21 Publications
2020
Evaluating the significance of contact maps in low-homology protein modeling using contact-assisted threading.
Bhattacharya, Sutanu and Bhattacharya, Debswapna
Scientific reports, vol. 10, (no. 1), pp. 2908, February 19, 2020. | Journal Article
 
QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks.
Shuvo, Md HossainBhattacharya, Sutanu and Bhattacharya, Debswapna
Bioinformatics (Oxford, England), vol. 36, pp. i285-i291, July 1, 2020. | Journal Article
 
SPECS: Integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural models
Alapati, Rahul and Bhattacharya, Debswapna
PLoS One, vol. 15, (no. 2), Feb 2020. | Journal Article
2019
Cover Image, Volume 87, Issue 7
Bhattacharya, Sutanu and Bhattacharya, Debswapna
Proteins: Structure, Function, and Bioinformatics, vol. 87, (no. 7), pp. C1, 2019-07-00. | Journal Article
 
Does inclusion of residue‐residue contact information boost protein threading?
Bhattacharya, Sutanu and Bhattacharya, Debswapna
Proteins: Structure, Function, and Bioinformatics, vol. 87, (no. 7), pp. 606, July 2019. | Journal Article
 
refineD: Improved protein structure refinement using machine learning based restrained relaxation.
Bhattacharya, Debswapna
Bioinformatics (Oxford, England), February 13, 2019. | Journal Article
2018
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
Keasar, ChenKeasar, ChenMcGuffin, Liam JMcGuffin, Liam JWallner, BjörnWallner, BjörnChopra, GauravChopra, GauravAdhikari, BadriAdhikari, BadriBhattacharya, DebswapnaBhattacharya, DebswapnaBlake, LaurenBlake, LaurenBortot, Leandro OliveiraBortot, Leandro OliveiraCao, RenzhiCao, RenzhiDhanasekaran, B KDhanasekaran, B KDimas, ItzhelDimas, ItzhelFaccioli, Rodrigo AntonioFaccioli, Rodrigo AntonioFaraggi, EshelFaraggi, EshelGanzynkowicz, RobertGanzynkowicz, RobertGhosh, SambitGhosh, SambitGhosh, SomaGhosh, SomaGiełdoń, ArturGiełdoń, ArturGolon, LukaszGolon, LukaszHe, YiHe, YiHeo, LimHeo, LimHou, JieHou, JieKhan, MainKhan, MainKhatib, FirasKhatib, FirasKhoury, George AKhoury, George AKieslich, ChrisKieslich, ChrisKim, David EKim, David EKrupa, PawelKrupa, PawelLee, Gyu RieLee, Gyu RieLi, HongboLi, HongboLi, JilongLi, JilongLipska, AgnieszkaLipska, AgnieszkaLiwo, AdamLiwo, AdamMaghrabi, Ali Hassan AMaghrabi, Ali Hassan AMirdita, MilotMirdita, MilotMirzaei, ShokoufehMirzaei, ShokoufehMozolewska, Magdalena AMozolewska, Magdalena AOnel, MelisOnel, MelisOvchinnikov, SergeyOvchinnikov, SergeyShah, AnandShah, AnandShah, UtkarshShah, UtkarshSidi, TomerSidi, TomerSieradzan, Adam KSieradzan, Adam KŚlusarz, MagdalenaŚlusarz, MagdalenaŚlusarz, RafalŚlusarz, RafalSmadbeck, JamesSmadbeck, JamesTamamis, PhanouriosTamamis, PhanouriosTrieber, NicholasTrieber, NicholasWirecki, TomaszWirecki, TomaszYin, YanpingYin, YanpingZhang, YangZhang, YangBacardit, JaumeBacardit, JaumeBaranowski, MaciejBaranowski, MaciejChapman, NicholasChapman, NicholasCooper, SethCooper, SethDefelicibus, AlexandreDefelicibus, AlexandreFlatten, JeffFlatten, JeffKoepnick, BrianKoepnick, BrianPopović, ZoranPopović, ZoranZaborowski, BartlomiejZaborowski, BartlomiejBaker, DavidBaker, DavidCheng, JianlinCheng, JianlinCzaplewski, CezaryCzaplewski, CezaryDelbem, Alexandre Cláudio BotazzoDelbem, Alexandre Cláudio BotazzoFloudas, ChristodoulosFloudas, ChristodoulosKloczkowski, AndrzejKloczkowski, AndrzejOłdziej, StanislawOłdziej, StanislawLevitt, MichaelLevitt, MichaelScheraga, HaroldScheraga, HaroldSeok, ChaokSeok, ChaokSöding, JohannesSöding, JohannesVishveshwara, SaraswathiVishveshwara, SaraswathiXu, DongXu, DongCrivelli, Silvia N and Crivelli, Silvia N
Scientific reports, vol. 8, (no. 1), pp. 18, 2018-Jul-02. | Journal Article
2017
Assessing Predicted Contacts for Building Protein Three-Dimensional Models
Adhikari, BadriAdhikari, BadriBhattacharya, DebswapnaBhattacharya, DebswapnaCao, RenzhiCao, RenzhiCheng, Jianlin and Cheng, Jianlin
Methods in molecular biology (Clifton, N.J.), vol. 1484, pp. 126, 2017-00-00. | Journal Article
 
