Pesquisa | BVS IEC

1.

DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction.

Terashi, Genki; Wang, Xiao; Prasad, Devashish; Nakamura, Tsukasa; Kihara, Daisuke.

Nat Methods ; 21(1): 122-131, 2024 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-38066344

2.

CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning.

Wang, Xiao; Terashi, Genki; Kihara, Daisuke.

Nat Methods ; 20(11): 1739-1747, 2023 Nov.

Artigo em Inglês | MEDLINE | ID: mdl-37783885

3.

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography.

Bukhman, Yury V; Morin, Phillip A; Meyer, Susanne; Chu, Li-Fang; Jacobsen, Jeff K; Antosiewicz-Bourget, Jessica; Mamott, Daniel; Gonzales, Maylie; Argus, Cara; Bolin, Jennifer; Berres, Mark E; Fedrigo, Olivier; Steill, John; Swanson, Scott A; Jiang, Peng; Rhie, Arang; Formenti, Giulio; Phillippy, Adam M; Harris, Robert S; Wood, Jonathan M D; Howe, Kerstin; Kirilenko, Bogdan M; Munegowda, Chetan; Hiller, Michael; Jain, Aashish; Kihara, Daisuke; Johnston, J Spencer; Ionkov, Alexander; Raja, Kalpana; Toh, Huishi; Lang, Aimee; Wolf, Magnus; Jarvis, Erich D; Thomson, James A; Chaisson, Mark J P; Stewart, Ron.

Mol Biol Evol ; 41(3)2024 Mar 01.

Artigo em Inglês | MEDLINE | ID: mdl-38376487

4.

Residue-wise local quality estimation for protein models from cryo-EM maps.

Terashi, Genki; Wang, Xiao; Maddhuri Venkata Subramaniya, Sai Raghavendra; Tesmer, John J G; Kihara, Daisuke.

Nat Methods ; 19(9): 1116-1125, 2022 09.

Artigo em Inglês | MEDLINE | ID: mdl-35953671

5.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

Lawson, Catherine L; Kryshtafovych, Andriy; Adams, Paul D; Afonine, Pavel V; Baker, Matthew L; Barad, Benjamin A; Bond, Paul; Burnley, Tom; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, Kevin; Dill, Ken A; DiMaio, Frank; Farrell, Daniel P; Fraser, James S; Herzik, Mark A; Hoh, Soon Wen; Hou, Jie; Hung, Li-Wei; Igaev, Maxim; Joseph, Agnel P; Kihara, Daisuke; Kumar, Dilip; Mittal, Sumit; Monastyrskyy, Bohdan; Olek, Mateusz; Palmer, Colin M; Patwardhan, Ardan; Perez, Alberto; Pfab, Jonas; Pintilie, Grigore D; Richardson, Jane S; Rosenthal, Peter B; Sarkar, Daipayan; Schäfer, Luisa U; Schmid, Michael F; Schröder, Gunnar F; Shekhar, Mrinal; Si, Dong; Singharoy, Abishek; Terashi, Genki; Terwilliger, Thomas C; Vaiana, Andrea; Wang, Liguo; Wang, Zhe; Wankowicz, Stephanie A; Williams, Christopher J; Winn, Martyn; Wu, Tianqi.

Nat Methods ; 18(2): 156-164, 2021 02.

Artigo em Inglês | MEDLINE | ID: mdl-33542514

6.

Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling.

Maddhuri Venkata Subramaniya, Sai Raghavendra; Terashi, Genki; Kihara, Daisuke.

Bioinformatics ; 39(8)2023 08 01.

Artigo em Inglês | MEDLINE | ID: mdl-37549063

7.

Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases.

Olek, Anna T; Rushton, Phillip S; Kihara, Daisuke; Ciesielski, Peter; Aryal, Uma K; Zhang, Zicong; Stauffacher, Cynthia V; McCann, Maureen C; Carpita, Nicholas C.

Plant Physiol ; 191(1): 142-160, 2023 01 02.

Artigo em Inglês | MEDLINE | ID: mdl-36250895

8.

PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features.

Harini, K; Kihara, Daisuke; Michael Gromiha, M.

Methods ; 213: 10-17, 2023 05.

Artigo em Inglês | MEDLINE | ID: mdl-36924867

9.

Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.

Christoffer, Charles; Kihara, Daisuke.

Proteomics ; 23(17): e2200322, 2023 09.

Artigo em Inglês | MEDLINE | ID: mdl-36529945

10.

Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.

Schweke, Hugo; Xu, Qifang; Tauriello, Gerardo; Pantolini, Lorenzo; Schwede, Torsten; Cazals, Frédéric; Lhéritier, Alix; Fernandez-Recio, Juan; Rodríguez-Lumbreras, Luis Angel; Schueler-Furman, Ora; Varga, Julia K; Jiménez-García, Brian; Réau, Manon F; Bonvin, Alexandre M J J; Savojardo, Castrense; Martelli, Pier-Luigi; Casadio, Rita; Tubiana, Jérôme; Wolfson, Haim J; Oliva, Romina; Barradas-Bautista, Didier; Ricciardelli, Tiziana; Cavallo, Luigi; Venclovas, Ceslovas; Olechnovic, Kliment; Guerois, Raphael; Andreani, Jessica; Martin, Juliette; Wang, Xiao; Terashi, Genki; Sarkar, Daipayan; Christoffer, Charles; Aderinwale, Tunde; Verburgt, Jacob; Kihara, Daisuke; Marchand, Anthony; Correia, Bruno E; Duan, Rui; Qiu, Liming; Xu, Xianjin; Zhang, Shuang; Zou, Xiaoqin; Dey, Sucharita; Dunbrack, Roland L; Levy, Emmanuel D; Wodak, Shoshana J.

