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A new method for modeling and solving the protein fold recognition problem (extended abstract)

Ying Xu, Dong Xu, Edward C. Uberbacher
1998 Proceedings of the second annual international conference on Computational molecular biology - RECOMB '98  
Acknowledgements This research was supported by the United States Department of Energy, under contract DE-AC05-840R21400 with Lockheed Martin Energy Systems, Inc.  ...  We expect this study will lead to new insights into the computational protein threading problem, and possibly new and better ways t o model the problem. (3,f) = ((31,31), ('s2,Z2), ......, (&,&)) be an  ...  Introduction Protein fold recognition concerns recognizing the native-like folds (3D structures) of an amino acid sequence, from a protein fold database.  ... 
doi:10.1145/279069.279134 dblp:conf/recomb/XuXU98 fatcat:ej7a6q44trbl5eztsa7kiewwmy

Extended Abstracts

2010 Cartilage  
Acknowledgments: We acknowledge the EU for financial support ("STEPS"; FP6-#NMP3-CT-2005-500465) Acknowledgments: This study was supported by a grant from the New Energy and Industrial Technology Development  ...  Organization, Japan, and Grantin-Aid for Scientific Research (B), Japan Society for the promotion of Science, Japan.  ...  These new lines, 1 healing and 4 non-healing, establish a new set of models that will now be used to 4 non-healing, establish a new set of models that will now be used to 4 non-healing, establish a new  ... 
doi:10.1177/1947603510386038 pmid:26075041 pmcid:PMC4300817 fatcat:m2mv3tnf6vhzndubvwdtltkh5y

Extended Abstracts

2003 Blood Purification  
Will transgenesis and gene targeting, as described above, solve the problem of vascular rejection?  ...  The reason for this is two fold.  ... 
doi:10.1159/000072553 fatcat:4nb76qsbazfzzhx5e5f7x5gkdi

Protein structure determination using protein threading and sparse NMR data (extended abstract)

Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Engin Serpersu
2000 Proceedings of the fourth annual international conference on Computational molecular biology - RECOMB '00  
It zs well known that the NMR method for protein structure determinatwn apphes to small proteins and that zts effectweness decreases very rapidly as the molecular weight increases beyond about 30 kD.  ...  We have recently developed a method for protein structure determmatwn that can fully utilize partzal NMR data as calculation constraints.  ...  Ed Uberbacher for his helpful discussion related to this work.  ... 
doi:10.1145/332306.332568 dblp:conf/recomb/XuXCES00 fatcat:bsa2kpi3hzexxnuon4tmmn7h4m

BioS2Net: Holistic Structural and Sequential Analysis of Biomolecules Using a Deep Neural Network

Albert Roethel, Piotr Biliński, Takao Ishikawa
2022 International Journal of Molecular Sciences  
for protein fold recognition.  ...  For decades, the rate of solving new biomolecular structures has been exceeding that at which their manual classification and feature characterisation can be carried out efficiently.  ...  Acknowledgments: Special thanks are addressed to Marcin Dziubak for the preparation of figures, as well as Natalia Szulc, Katarzyna Grudzi ą ż, and Paulina Smaruj for comments on the manuscript.  ... 
doi:10.3390/ijms23062966 pmid:35328384 pmcid:PMC8954277 fatcat:u7k4k2chxnckdi3v7mn4kkxtee

Application of Bioinformatics on Protein Structure Prediction

XIAODAN LIU
2017 DEStech Transactions on Computer Science and Engineering  
This paper describes the establishment and development of common database of protein, protein structure analysis, protein secondary and tertiary structure prediction; The application of bioinformatics  ...  in protein structure analysis is comprehensively summarized, which provides theoretical basis for the wide application of bioinformatics in protein engineering.  ...  At present, the main methods of 3D spatial structure prediction are homology modeling, fold type recognition and ab initio prediction.  ... 
doi:10.12783/dtcse/cib2015/16173 fatcat:zywns4pb5bezfc6dw77y5rfbly

DelPhi Suite: New Developments and Review of Functionalities

Chuan Li, Zhe Jia, Arghya Chakravorty, Swagata Pahari, Yunhui Peng, Sankar Basu, Mahesh Koirala, Shailesh Kumar Panday, Marharyta Petukh, Lin Li, Emil Alexov
2019 Journal of Computational Chemistry  
The new DelPhi is a C++ object-oriented package supporting various levels of multiprocessing and memory distribution.  ...  Here, we report a new edition of the popular software package DelPhi along with describing its functionalities.  ...  Acknowledgments The work was supported by a grant from NIH, grant number R01GM093937. We thank Chitra Karki for the help preparing  ... 
doi:10.1002/jcc.26006 pmid:31237360 pmcid:PMC6771749 fatcat:2hvhb72exbarhipvw7p376ekhu

