[207] [Abstract] Kryshtafovych A., Moult J.,, & CASP-COVID paricipants (including Charles Christoffer, Genki Terashi, Daipayan Sarkar, Daisuke Kihara), Modeling SARS-CoV-2 proteins in the CASP-commons experiment. Proteins, doi: 10.1002/prot.26231, in press, (2021)
[206] [Abstract] M.F. Lensink, ,, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, ,, & S.J. Wodak (108 authors), Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins, doi: 10.1002/prot.26222, in press, (2021)
[205] M. Shekhar*, Genki Terashi*, C. Gupta, Daipayan Sarkar, G. Debussche, N.J. Sisco, J. Nguyen, A. Mondal, J. Vant, P. Fromme, W.D. Van Horn, E. Tajkhorshid, Daisuke Kihara, K. Dill, A. Perez, & A. Singharoy (*co-first authors), CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps. Matter, in press, (2021)
[204] B.K. Broyles, A.T. Gutierrez, T.P. Maris, D.A. Coil, T.M. Wagner, Xiao Wang, Daisuke Kihara, C.A. Class, A.M. Erkine, Activation of gene expression by detergent-like protein domains. iScience, 24: 9, (2021)
[203] [PDF] Charles Christoffer, Vijay Bharadwaj, Ryan Luu, & Daisuke Kihara, LZerD protein-protein docking webserver enhanced with de novo structure prediction. Frontiers in Molecular Biosciences, doi: 10.3389/fmolb.2021.724947 (2021) [ LZerD Protein Docking Server ]
[202] [Abstract] Jacob Verburgt & Daisuke Kihara, Benchmarking of structure refinement methods for protein complex models. Proteins, doi: 10.1002/prot.26188 (2021)
[201] A. Raffo, U. Fugacci, S. Biasotti, W. Rocchia, Y. Liu, E. Otu, R. Zwiggelaar, D. Hunter, E.I. Zacharaki, E. Psatha, D. Laskos, G. Arvanitis, K. Moustakas, Tunde Aderinwale, Charles Christoffer, Woong-Hee Shin, Daisuke Kihara, A. Giachetti, H.-N. Nguyen, T.-D. Nguyen, V.-T. Nguyen-Truong, D. Le-Thanh, H.-D. Ngyuen, & M.-T. Tran, SHREC 2021: Retrieval and classification of protein surfaces equipped with physical and chemical properties. Computers & Graphics, 99: 1-21, (2021)
[200] [Abstract] Takaharu Mori, Genki Terashi, Daisuke Matsuoka, Daisuke Kihara, & Yuji Sugita, Efficient flexible fitting refinement with automatic error fixing for de novo structure modeling from cryo-EM density maps. J. Chem. Inf. Model., 61: 3516-3528 (2021)
[199] [PDF] [Abstract] Xiao Wang, Sean Flannery, & Daisuke Kihara, Protein docking model evaluation by graph neural networks. Frontiers in Molecular Biosciences, 8: 647915 (2021) [GitHub page of GNN_DOVE]
[198] [Abstract] Charles Christoffer, Siyang Chen, Vijay Bharadwaj, Tunde Aderinwale, Vidhur Kumar, Matin Hormati, & Daisuke Kihara, LZerD webserver for pairwise and multiple protein-protein docking. Nucleic Acid Research, in press, (2021) [LZerD Server]
[197] [Abstract] Anwesha Sanyal, Erica A. Zbornik, Ben G. Watson, Charles Christoffer, Jia Ma, Daisuke Kihara, & Seema Mattoo, Kinetic and strutctural parameters governing Fic-mediated adenylylation/AMPylation of the Hsp70 chaperone, BiP/GRP78. Cell Stress & Chaperones, in press, (2021)
[196] [PDF] [Abstract] Xiao Wang, Eman Alnabati, Tunde W. Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, & Daisuke Kihara, Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning. Nature Communications, 12: 2302 (2021) [Emap2sec+]
