27 Publications (Page 1 of 2)
2023
Contact-Assisted Threading in Low-Homology Protein Modeling.Bhattacharya, Sutanu⋅Bhattacharya, Sutanu⋅Roche, Rahmatullah⋅Roche, Rahmatullah⋅Shuvo, Md Hossain⋅Shuvo, Md Hossain⋅Moussad, Bernard⋅Moussad, Bernard⋅Bhattacharya, Debswapna and Bhattacharya, DebswapnaMethods in molecular biology (Clifton, N.J.), vol. 2627, pp. 41-59, 2023.
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The transformative power of transformers in protein structure prediction.Moussad, Bernard⋅Roche, Rahmatullah and Bhattacharya, DebswapnaProceedings of the National Academy of Sciences of the United States of America, vol. 120, (no. 32), pp. e2303499120, August 8, 2023.
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2022
rrQNet: protein contact map quality estimation by deep evolutionary reconciliation.Roche, Rahmatullah⋅Roche, Rahmatullah⋅Bhattacharya, Sutanu⋅Bhattacharya, Sutanu⋅Shuvo, Md Hossain⋅Shuvo, Md. Hossain⋅Bhattacharya, Debswapna and Bhattacharya, DebswapnaProteins, June 25, 2022.
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2021
DeepRefiner: high-accuracy protein structure refinement by deep network calibration.Shuvo, Md Hossain⋅Gulfam, Muhammad and Bhattacharya, DebswapnaNucleic acids research, May 17, 2021.
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Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins.Roche, Rahmatullah⋅Roche, Rahmatullah⋅Bhattacharya, Sutanu⋅Bhattacharya, Sutanu⋅Bhattacharya, Debswapna and Bhattacharya, DebswapnaPLoS computational biology, vol. 17, (no. 2), pp. e1008753, February 23, 2021.
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Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading.Bhattacharya, Sutanu⋅Bhattacharya, Sutanu⋅Roche, Rahmatullah⋅Roche, Rahmatullah⋅Shuvo, Md Hossain⋅Shuvo, Md Hossain⋅Bhattacharya, Debswapna and Bhattacharya, DebswapnaFrontiers in molecular biosciences, vol. 8, pp. 643752, 2021.
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2020
Evaluating the significance of contact maps in low-homology protein modeling using contact-assisted threading.Bhattacharya, Sutanu and Bhattacharya, DebswapnaScientific reports, vol. 10, (no. 1), pp. 2908, February 19, 2020.
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QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks.Shuvo, Md Hossain⋅Bhattacharya, Sutanu and Bhattacharya, DebswapnaBioinformatics (Oxford, England), vol. 36, pp. i285-i291, July 1, 2020.
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SPECS: Integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural modelsAlapati, Rahul and Bhattacharya, DebswapnaPLoS One, vol. 15, (no. 2), Feb 2020.
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2019
Cover Image, Volume 87, Issue 7Bhattacharya, Sutanu and Bhattacharya, DebswapnaProteins: Structure, Function, and Bioinformatics, vol. 87, (no. 7), pp. C1, 2019-07-00.
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Does inclusion of residue‐residue contact information boost protein threading?Bhattacharya, Sutanu and Bhattacharya, DebswapnaProteins: Structure, Function, and Bioinformatics, vol. 87, (no. 7), pp. 606, July 2019.
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refineD: Improved protein structure refinement using machine learning based restrained relaxation.Bhattacharya, DebswapnaBioinformatics (Oxford, England), February 13, 2019.
