Qiwen Dong

Qiwen Dong

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Qiwen Dong

Qiwen Dong

Publications by authors named "Qiwen Dong"

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Predicting protein-ligand binding residues with deep convolutional neural networks.

BMC Bioinformatics 2019 Feb 26;20(1):93. Epub 2019 Feb 26.

The High School Affiliated of Liaoning Normal University, Dalian, China.

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http://dx.doi.org/10.1186/s12859-019-2672-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390579PMC
February 2019

RRCRank: a fusion method using rank strategy for residue-residue contact prediction.

BMC Bioinformatics 2017 Sep 2;18(1):390. Epub 2017 Sep 2.

School of Computer Science, Fudan University, Shanghai, 200433, People's Republic of China.

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http://dx.doi.org/10.1186/s12859-017-1811-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581475PMC
September 2017

MQAPRank: improved global protein model quality assessment by learning-to-rank.

BMC Bioinformatics 2017 May 25;18(1):275. Epub 2017 May 25.

School of Data Science and Engineering, East China Normal University, Shanghai, 200062, People's Republic of China.

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http://dx.doi.org/10.1186/s12859-017-1691-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445322PMC
May 2017

Identifying the missing proteins in human proteome by biological language model.

BMC Syst Biol 2016 Dec 23;10(Suppl 4):113. Epub 2016 Dec 23.

College of Engineering, Shanghai Ocean University, Shanghai, 201303, People's Republic of China.

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http://dx.doi.org/10.1186/s12918-016-0352-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259966PMC
December 2016

Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals.

Bioinformatics 2016 11 4;32(21):3260-3269. Epub 2016 Jul 4.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079472PMC
November 2016

Protein ligand-specific binding residue predictions by an ensemble classifier.

BMC Bioinformatics 2016 Nov 17;17(1):470. Epub 2016 Nov 17.

Institute for Data Science and Engineering, East China Normal University, Shanghai, 200062, People's Republic of China.

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http://dx.doi.org/10.1186/s12859-016-1348-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114821PMC
November 2016

Sorting protein decoys by machine-learning-to-rank.

Sci Rep 2016 08 17;6:31571. Epub 2016 Aug 17.

Institute for Data Science and Engineering, East China Normal University, Shanghai 200062, People's Republic of China.

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http://dx.doi.org/10.1038/srep31571DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987638PMC
August 2016

Characterization and Prediction of Protein Flexibility Based on Structural Alphabets.

Biomed Res Int 2016;2016:4628025. Epub 2016 Aug 30.

College of Engineering, Shanghai Ocean University, Shanghai 201303, China.

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http://dx.doi.org/10.1155/2016/4628025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021887PMC
August 2016

Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome.

J Proteome Res 2015 Sep 30;14(9):3750-61. Epub 2015 Jul 30.

School of Computer Science, Fudan University , Shanghai, 204433, China.

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http://pubs.acs.org/doi/10.1021/acs.jproteome.5b00516
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http://dx.doi.org/10.1021/acs.jproteome.5b00516DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878405PMC
September 2015

Murine Gammaherpesvirus 68 Pathogenesis Is Independent of Caspase-1 and Caspase-11 in Mice and Impairs Interleukin-1β Production upon Extrinsic Stimulation in Culture.

J Virol 2015 Jul 8;89(13):6562-74. Epub 2015 Apr 8.

Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York, USA

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http://dx.doi.org/10.1128/JVI.00658-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4468508PMC
July 2015

Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection.

Bioinformatics 2014 Feb 5;30(4):472-9. Epub 2013 Dec 5.

School of Computer Science and Technology and Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Shanghai Key Laboratory of Intelligent Information Processing, Shanghai 200433, China, Gordon Life Science Institute, Belmont, MA 02478, USA, School of Computer, Shenyang Aerospace University, Shenyang, Liaoning, China, School of Computer Science, Fudan University, Shanghai 200433, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/btt709DOI Listing
February 2014

Protein Remote Homology Detection by Combining Chou's Pseudo Amino Acid Composition and Profile-Based Protein Representation.

Mol Inform 2013 Oct 24;32(9-10):775-82. Epub 2013 Jul 24.

School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen Graduate School, Shenzhen, Guangdong, P. R. China phone: +86-755-26033283.

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http://dx.doi.org/10.1002/minf.201300084DOI Listing
October 2013

Using amino acid physicochemical distance transformation for fast protein remote homology detection.

PLoS One 2012 28;7(9):e46633. Epub 2012 Sep 28.

School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, People's Republic of China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0046633PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460876PMC
February 2013

A Protein Classification Method Based on Latent Semantic Analysis*.

