32 Publications (Page 1 of 2)
2025
RNAbpFlow: Base pair-augmented SE(3)-flow matching for conditional RNA 3D structure generation
Tarafder, Sumit and Bhattacharya, Debswapna
bioRxiv : the preprint server for biology, Jan 26, 2025. | Journal Article
 
To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era
Vangaru, Sriniketh and Bhattacharya, Debswapna
bioRxiv : the preprint server for biology, Feb 27, 2025. | Journal Article
2024
Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules
Norton, Trevor and Bhattacharya, Debswapna
Journal of molecular biology, pp. 168818, Oct 8, 2024. | Journal Article
 
The landscape of RNA 3D structure modeling with transformer networks
Tarafder, SumitRoche, Rahmatullah and Bhattacharya, Debswapna
Biology methods & protocols, vol. 9, (no. 1), pp. bpae047, Jan 2024. | Journal Article
2023
Contact-Assisted Threading in Low-Homology Protein Modeling.
Bhattacharya, SutanuBhattacharya, SutanuRoche, RahmatullahRoche, RahmatullahShuvo, Md HossainShuvo, Md HossainMoussad, BernardMoussad, BernardBhattacharya, Debswapna and Bhattacharya, Debswapna
Methods in molecular biology (Clifton, N.J.), vol. 2627, pp. 41-59, 2023. | Journal Article
 
E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction
Roche, RahmatullahMoussad, BernardShuvo, Md Hossain and Bhattacharya, Debswapna
PLoS computational biology, vol. 19, (no. 8), pp. e1011435, Aug 2023. | Journal Article
 
The transformative power of transformers in protein structure prediction.
Moussad, BernardRoche, Rahmatullah and Bhattacharya, Debswapna
Proceedings of the National Academy of Sciences of the United States of America, vol. 120, (no. 32), pp. e2303499120, August 8, 2023. | Journal Article
2022
rrQNet: protein contact map quality estimation by deep evolutionary reconciliation.
Roche, RahmatullahRoche, RahmatullahBhattacharya, SutanuBhattacharya, SutanuShuvo, Md HossainShuvo, Md. HossainBhattacharya, Debswapna and Bhattacharya, Debswapna
Proteins, June 25, 2022. | Journal Article
2021
DeepRefiner: high-accuracy protein structure refinement by deep network calibration.
Shuvo, Md HossainGulfam, Muhammad and Bhattacharya, Debswapna
Nucleic acids research, May 17, 2021. | Journal Article
 
Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins.
Roche, RahmatullahRoche, RahmatullahBhattacharya, SutanuBhattacharya, SutanuBhattacharya, Debswapna and Bhattacharya, Debswapna
PLoS computational biology, vol. 17, (no. 2), pp. e1008753, February 23, 2021. | Journal Article
 
Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading.
Bhattacharya, SutanuBhattacharya, SutanuRoche, RahmatullahRoche, RahmatullahShuvo, Md HossainShuvo, Md HossainBhattacharya, Debswapna and Bhattacharya, Debswapna
Frontiers in molecular biosciences, vol. 8, pp. 643752, 2021. | Journal Article
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, ChenKeasar, ChenMcGuffin, Liam JMcGuffin, Liam JMcGuffin, Liam JWallner, BjörnWallner, BjörnWallner, BjörnWallner, BjörnChopra, GauravChopra, GauravChopra, GauravChopra, GauravAdhikari, BadriAdhikari, BadriAdhikari, BadriAdhikari, BadriBhattacharya, DebswapnaBhattacharya, DebswapnaBhattacharya, DebswapnaBhattacharya, DebswapnaBlake, LaurenBlake, LaurenBlake, LaurenBlake, LaurenBortot, Leandro OliveiraBortot, Leandro OliveiraBortot, Leandro OliveiraCao, RenzhiCao, RenzhiCao, RenzhiCao, RenzhiDhanasekaran, B KDhanasekaran, B KDhanasekaran, B KDhanasekaran, BKDimas, ItzhelDimas, ItzhelDimas, ItzhelDimas, ItzhelFaccioli, Rodrigo AntonioFaccioli, Rodrigo AFaccioli, Rodrigo AntonioFaraggi, EshelFaraggi, EshelFaraggi, EshelGanzynkowicz, RobertGanzynkowicz, RobertGanzynkowicz, RobertGanzynkowicz, RobertGhosh, SambitGhosh, SambitGhosh, SambitGhosh, SambitGhosh, SomaGhosh, SomaGhosh, SomaGhosh, SomaGiełdoń, ArturGiełdoń, ArturGiełdoń, ArturGiełdoń, ArturGolon, LukaszGolon, LukaszGolon, LukaszGolon, LukaszHe, YiHe, YiHe, YiHe, YiHeo, LimHeo, LimHeo, LimHeo, LimHou, JieHou, JieHou, JieHou, JieKhan, MainKhan, MainKhan, MainKhan, MainKhatib, FirasKhatib, FirasKhatib, FirasKhatib, FirasKhoury, George AKhoury, George AKhoury, George AKieslich, ChrisKieslich, ChrisKieslich, ChrisKieslich, ChrisKim, David EKim, David EKim, David EKrupa, PawelKrupa, PawelKrupa, PawelKrupa, PawelLee, Gyu RieLee, Gyu RieGyu, Rie LLee, Gyu RieLi, HongboLi, HongboLi, HongboLi, HongboLi, JilongLi, JilongLi, JilongLi, JilongLipska, AgnieszkaLipska, AgnieszkaLipska, AgnieszkaLipska, AgnieszkaLiwo, AdamLiwo, AdamLiwo, AdamLiwo, AdamMaghrabi, Ali HMaghrabi, Ali Hassan AMaghrabi, Ali Hassan AMirdita, MilotMirdita, MilotMirdita, MilotMirzaei, ShokoufehMirzaei, ShokoufehMirzaei, ShokoufehMirzaei, ShokoufehMozolewska, Magdalena AMozolewska, Magdalena AMozolewska, Magdalena AOnel, MelisOnel, MelisOnel, MelisOnel, MelisOvchinnikov, SergeyOvchinnikov, SergeyOvchinnikov, SergeyOvchinnikov, SergeyShah, AnandShah, AnandShah, AnandShah, AnandShah, UtkarshShah, UtkarshShah, UtkarshShah, UtkarshSidi, TomerSidi, TomerSidi, TomerSidi, TomerSieradzan, Adam KSieradzan, Adam KSieradzan, Adam KŚlusarz, MagdalenaŚlusarz, MagdalenaŚlusarz, MagdalenaŚlusarz, MagdalenaŚlusarz, RafalŚlusarz, RafalŚlusarz, RafalŚlusarz, RafalSmadbeck, JamesSmadbeck, JamesSmadbeck, JamesSmadbeck, JamesTamamis, PhanouriosTamamis, PhanouriosTamamis, PhanouriosTamamis, PhanouriosTrieber, NicholasTrieber, NicholasTrieber, NicholasTrieber, NicholasWirecki, TomaszWirecki, TomaszWirecki, TomaszWirecki, TomaszYin, YanpingYin, YanpingYin, YanpingYin, YanpingZhang, YangZhang, YangZhang, YangZhang, YangBacardit, JaumeBacardit, JaumeBacardit, JaumeBacardit, JaumeBaranowski, MaciejBaranowski, MaciejBaranowski, MaciejBaranowski, MaciejChapman, NicholasChapman, NicholasChapman, NicholasChapman, NicholasCooper, SethCooper, SethCooper, SethCooper, SethDefelicibus, AlexandreDefelicibus, AlexandreDefelicibus, AlexandreDefelicibus, AlexandreFlatten, JeffFlatten, JeffFlatten, JeffFlatten, JeffKoepnick, BrianKoepnick, BrianKoepnick, BrianKoepnick, BrianPopović, ZoranPopović, ZoranPopović, ZoranPopović, ZoranZaborowski, BartlomiejZaborowski, BartlomiejZaborowski, BartlomiejZaborowski, BartlomiejBaker, DavidBaker, DavidBaker, DavidBaker, DavidCheng, JianlinCheng, JianlinCheng, JianlinCzaplewski, CezaryCzaplewski, CezaryCzaplewski, CezaryCzaplewski, CezaryDelbem, Alexandre Cláudio BotazzoDelbem, Alexandre Cláudio BotazzoDelbem, Alexandre Cláudio BotazzoFloudas, ChristodoulosFloudas, ChristodoulosFloudas, ChristodoulosFloudas, ChristodoulosKloczkowski, AndrzejKloczkowski, AndrzejKloczkowski, AndrzejKloczkowski, AndrzejOłdziej, StanislawOłdziej, StanislawOłdziej, StanislawOłdziej, StanislawLevitt, MichaelLevitt, MichaelLevitt, MichaelLevitt, MichaelScheraga, HaroldScheraga, HaroldScheraga, HaroldScheraga, HaroldSeok, ChaokSeok, ChaokSeok, ChaokSöding, JohannesSöding, JohannesSöding, JohannesSöding, JohannesVishveshwara, SaraswathiVishveshwara, SaraswathiVishveshwara, SaraswathiVishveshwara, SaraswathiXu, DongXu, DongXu, DongXu, DongCrivelli, Silvia NCaglar, AhmetCrivelli, Silvia NFoldit Players consortiumCoral, AlanMacMillan, AlisonAllen, LubowFailer, BarbaraKestemont, BrunoLanders, Catherine RPainter, Charles RGarnier, ChristopheSellin, ClaudineJanz, DietmarWheeler, Douglas CSimon, VeraFlear, Dylan MCroze, EmmanuelMcIlvaine, George VBeecher, GilLawrie, GordonYkman, GuyFeldmann, HaraldFuentes, Heidemarie KKovanecz, IstvanLongino, James ANijland, Jan HDiderich, Jasper ACanfield, Jeffrey MEriksson, JesperSlone, Jesse DMitchell, JoanneMitch, JohnLoots-Boiy, JornBrownlee, June MWilson, KarstenClayton, Keith TDeFord, Kenneth EAbbey, Kirk JWithers, LarryWei, LindaIves, LloydMiller, Lori ACarpenter, LynnSharma, Manasa GRicci, ManuelDavids, Matthew JGaebel, MatthiasCassidy, Michael DFagiola, MichaelPfützenreuter, MichaelBarlow, NovaTriggiani, Peter JLeduc, RobertMorneau, Rosemarie LZaccanelli, Scott JKleinfelter, Susan CBausewein, ThomasGeorge, Thomas JBarmettler, Walter 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