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2018
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12Keasar, Chen⋅Keasar, Chen⋅McGuffin, Liam J⋅McGuffin, Liam J⋅McGuffin, Liam J⋅Wallner, Björn⋅Wallner, Björn⋅Wallner, Björn⋅Chopra, Gaurav⋅Chopra, Gaurav⋅Chopra, Gaurav⋅Adhikari, Badri⋅Adhikari, Badri⋅Adhikari, Badri⋅Bhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Blake, Lauren⋅Blake, Lauren⋅Blake, Lauren⋅Bortot, Leandro Oliveira⋅Bortot, Leandro Oliveira⋅Cao, Renzhi⋅Cao, Renzhi⋅Cao, Renzhi⋅Dhanasekaran, B K⋅Dhanasekaran, B K⋅Dhanasekaran, B K⋅Dimas, Itzhel⋅Dimas, Itzhel⋅Dimas, Itzhel⋅Faccioli, Rodrigo A⋅Faccioli, Rodrigo Antonio⋅Faccioli, Rodrigo Antonio⋅Faraggi, Eshel⋅Faraggi, Eshel⋅Ganzynkowicz, Robert⋅Ganzynkowicz, Robert⋅Ganzynkowicz, Robert⋅Ghosh, Sambit⋅Ghosh, Sambit⋅Ghosh, Sambit⋅Ghosh, Soma⋅Ghosh, Soma⋅Ghosh, Soma⋅Giełdoń, Artur⋅Giełdoń, Artur⋅Giełdoń, Artur⋅Golon, Lukasz⋅Golon, Lukasz⋅Golon, Lukasz⋅He, Yi⋅He, Yi⋅He, Yi⋅Heo, Lim⋅Heo, Lim⋅Heo, Lim⋅Hou, Jie⋅Hou, Jie⋅Hou, Jie⋅Khan, Main⋅Khan, Main⋅Khan, Main⋅Khatib, Firas⋅Khatib, Firas⋅Khatib, Firas⋅Khoury, George A⋅Khoury, George A⋅Khoury, George A⋅Kieslich, Chris⋅Kieslich, Chris⋅Kieslich, Chris⋅Kim, David E⋅Kim, David E⋅Kim, David E⋅Krupa, Pawel⋅Krupa, Pawel⋅Krupa, Pawel⋅Lee, Gyu Rie⋅Lee, Gyu Rie⋅Gyu, Rie L⋅Li, Hongbo⋅Li, Hongbo⋅Li, Hongbo⋅Li, Jilong⋅Li, Jilong⋅Li, Jilong⋅Lipska, Agnieszka⋅Lipska, Agnieszka⋅Lipska, Agnieszka⋅Liwo, Adam⋅Liwo, Adam⋅Liwo, Adam⋅Maghrabi, Ali H⋅Maghrabi, Ali Hassan A⋅Maghrabi, Ali Hassan A⋅Mirdita, Milot⋅Mirdita, Milot⋅Mirzaei, Shokoufeh⋅Mirzaei, Shokoufeh⋅Mirzaei, Shokoufeh⋅Mozolewska, Magdalena A⋅Mozolewska, Magdalena A⋅Mozolewska, Magdalena A⋅Onel, Melis⋅Onel, Melis⋅Onel, Melis⋅Ovchinnikov, Sergey⋅Ovchinnikov, Sergey⋅Ovchinnikov, Sergey⋅Shah, Anand⋅Shah, Anand⋅Shah, Anand⋅Shah, Utkarsh⋅Shah, Utkarsh⋅Shah, Utkarsh⋅Sidi, Tomer⋅Sidi, Tomer⋅Sidi, Tomer⋅Sieradzan, Adam K⋅Sieradzan, Adam K⋅Sieradzan, Adam