[195] [Abstract] Nagib Ahsan, R.S.P. Rao, R.S. Wilson, U. Punyamurtula, F. Salvato, M. Petersen, M.K. Ahmed, M.R. Abid, Jacob C. Verburght, Daisuke Kihara, L. Fornelli, S.B. Foster, B. Ramratnam, Mass spectrometry-based proteomics platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches. PROTEOMICS, in press, (2021)
[---] Daisuke Kihara, Breakthrough in protein structure prediction - Alphafold2. Jikken Igaku (Experimental Medicine), 39: 906-908. (in Japanese) (2021)
[194] [PDF] [Abstract] Xusi Han#, Genki Terashi#, Charles Christoffer, Siyang Chen, & Daisuke Kihara (# co-first authors), VESPER: global and local cryo-EM map alignment using local density vectors. Nature Communications, 12: 2090. [Web server: VESPER Server] [Github: VESPER] (2021)
[193] [PDF] [Abstract] Aashish Jain, Genki Terashi, Yuki Kagaya, Sai Raghavendra Venkata Maddhuri Subramaniya, Charles Christoffer, & Daisuke Kihara, Analyzing effect of quadraple multiple sequence alignments on deep learning based protein inter-residue distance prediction. Scientific Reports, 11: 7574. [Github: AttentiveDist"] (2021)
[192] [Abstract] Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Aashish Jain, Yuki Kagaya, & Daisuke Kihara, Protein contact map refinement for improving protein structure prediction using generative adversarial networks. Bioinformatics, doi: 10.1093/bioinformatics/btab220 [GitHub: ContactGAN] (2021)
[191] [PDF] [Abstract] Catherine L. Lawson, ,,, Daisuke Kihara, ,,, Daipayan Sarkar , ,,, Genki Terashi , ,,, Helen M. Berman, & Wah Chiu (54 authors), Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods, 18: 156-164 (2021)
[190] [Abstract] Swetha Ramadesikan, Lisette Skiba, Jennifer Lee, Kayalviszhi Madhivanan, Daipayan Sarkar, Agustina De La Fuente, Claudia B. Hanna, Genki Terashi, Tony Hazbinpress Daisuke Kihara, & R. Claudio Aguilar, Genotype & phenotype in Lowe syndrome: Specific OCRL1 patient mutations differentially impact cellular phenotypes. Human Mol. Genet., doi: 10.1093/hmg/ddab025, in press (2021)
[189] [Abstract] Xiao Wang, Daisuke Kihara, Jiebo Luo, & Guo-Jun Qi, EnAET: A self-trained framework for semi-supervised learning with ensemble transformations. IEEE Trans Image Process., 30: 1639-1647 (2021)
[188] [Abstract] Ramanathan Karuppasamy, Shanthi Veerappapillai, Sayoni Maiti, Woong-Hee Shin & Daisuke Kihara, Current progress and future perspective of polypharmacology: From the view of non-small cell lung cancer. Seminars in Cancer Biol. 68: 84-91, (2021)
[187] [PDF] [Abstract] Woong-Hee Shin, Keiko Kumazawa, Kenichiro Imai, Takatsugu Hirokawa, & Daisuke Kihara, Current challenges and opportunities in designing protein-protein interaction targeted drugs. Advances and Applications in Bioinformatics and Chemistry, 13: 11-25 (2020)
[186] Daisuke Kihara, Charles Christoffer, Siyang Chen, Vijay Bharadwaj, & Tunde Aderinwale, LZerD: Software for protein docking modeling. Jikken Igaku (Experimental Medicine), 38: 3271-3276 (in Japanese) (2020)
[---] [PDF] [Abstract] Daisuke Kihara, Turning points in my career path. Seibutsu Butsuri (Biophysics), (in Japanese), 61: 44-45 (2020)
[185] [Abstract] I. Gubins, M.L. Chaillet, G.v.d. Schot, R.C. Veltkamp, F. Foerster, Y. Hao, X. Wan, X. Cui, F. Zhang, E. Moebel, Xiao Wang, Daisuke Kihara, X. Zeng, M. Xu, N.P. Nguyen, T. White, & F. Bunyak, SHREC2020: Classification in cryo-electron tomograms. Computers & Graphics, 91: 279-289 (2020)