Biomedical named entity recognition using two-phase model based on SVMs

Ki-Joong Lee, Young-Sook Hwang, Seonho Kim, Hae-Chang Rim
2004 Journal of Biomedical Informatics  
We try to solve these problems by separating the NE recognition task into two subtasks, where we use appropriate SVM classifiers and relevant features for each subtask.  ...  In addition, by employing a hierarchical classification method based on ontology, we effectively solve the multiclass problem concerning semantic classification.  ...  For instance, the MEDLINE database [11] contains over 12 million abstracts and many new abstracts are added monthly.  ... 
doi:10.1016/j.jbi.2004.08.012 pmid:15542017 fatcat:iocpoyozvbfvfh7bmtc7mp2whq

Recognition of Structure Similarities in Proteins

Lin WANG, Yuqing QIU, Jiguang WANG, Xiangsun ZHANG
2008 Journal of Systems Science and Complexity  
Most of those methods can be available on the World Wide Web, but evaluation of all the methods is still a hard problem.  ...  Protein fold structure is more conserved than its amino acid sequence and closely associated with biological function, so calculating the similarity of protein structures is a fundamental problem in structural  ...  So recognition of common substructures (the local structural motifs or binding sites) is important for studies in protein function and protein fold changes in evolution [10] .  ... 
doi:10.1007/s11424-008-9143-5 fatcat:ashntqwlzvbz7hamv2j4mh4pfi

Physical Biomodeling: a new field enabled by 3-D printing in biomodeling [article]

Promita Chakraborty
2015 arXiv   pre-print
Now 3D printing technology opens the door for a new field, Physical Biomodeling, at the intersection of experimental data, computational biology and physical modeling for study of biological systems, such  ...  as protein folding at nano-scale.  ...  New frontiers for protein folding with physical models: A few exciting and important possibilities, particularly for research in the protein folding problem is as follows.  ... 
arXiv:1502.04687v2 fatcat:mjgzyuy7efacxep3hew6ynr56u

Gene finding for the helical cytokines

D. Conklin, B. Haldeman, Z. Gao
2005 Bioinformatics  
The low gene sensitivity of current methods is a problem for divergent protein families, because fairly accurate exon assemblies are required before sensitive fold recognition algorithms can be applied  ...  This paper presents a new genomic threading algorithm which integrates the gene finding and fold recognition steps into a single process.  ...  the preparation of Figure 2 and Patrick O'Hara.  ... 
doi:10.1093/bioinformatics/bti283 pmid:15661800 fatcat:bnkaovhcmndirjl4zukfugwgti

A Promising Similarity Based Secondary Structure Prediction Method

Faruk Berat Akcesme, Mehmet Can
2016 Southeast Europe Journal of Soft Computing  
., 1996; Fischer and Eisenberg, 1996; rotein folding problem is on a long way to are protein structure prediction methods, modeling and threading that work for some special cases.  ...  Although protein folding problem is solution, there are protein structure prediction methods, such as comparative modeling and well, but unfortunately only for some special cases.  ... 
doi:10.21533/scjournal.v5i1.103 fatcat:snehjwk5dzb4jnokmuiluixmve

Protein structure prediction by AlphaFold2: are attention and symmetries all you need?

Nazim Bouatta, Peter Sorger, Mohammed AlQuraishi
2021 Acta Crystallographica Section D: Structural Biology  
The rules of protein folding are ultimately encoded in the physical principles that underpin it; to conclude, the implications of having a powerful computational model for structure prediction that does  ...  Recent advances in deep learning, combined with the availability of genomic data for inferring co-evolutionary patterns, provide a new approach to protein structure prediction that is complementary to  ...  Acknowledgements The following competing interests are declared. MA is a member of the SAB of FL2021-002, a Foresite Labs company, and consults for Interline Therapeutics.  ... 
doi:10.1107/s2059798321007531 pmid:34342271 pmcid:PMC8329862 fatcat:sam47cns4fhg3hgo273qoshlta

Protein structure alignment considering phenotypic plasticity

G. Csaba, F. Birzele, R. Zimmer
2008 Bioinformatics  
Results: Here, we introduce a new measure for protein structure similarity and propose a novel method called phenotypic plasticity method (PPM) which explicitly tries to model the evolutionary distance  ...  method which models the cost of mutations, insertions and deletions occurring in protein sequences on the structure level is still missing.  ...  This set-up becomes for example important for folds which contain only one family and need to be extended by a new family ('protein structure threading').  ... 
doi:10.1093/bioinformatics/btn271 pmid:18689847 fatcat:6hl6gu4fjbh5vg4iteab3sx2ie
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