K⋅Ślusarz, Magdalena⋅Ślusarz, Magdalena⋅Ślusarz, Magdalena⋅Ślusarz, Rafal⋅Ślusarz, Rafal⋅Ślusarz, Rafal⋅Smadbeck, James⋅Smadbeck, James⋅Smadbeck, James⋅Tamamis, Phanourios⋅Tamamis, Phanourios⋅Tamamis, Phanourios⋅Trieber, Nicholas⋅Trieber, Nicholas⋅Trieber, Nicholas⋅Wirecki, Tomasz⋅Wirecki, Tomasz⋅Wirecki, Tomasz⋅Yin, Yanping⋅Yin, Yanping⋅Yin, Yanping⋅Zhang, Yang⋅Zhang, Yang⋅Zhang, Yang⋅Bacardit, Jaume⋅Bacardit, Jaume⋅Bacardit, Jaume⋅Baranowski, Maciej⋅Baranowski, Maciej⋅Baranowski, Maciej⋅Chapman, Nicholas⋅Chapman, Nicholas⋅Chapman, Nicholas⋅Cooper, Seth⋅Cooper, Seth⋅Cooper, Seth⋅Defelicibus, Alexandre⋅Defelicibus, Alexandre⋅Defelicibus, Alexandre⋅Flatten, Jeff⋅Flatten, Jeff⋅Flatten, Jeff⋅Koepnick, Brian⋅Koepnick, Brian⋅Koepnick, Brian⋅Popović, Zoran⋅Popović, Zoran⋅Popović, Zoran⋅Zaborowski, Bartlomiej⋅Zaborowski, Bartlomiej⋅Zaborowski, Bartlomiej⋅Baker, David⋅Baker, David⋅Baker, David⋅Cheng, Jianlin⋅Cheng, Jianlin⋅Cheng, Jianlin⋅Czaplewski, Cezary⋅Czaplewski, Cezary⋅Czaplewski, Cezary⋅⋅Delbem, Alexandre Cláudio Botazzo⋅Delbem, Alexandre Cláudio Botazzo⋅Floudas, Christodoulos⋅Floudas, Christodoulos⋅Floudas, Christodoulos⋅Kloczkowski, Andrzej⋅Kloczkowski, Andrzej⋅Kloczkowski, Andrzej⋅Ołdziej, Stanislaw⋅Ołdziej, Stanislaw⋅Ołdziej, Stanislaw⋅Levitt, Michael⋅Levitt, Michael⋅Levitt, Michael⋅Scheraga, Harold⋅Scheraga, Harold⋅Scheraga, Harold⋅Seok, Chaok⋅Seok, Chaok⋅Söding, Johannes⋅Söding, Johannes⋅Söding, Johannes⋅Vishveshwara, Saraswathi⋅Vishveshwara, Saraswathi⋅Vishveshwara, Saraswathi⋅Xu, Dong⋅Xu, Dong⋅Xu, Dong⋅Crivelli, Silvia N⋅Caglar, Ahmet⋅Crivelli, Silvia N⋅Coral, Alan⋅MacMillan, Alison⋅Allen, Lubow⋅Failer, Barbara⋅Kestemont, Bruno⋅Landers, Catherine R⋅Painter, Charles R⋅Garnier, Christophe⋅Sellin, Claudine⋅Janz, Dietmar⋅Wheeler, Douglas C⋅Simon, Vera⋅Flear, Dylan M⋅Croze, Emmanuel⋅McIlvaine, George V⋅Beecher, Gil⋅Lawrie, Gordon⋅Ykman, Guy⋅Feldmann, Harald⋅Fuentes, Heidemarie K⋅Kovanecz, Istvan⋅Longino, James A⋅Nijland, Jan H⋅Diderich, Jasper A⋅Canfield, Jeffrey M⋅Eriksson, Jesper⋅Slone, Jesse D⋅Mitchell, Joanne⋅Mitch, John⋅Loots-Boiy, Jorn⋅Brownlee, June M⋅Wilson, Karsten⋅Clayton, Keith T⋅DeFord, Kenneth E⋅Abbey, Kirk J⋅Withers, Larry⋅Wei, Linda⋅Ives, Lloyd⋅Miller, Lori A⋅Carpenter, Lynn⋅Sharma, Manasa G⋅Ricci, Manuel⋅Davids, Matthew J⋅Gaebel, Matthias⋅Cassidy, Michael D⋅Fagiola, Michael⋅Pfützenreuter, Michael⋅Barlow, Nova⋅Triggiani, Peter J⋅Leduc, Robert⋅Morneau, Rosemarie L⋅Zaccanelli, Scott J⋅Kleinfelter, Susan C⋅Bausewein, Thomas⋅George, Thomas J⋅Barmettler, Walter and Crivelli, Silvia NScientific reports, vol. 8, (no. 1), pp. 18, 2018-Jul-02.