[184] [Abstract] F. Langenfeld, Y. Peng, Y.-K. Lai, P.L. Rosin, Tunde Aderinwale, Genki Terashi, Charles Christoffer, Daisuke Kihara, H. Benhabiles, K. Hammoudi, A. Cabani, F. Windal, M. Melkemi, A. Giachetti, S. Mylonas, A. Axenopoulos, P. Daras, E. Otu, R. Zwiggelaar, D. Hunter, Y. Liu, & M. Montes, SHREC2020: Multi-domain protein shape retrieval challenge. Computers & Graphics, 91: 189-198 (2020)
[183] [Abstract] Genki Terashi, Yuhong Zha, & Daisuke Kihara Protein structure modeling from cryo-EMmap using MAINMAST and MAINMAST-GUI Plugin. Methods in Mol. Biol., 2165: 317-336 (2020)
[182] [Abstract] Charles Christoffer & Daisuke Kihara IDP-LZerD: Software for modeling disordered protein interactions. Methods Mol. Biol., 2165: 231-244 (2020)
[181] [Abstract] Tunde Aderinwale, Charles W. Christoffer, Daipayan Sarkar, Eman Alnabati, & Daisuke Kihara Computational structure modeling for diverse categories of macromolecular interactions. Curr. Opin. Struct. Biol., 64: 1-8 (2020)
[180] [Abstract] Brenda Gonzalez, Lyman Monroe, Kunpeng Li, Rui Yan, Elena Wright, Thomas Walter, Daisuke Kihara, Susan T. Weintraub, Julie A Thomas, Philip Serwer, & Wen Jiang Phage G structure at 6.1 A resolution, condensed DNA, and host identity revision to a Lysinibacillus. J. Mol. Biol., 432: 4139-4153 (2020)
[179] [Abstract] Genki Terashi, Yuki Kagaya, & Daisuke Kihara, MAINMASTseg: Automated map segmentation method for cryo-EM density with symmetry. J. Chem. Inf. Model., 60: 2634-2643 (2020) [MAINMASTseg]
[178] Daisuke Kihara, Trends in software developments of biomolecular structural modeling and prediction. Jikken Igaku (Experimental Medicine), 38: 866-871, (in Japanese) (2020)
[177] [pdf] [Abstract] Tuan Lai, Quan Huang Tran, Trung Bui, & Daisuke Kihara, A simple but effective BERT model for dialog state tracking on resource-limited systems. ICASSP 2020, (2020)
[176] [Abstract] Genki Terashi, Charles Christoffer & Daisuke Kihara, Path-LZerD: Predicting assembly order of multimeric protein complexes Methods in Mol. Biol., 2074: 95-112, (2020) [Path-LZerD]
[175] Genki Terashi, Sai Raghavendra Maddhuri Venkata Subramaniya & Daisuke Kihara, Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning. Jikken Igaku (Experimental Medicine), 38: 82-86, (in Japanese) (2020)
[174] [pdf] [Abstract] Julian S. Deville, Daisuke Kihara, & Atilla Sit, 2DKD: A toolkit for content-based local image search. Source Code for Biology and Medicine, 15:1, (2020) [2DKD code at Gihub]
[173] [Abstract] Xiao Wang, Genki Terashi, Charles Christoffer, Mengmeng Zhu, & Daisuke Kihara, Protein docking model evaluation by 3D convolutional neural networks. Bioinformtics, 36: 2113-2118 (2020) [DOVE code at Gihub] [Dove webserver]
[172] [Abstract] Charles Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Lenna Peterson, Jacob Verburgt, & Daisuke Kihara, Performance and enhancement of the LZerD protein asssembly pipeline in CAPRI 38-46. Proteins: Strucure, Function, and Bioinformtics, 88: 948-961 (2020)
[171] [pdf] [Abstract] Eman Alnabati & Daisuke Kihara, Advances in structure modeling methods in cryo-electon microscopy maps. Molecules, 25: 82, (2019)