Conf Proc IEEE Eng Med Biol Soc 2005 ;7:7738-41

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http://dx.doi.org/10.1109/IEMBS.2005.1616306DOI Listing
October 2012

An improved genetic algorithm for statistical potential function design and protein structure prediction.

Int J Data Min Bioinform 2012 ;6(2):162-77

Department of Computer Science and Technology, Tongji University, Shanghai 201804, China.

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September 2012

Protein remote homology detection based on auto-cross covariance transformation.

Comput Biol Med 2011 Aug 12;41(8):640-7. Epub 2011 Jun 12.

College of Engineering, Shanghai Ocean University, Shanghai 201303, China.

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http://dx.doi.org/10.1016/j.compbiomed.2011.05.015DOI Listing
August 2011

Novel nonlinear knowledge-based mean force potentials based on machine learning.

IEEE/ACM Trans Comput Biol Bioinform 2011 Mar-Apr;8(2):476-86

Shanghai Key Lab of Intelligent Information Processing and the School of Computer Science, Fudan University, Old Yifu Building, Room 202-5, 220 Handan Road, Shanhai 200433, China.

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http://dx.doi.org/10.1109/TCBB.2010.86DOI Listing
June 2011

An improved profile-level domain linker propensity index for protein domain boundary prediction.

Protein Pept Lett 2011 Jan;18(1):7-16

Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, China.

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January 2011

Prediction of protein-protein interactions from primary sequences.

Int J Data Min Bioinform 2010 ;4(2):211-27

Shanghai Key Lab of Intelligent Information Processing, School of Computer Science, Fudan University, Shanghai 200433, China.

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July 2010

Gene ontology-based protein function prediction by using sequence composition information.

Protein Pept Lett 2010 Jun;17(6):789-95

Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.

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June 2010

Prediction of protein-protein interaction sites using an ensemble method.

BMC Bioinformatics 2009 Dec 16;10:426. Epub 2009 Dec 16.

Department of Computer Science and Technology, Tongji University, Shanghai 201804, China.

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http://dx.doi.org/10.1186/1471-2105-10-426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808167PMC
December 2009

Prediction of protein binding sites in protein structures using hidden Markov support vector machine.

BMC Bioinformatics 2009 Nov 20;10:381. Epub 2009 Nov 20.

Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, PR China.

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http://dx.doi.org/10.1186/1471-2105-10-381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785799PMC
November 2009

A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation.

Bioinformatics 2009 Oct 25;25(20):2655-62. Epub 2009 Aug 25.

Shanghai Key Lab of Intelligent Information Processing, School of Computer Science, Fudan University and Department of Computer Science and Technology, Tongji University, Shanghai, China.

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http://dx.doi.org/10.1093/bioinformatics/btp500DOI Listing
October 2009

Exploiting three kinds of interface propensities to identify protein binding sites.

Comput Biol Chem 2009 Aug 9;33(4):303-11. Epub 2009 Jul 9.

Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, China.

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http://dx.doi.org/10.1016/j.compbiolchem.2009.07.001DOI Listing
August 2009

A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis.

BMC Bioinformatics 2008 Dec 1;9:510. Epub 2008 Dec 1.

Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, PR China.

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http://dx.doi.org/10.1186/1471-2105-9-510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613933PMC
December 2008

Prediction of protein local structures and folding fragments based on building-block library.

Proteins 2008 Jul;72(1):353-66

School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.

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http://dx.doi.org/10.1002/prot.21931DOI Listing
July 2008

Analysis and prediction of protein local structure based on structure alphabets.

Proteins 2008 Jul;72(1):163-72

School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.

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http://doi.wiley.com/10.1002/prot.21904
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http://dx.doi.org/10.1002/prot.21904DOI Listing
July 2008

Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins.

BMC Bioinformatics 2007 May 5;8:147. Epub 2007 May 5.

School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.

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http://dx.doi.org/10.1186/1471-2105-8-147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885810PMC
May 2007

Novel knowledge-based mean force potential at the profile level.

BMC Bioinformatics 2006 Jun 27;7:324. Epub 2006 Jun 27.

School of Computer Science and Technology, Harbin Institute of Technology, Harbin, PR China.

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http://dx.doi.org/10.1186/1471-2105-7-324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1534065PMC
June 2006

Domain boundary prediction based on profile domain linker propensity index.

Comput Biol Chem 2006 Apr 13;30(2):127-33. Epub 2006 Mar 13.

School of Computer Science and Technology, Harbin Institute of Technology, Harbin, PR China.

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http://dx.doi.org/10.1016/j.compbiolchem.2006.01.001DOI Listing
April 2006

A seqlet-based maximum entropy Markov approach for protein secondary structure prediction.

Sci China C Life Sci 2005 Aug;48(4):394-405

School of Computer Science and Technology, Harbin Institute of Technology, China.

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August 2005