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2017
Assessing Predicted Contacts for Building Protein Three-Dimensional ModelsAdhikari, Badri⋅Adhikari, Badri⋅Bhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Cao, Renzhi⋅Cao, Renzhi⋅Cheng, Jianlin and Cheng, JianlinMethods in molecular biology (Clifton, N.J.), vol. 1484, pp. 126, 2017-00-00.
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QAcon: single model quality assessment using protein structural and contact information with machine learning techniquesCao, Renzhi⋅Cao, Renzhi⋅Adhikari, Badri⋅Adhikari, Badri⋅Bhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Sun, Miao⋅Sun, Miao⋅Hou, Jie⋅Hou, Jie⋅Cheng, Jianlin and Cheng, JianlinBioinformatics (Oxford, England), vol. 33, (no. 4), pp. 588, 2017-02-15.
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2016
3Drefine: an interactive web server for efficient protein structure refinementBhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Nowotny, Jackson⋅Nowotny, Jackson⋅Cao, Renzhi⋅Cao, Renzhi⋅Cheng, Jianlin and Cheng, JianlinNucleic acids research, vol. 44, (no. W1), pp. W409, 2016-07-08.
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ConEVA: a toolbox for comprehensive assessment of protein contactsAdhikari, Badri⋅Adhikari, Badri⋅Nowotny, Jackson⋅Nowotny, Jackson⋅Bhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Hou, Jie⋅Hou, Jie⋅Cheng, Jianlin and Cheng, JianlinBMC bioinformatics, vol. 17, (no. 1), pp. 517, 2016-Dec-07.
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DeepQA: improving the estimation of single protein model quality with deep belief networksCao, Renzhi⋅Cao, Renzhi⋅Bhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Hou, Jie⋅Hou, Jie⋅Cheng, Jianlin and Cheng, JianlinBMC bioinformatics, vol. 17, (no. 1), pp. 495, 2016-Dec-05.
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FRAGSION: ultra-fast protein fragment library generation by IOHMM samplingBhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Adhikari, Badri⋅Adhikari, Badri⋅Li, Jilong⋅Li, Jilong⋅Cheng, Jianlin and Cheng, JianlinBioinformatics (Oxford, England), vol. 32, (no. 13), pp. 2061, 2016-07-01.
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Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11Cao, Renzhi⋅Cao, Renzhi⋅Bhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Adhikari, Badri⋅Adhikari, Badri⋅Li, Jilong⋅Li, Jilong⋅Cheng, Jianlin and Cheng, JianlinProteins: Structure, Function, and Bioinformatics, vol. 84, pp. 259, 2016-09-00.
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UniCon3D:de novoprotein structure prediction using united-residue conformational search via stepwise, probabilistic samplingBhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Cao, Renzhi⋅Cao, Renzhi⋅Cheng, Jianlin and Cheng, JianlinBioinformatics, vol. 32, (no. 18), pp. 2799, 2016-09-15.
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2015
CONFOLD: Residue‐residue contact‐guided ab initio protein foldingAdhikari, Badri⋅Adhikari, Badri⋅Bhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Cao, Renzhi⋅Cao, Renzhi⋅Cheng, Jianlin and Cheng, JianlinProteins: Structure, Function, and Bioinformatics, vol. 83, (no. 8), pp. 1449, August 2015.
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Large-scale model quality assessment for improving protein tertiary structure predictionCao, Renzhi⋅Cao, Renzhi⋅Bhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Adhikari, Badri⋅Adhikari, Badri⋅Li, Jilong⋅Li, Jilong⋅Cheng, Jianlin and Cheng, JianlinBioinformatics (Oxford, England), vol. 31, (no. 12), pp. i123, 2015-Jun-15.
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2014
The MULTICOM protein tertiary structure prediction systemLi, Jilong⋅Li, Jilong⋅Bhattacharya, Debswapna⋅Bhattacharya, Debswapna⋅Cao, Renzhi⋅Cao, Renzhi⋅Adhikari, Badri⋅Adhikari, Badri⋅Deng, Xin⋅Deng, Xin⋅Eickholt, Jesse⋅Eickholt, Jesse⋅Cheng, Jianlin and Cheng, JianlinMethods in molecular biology (Clifton, N.J.), vol. 1137, pp. 41, 2014-00-00.
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