.  ...  The authors are grateful to Liefeng Bo and Kristian Kersting for their help with the gradient tree boosting technique. We also thank Chuong Do for his help with the CONTRAlign software.  ... 
doi:10.1007/978-3-642-02008-7_3 pmid:22506254 pmcid:PMC3325114 fatcat:oz2hfjleevec5htbr35mq6rkt4

PROTEIN FOLD RECOGNITION USING THE GRADIENT BOOST ALGORITHM

Feng Jiao, Jinbo Xu, Libo Yu, Dale Schuurmans
2006 Computational Systems Bioinformatics  
Protein threading represents one of the most promising techniques for this problem.  ...  One of the critical steps in protein threading, called fold recognition, is to choose the best-fit template for the query protein with the structure to be predicted.  ...  EXPERIMENTAL RESULTS When one protein structure is to be predicted, we thread its sequence to each template in the database and obtain the predicted alignment accuracy using the LS Boost algorithm.  ... 
doi:10.1142/9781860947575_0012 fatcat:cx4vds4torbfznybbxpjq5f67a

PROTEIN FOLD RECOGNITION USING THE GRADIENT BOOST ALGORITHM

Feng Jiao, Jinbo Xu, Libo Yu, Dale Schuurmans
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
Protein threading represents one of the most promising techniques for this problem.  ...  One of the critical steps in protein threading, called fold recognition, is to choose the best-fit template for the query protein with the structure to be predicted.  ...  EXPERIMENTAL RESULTS When one protein structure is to be predicted, we thread its sequence to each template in the database and obtain the predicted alignment accuracy using the LS Boost algorithm.  ... 
doi:10.1142/18609475730015 fatcat:utn6blaf4zhrfkkwjwuvjmjcdy

PROTEIN FOLD RECOGNITION USING THE GRADIENT BOOST ALGORITHM

Feng Jiao, Jinbo Xu, Libo Yu, Dale Schuurmans
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
Protein threading represents one of the most promising techniques for this problem.  ...  One of the critical steps in protein threading, called fold recognition, is to choose the best-fit template for the query protein with the structure to be predicted.  ...  EXPERIMENTAL RESULTS When one protein structure is to be predicted, we thread its sequence to each template in the database and obtain the predicted alignment accuracy using the LS Boost algorithm.  ... 
doi:10.1142/1860947573_0015 fatcat:ilo5zoup2bgqxki2m4qsxka7ya

Evaluating the significance of contact maps in low-homology protein modeling using contact-assisted threading

Sutanu Bhattacharya, Debswapna Bhattacharya
2020 Scientific Reports  
We have recently demonstrated the utility of contact information to boost protein threading by developing a new contact-assisted threading method.  ...  Collectively, our study uncovers the mutual association between the quality of predicted contacts and its possible utility in boosting threading performance for improving low-homology protein modeling.  ...  Consequently, residue-residue contact or distance has become valuable new information to explore in boosting the accuracy of protein threading.  ... 
doi:10.1038/s41598-020-59834-2 pmid:32076047 pmcid:PMC7031282 fatcat:zs32fxlxv5hptjrwrkx4rhhzk4

iWRAP: An Interface Threading Approach with Application to Prediction of Cancer-Related Protein–Protein Interactions

Raghavendra Hosur, Jinbo Xu, Jadwiga Bienkowska, Bonnie Berger
2011 Journal of Molecular Biology  
We introduce a threading approach, iWRAP, which focuses on only the protein interface.  ...  Threading methods extend coverage further into the twilight zone by aligning primary sequences for a pair of proteins to a best-fit template complex to predict an entire three-dimensional structure.  ...  In the combined method, DBLRAP threading results are boosted and combined with iWRAP predictions.  ... 
doi:10.1016/j.jmb.2010.11.025 pmid:21130772 pmcid:PMC3028939 fatcat:zvhimtwyibevjch4aul6jvpwby

Boosting Methods for Protein Fold Recognition: An Empirical Comparison

Yazhene Krishnaraj, Chandan K. Reddy
2008 2008 IEEE International Conference on Bioinformatics and Biomedicine  
Overall, Boosting methods achieve 60% fold recognition accuracy on an independent test protein dataset which is the highest prediction achieved when compared with the accuracy values obtained with other  ...  Prediction accuracy is measured on a dataset with proteins from 27 most populated folds from the SCOP database, and is compared with results from other literature using SVM, KNN and NN algorithms on the  ...  (2) Threading [6] , which detects the structural similarities by comparison with a library of known structures even for low similarity protein sequences.  ... 
doi:10.1109/bibm.2008.83 dblp:conf/bibm/KrishnarajR08 fatcat:tdsku2sefzabncrysmjcwvryki

Statistical inference for template-based protein structure prediction [article]

Jian Peng
2013 arXiv   pre-print
Although substantial effort has been made to improve protein sequence alignment, the accuracy of alignments between distantly related proteins is still unsatisfactory.  ...  For a protein with multiple good templates, we design a probabilistic consistency approach to thread the protein to all templates simultaneously.  ...  Thus, almost all existing protein threading methods takes sequence profiles as their input. The accuracy of protein threading thus is heavily relied on the quality of sequence profiles.  ... 
arXiv:1306.4420v1 fatcat:nqllgpxl2nbkndm2blh6tmcggq