Proteomics ; 23(17): e2200323, 2023 09.

Artigo em Inglês | MEDLINE | ID: mdl-37365936

11.

Genotype & phenotype in Lowe Syndrome: specific OCRL1 patient mutations differentially impact cellular phenotypes.

Ramadesikan, Swetha; Skiba, Lisette; Lee, Jennifer; Madhivanan, Kayalvizhi; Sarkar, Daipayan; De La Fuente, Agustina; Hanna, Claudia B; Terashi, Genki; Hazbun, Tony; Kihara, Daisuke; Aguilar, R Claudio.

Hum Mol Genet ; 30(3-4): 198-212, 2021 04 26.

Artigo em Inglês | MEDLINE | ID: mdl-33517444

12.

Multi-level analysis of intrinsically disordered protein docking methods.

Verburgt, Jacob; Zhang, Zicong; Kihara, Daisuke.

Methods ; 204: 55-63, 2022 08.

Artigo em Inglês | MEDLINE | ID: mdl-35609776

13.

LZerD webserver for pairwise and multiple protein-protein docking.

Christoffer, Charles; Chen, Siyang; Bharadwaj, Vijay; Aderinwale, Tunde; Kumar, Vidhur; Hormati, Matin; Kihara, Daisuke.

Nucleic Acids Res ; 49(W1): W359-W365, 2021 07 02.

Artigo em Inglês | MEDLINE | ID: mdl-33963854

14.

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.

Toh, Huishi; Yang, Chentao; Formenti, Giulio; Raja, Kalpana; Yan, Lily; Tracey, Alan; Chow, William; Howe, Kerstin; Bergeron, Lucie A; Zhang, Guojie; Haase, Bettina; Mountcastle, Jacquelyn; Fedrigo, Olivier; Fogg, John; Kirilenko, Bogdan; Munegowda, Chetan; Hiller, Michael; Jain, Aashish; Kihara, Daisuke; Rhie, Arang; Phillippy, Adam M; Swanson, Scott A; Jiang, Peng; Clegg, Dennis O; Jarvis, Erich D; Thomson, James A; Stewart, Ron; Chaisson, Mark J P; Bukhman, Yury V.

BMC Biol ; 20(1): 245, 2022 11 08.

Artigo em Inglês | MEDLINE | ID: mdl-36344967

15.

Current progress and future perspectives of polypharmacology : From the view of non-small cell lung cancer.

Karuppasamy, Ramanathan; Veerappapillai, Shanthi; Maiti, Sayoni; Shin, Woong-Hee; Kihara, Daisuke.

Semin Cancer Biol ; 68: 84-91, 2021 01.

Artigo em Inglês | MEDLINE | ID: mdl-31698087

16.

Benchmarking of structure refinement methods for protein complex models.

Verburgt, Jacob; Kihara, Daisuke.

Proteins ; 90(1): 83-95, 2022 01.

Artigo em Inglês | MEDLINE | ID: mdl-34309909

17.

Using steered molecular dynamic tension for assessing quality of computational protein structure models.

Monroe, Lyman; Kihara, Daisuke.

J Comput Chem ; 43(17): 1140-1150, 2022 06 30.

Artigo em Inglês | MEDLINE | ID: mdl-35475517

18.

Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning.

Maddhuri Venkata Subramaniya, Sai Raghavendra; Terashi, Genki; Kihara, Daisuke.

Nat Methods ; 16(9): 911-917, 2019 09.

Artigo em Inglês | MEDLINE | ID: mdl-31358979

19.

Protein contact map refinement for improving structure prediction using generative adversarial networks.

Maddhuri Venkata Subramaniya, Sai Raghavendra; Terashi, Genki; Jain, Aashish; Kagaya, Yuki; Kihara, Daisuke.

Bioinformatics ; 37(19): 3168-3174, 2021 Oct 11.

Artigo em Inglês | MEDLINE | ID: mdl-33787852

20.

Mass spectrometry-based proteomic platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches.

Ahsan, Nagib; Rao, R Shyama Prasad; Wilson, Rashaun S; Punyamurtula, Ujwal; Salvato, Fernanda; Petersen, Max; Ahmed, Mohammad Kabir; Abid, M Ruhul; Verburgt, Jacob C; Kihara, Daisuke; Yang, Zhibo; Fornelli, Luca; Foster, Steven B; Ramratnam, Bharat.

Proteomics ; 21(10): e2000279, 2021 05.

Artigo em Inglês | MEDLINE | ID: mdl-33860983

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Instituto Evandro Chagas

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