QAcon: single model quality assessment using protein structural and contact information with machine learning techniques
Cao, RenzhiCao, RenzhiAdhikari, BadriAdhikari, BadriBhattacharya, DebswapnaBhattacharya, DebswapnaSun, MiaoSun, MiaoHou, JieHou, JieCheng, Jianlin and Cheng, Jianlin
Bioinformatics (Oxford, England), vol. 33, (no. 4), pp. 588, 2017-02-15. | Journal Article
2016
3Drefine: an interactive web server for efficient protein structure refinement
Bhattacharya, DebswapnaBhattacharya, DebswapnaNowotny, JacksonNowotny, JacksonCao, RenzhiCao, RenzhiCheng, Jianlin and Cheng, Jianlin
Nucleic acids research, vol. 44, (no. W1), pp. W409, 2016-07-08. | Journal Article
 
ConEVA: a toolbox for comprehensive assessment of protein contacts
Adhikari, BadriAdhikari, BadriNowotny, JacksonNowotny, JacksonBhattacharya, DebswapnaBhattacharya, DebswapnaHou, JieHou, JieCheng, Jianlin and Cheng, Jianlin
BMC bioinformatics, vol. 17, (no. 1), pp. 517, 2016-Dec-07. | Journal Article
 
DeepQA: improving the estimation of single protein model quality with deep belief networks
Cao, RenzhiCao, RenzhiBhattacharya, DebswapnaBhattacharya, DebswapnaHou, JieHou, JieCheng, Jianlin and Cheng, Jianlin
BMC bioinformatics, vol. 17, (no. 1), pp. 495, 2016-Dec-05. | Journal Article
 
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling
Bhattacharya, DebswapnaBhattacharya, DebswapnaAdhikari, BadriAdhikari, BadriLi, JilongLi, JilongCheng, Jianlin and Cheng, Jianlin
Bioinformatics (Oxford, England), vol. 32, (no. 13), pp. 2061, 2016-07-01. | Journal Article
 
Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11
Cao, RenzhiCao, RenzhiBhattacharya, DebswapnaBhattacharya, DebswapnaAdhikari, BadriAdhikari, BadriLi, JilongLi, JilongCheng, Jianlin and Cheng, Jianlin
Proteins: Structure, Function, and Bioinformatics, vol. 84, pp. 259, 2016-09-00. | Journal Article
 
UniCon3D:de novoprotein structure prediction using united-residue conformational search via stepwise, probabilistic sampling
Bhattacharya, DebswapnaBhattacharya, DebswapnaCao, RenzhiCao, RenzhiCheng, Jianlin and Cheng, Jianlin
Bioinformatics, vol. 32, (no. 18), pp. 2799, 2016-09-15. | Journal Article
2015
CONFOLD: Residue‐residue contact‐guided ab initio protein folding
Adhikari, BadriAdhikari, BadriBhattacharya, DebswapnaBhattacharya, DebswapnaCao, RenzhiCao, RenzhiCheng, Jianlin and Cheng, Jianlin
Proteins: Structure, Function, and Bioinformatics, vol. 83, (no. 8), pp. 1449, August 2015. | Journal Article
 
De novo protein conformational sampling using a probabilistic graphical model
Bhattacharya, DebswapnaBhattacharya, DebswapnaCheng, Jianlin and Cheng, Jianlin
Scientific reports, vol. 5, (no. 1), pp. 16332, 2015-Nov-06. | Journal Article
 
Large-scale model quality assessment for improving protein tertiary structure prediction
Cao, RenzhiCao, RenzhiBhattacharya, DebswapnaBhattacharya, DebswapnaAdhikari, BadriAdhikari, BadriLi, JilongLi, JilongCheng, Jianlin and Cheng, Jianlin
Bioinformatics (Oxford, England), vol. 31, (no. 12), pp. i123, 2015-Jun-15. | Journal Article
2014
The MULTICOM protein tertiary structure prediction system
Li, JilongLi, JilongBhattacharya, DebswapnaBhattacharya, DebswapnaCao, RenzhiCao, RenzhiAdhikari, BadriAdhikari, BadriDeng, XinDeng, XinEickholt, JesseEickholt, JesseCheng, Jianlin and Cheng, Jianlin
Methods in molecular biology (Clifton, N.J.), vol. 1137, pp. 41, 2014-00-00. | Journal Article
2013
3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic‐level energy minimization
Bhattacharya, DebswapnaBhattacharya, DebswapnaCheng, Jianlin and Cheng, Jianlin
Proteins: Structure, Function, and Bioinformatics, vol. 81, (no. 1), pp. 131, January 2013. | Journal Article
 
i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10
Bhattacharya, DebswapnaBhattacharya, DebswapnaCheng, Jianlin and Cheng, Jianlin
PloS one, vol. 8, (no. 7), pp. e69648, 2013-00-00. | Journal Article