Raptorx: Exploiting structure information for protein alignment by statistical inference

Jian Peng, Jinbo Xu
2011 Proteins: Structure, Function, and Bioinformatics  
This paper presents RaptorX, a statistical method for template-based protein modeling that improves alignment accuracy by exploiting structural information in a single or multiple templates.  ...  Our results show that template structural information helps a lot with both single-template and multiple-template protein threading especially when closely-related templates are unavailable and there is  ...  RaptorX-Boost performed worse than RaptorX-MSA in CASP9, maybe because we did not correctly use TASSER. RaptorX is a combination of RaptorX-MSA and RaptorX-Boost.  ... 
doi:10.1002/prot.23175 pmid:21987485 pmcid:PMC3226909 fatcat:uvvsv2pwpfcwbati2nig3dqryi

Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination

Srayanta Mukherjee, Yang Zhang
2011 Structure  
We present a threading-recombination approach, COTH, to boost the protein complex structure library by combining tertiary structure templates with complex alignments.  ...  It also shows a higher accuracy in interface modeling than rigid-body docking of unbound structures from ZDOCK although with lower coverage.  ...  To boost the capacity of the protein complex library, a monomer-based threading was performed in parallel through the tertiary structure library with the resultant alignments shifted to complex framework  ... 
doi:10.1016/j.str.2011.04.006 pmid:21742262 pmcid:PMC3134792 fatcat:vbcw32t2mvg3vhi4cri3r3udum

IMPROVEMENT IN PROTEIN SEQUENCE-STRUCTURE ALIGNMENT USING INSERTION/DELETION FREQUENCY ARRAYS

Kyle Ellrott, Jun-tao Guo, Victor Olman, Ying Xu
2007 Computational Systems Bioinformatics  
By applying IFA to the protein threading problem, we have been able to improve the alignment accuracy, especially for proteins with low sequence identity.  ...  the protein structure.  ...  Once applied, this technique can improve protein threading alignment accuracy.  ... 
doi:10.1142/9781860948732_0034 fatcat:67nfl6acnzgrxdaqwo4i2qpwmy

Improved protein fold assignment using support vector machines

Robert E. Langlois, Alice Diec, Ognjen Perisic, Yang Dai, Hui Lu
2006 International Journal of Bioinformatics Research and Applications  
The current implementation demonstrates better prediction accuracy than previous similar approaches, and has similar performance when compared with straightforward threading. ) 'Improved protein fold assignment  ...  Because of the relatively large gap of knowledge between number of protein sequences and protein structures, the ability to construct a computational model predicting structure from sequence information  ...  Improved protein fold assignment using support vector machines  ... 
doi:10.1504/ijbra.2006.007909 fatcat:xdeenes2lrdu5nni5loxt3apeq

Improved protein fold assignment using support vector machines

Robert E. Langlois, Alice Diec, Ognjen Perisic, Yang Dai, Hui Lu
2005 International Journal of Bioinformatics Research and Applications  
The current implementation demonstrates better prediction accuracy than previous similar approaches, and has similar performance when compared with straightforward threading. ) 'Improved protein fold assignment  ...  Because of the relatively large gap of knowledge between number of protein sequences and protein structures, the ability to construct a computational model predicting structure from sequence information  ...  Improved protein fold assignment using support vector machines  ... 
doi:10.1504/ijbra.2005.007909 pmid:18048139 fatcat:aottt2pksfae3hmzlv4ewqhob4

Efficient computation of Hash Hirschberg protein alignment utilizing hyper threading multi‐core sharing technology

Muhannad Abu‐Hashem, Adnan Gutub
2021 CAAI Transactions on Intelligence Technology  
The authors propose using parallel shared memory architecture via Hyper Threading to improve the performance of molecular dataset protein pairwise alignment.  ...  The benefit of this work improvement is shown preserving acceptable accuracy, that is, reaching 2.08, 2.88, and 3.87 boost-up as well as the efficiency of 1.04, 0.96, and 0.97, using 2, 3, and 4 cores,  ...  This section discusses the results in terms of time performance and accuracy, along with the performance's gains of applying the hyper threading technique by assigning multiple threads for each core concurrently  ... 
doi:10.1049/cit2.12070 fatcat:usku2nnyfvcildjjrd53o4rebu

Predicting highly-connected hubs in protein interaction networks by QSAR and biological data descriptors

Michael Hsing, Kendall Byler, Artem Cherkasov
2009 Bioinformation  
Those protein descriptors, together with available protein interaction data have been processed by a machine learning method (boosting trees) and resulted in the development of hub classifiers that are  ...  Hub proteins (those engaged in most physical interactions in a protein interaction network (PIN) have recently gained much research interest due to their essential role in mediating cellular processes  ...  Furthermore we have demonstrated the feasibility of combining numerous protein descriptors to construct boosting treesbased hub classifiers.  ... 
doi:10.6026/97320630004164 pmid:20198194 pmcid:PMC2825595 fatcat:debydckkrbbbvefe4ghuhgibky
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