[170] [pdf] [Abstract] Manuel Zumbado-Corrales, Luis Castillo-Valverde, Jose Salas-Bonilla, Julio Viquez-Murillo, Daisuke Kihara, & Juan Esquivel-Rodriguez, Matching of EM map segments to structurally-relevant Bio-molecular regions. Latin American High Performance Computing Conference, 464-478, (2019)
[169] [pdf] [Abstract] Chiba S., ,,, Woong-Hee Shin, Daisuke Kihara,,, & Sekijima M., A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Scientific Reports, 9: 19585, (2019)
[168] [pdf] [Abstract] Aashish Jain & Daisuke Kihara, NNTox: Gene ontology-based protein toxicity prediction using neural network. Scientific Reports, 9: 17923, (2019) [NNTox code at Gihub]
[167] [pdf] [Abstract] Mark F. Lensink,,, Charles Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Daisuke Kihara ,,,, & Shoshana J Wodak, Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins: Structure, Function, and Bioinformatics, 87: 1200-1221 (2019)
[166] [pdf] [Abstract] Naihui Zhou,,, Aashish Jain,,,, Daisuke Kihara, ,,, Predrag Radivojac, & Iddo Friedberg, The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology, 20: 244, (2019)
[165] [pdf] [Abstract] Woong-Hee Shin, Daisuke Kihara, Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-ParchSurfer2.0. J. Computer-Aided Molecular Design, 33: 1083-1094, (2019)
[164] [pdf] [Abstract] Tuan Lai, Quan Huang Tran, Trung Bui, & Daisuke Kihara, A gated self-attention memory network for answer selection. The 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP) , (2019)
[163] [pdf] [Abstract] Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, & Daisuke Kihara, Protein secondary structure detection in intermediate-resolution cyor-EM maps using deep learning. Nature Methods, 16: 911-917 (2019) [Journal Cover Art] [Blog] [Emap2Sec page] [Github: Emap2sec] [In CodeOcean] (2019)
[162] [pdf] [Abstract] Ramanathan Karuppaswamy, Sayoni V. Shanthi, Woong-Hee Shin & Daisuke Kihara, Implementationof Pharmacophore-based 3D QSAR model and scafford analysis in order to excavate pristine ALK inhibitors. Medicinal Chemistry Research, 28: 1726-1739, (2019)
[161] [pdf] [Abstract] Ziyun Ding & Daisuke Kihara, Computational identification of protein-protein interactions in model plan proteomes. Scientific Reports, 9: 8740 (2019)
[160] [pdf] [Absract] Atilla Sit, Woong-Hee Shin, & Daisuke Kihara, Three-dimensional Krawtchouk descriptors for protein local surface shape comparison. Pattern Recognition, 93: 534-545 (2019)
[159] [pdf] [Absract] Ilja Gubins, Gijs van der Shot, Remo C. Veltkamp, Frierich Foerster, Xuefeng Du, Xiangrui Zeng, Zhenxi zhu, Lufan Chang, Min Xu, Emmanuel Moebel, Tuan M. Lai, Xusi Han, Genki Terashi, Daisuke Kihara, Benjamin A. Himes, Xiaohua Wan, Jingrong Zhang, Shan Gao, Yu Hao, Zhilong Lv, Zhidong, Yang, Zijun Ding, Xuefeng Cui, & Fa Zhang, SHREC'19 Track: Classification in cryo-electron tomograms. 12th EG Workshop 3D Object Retrieval 2019, (2019)
[158] [pdf] [Absract] Florent Langenfeld, Apostolos Axenopoulos, Halim Benhabiles, Petros Daras, Andrea Giachetti, Xusi Han, Karim Hammoudi, Daisuke Kihara, Tuan M. Lai , Mahmoud Melkemi, Stelios K. Mylonas, Genki Terashi , Yufan Wang, Feryal Windal, & Matthieu Montes, SHREC'19 Protein shape retrieval contest. 12th EG Workshop 3D Object Retrieval 2019, (2019)
[157] [pdf] [Abstract] Xusi Han, Atilla Sit, Charles Christoffer, Siyang Chen, & Daisuke Kihara, A global map of the protein shape universe. PloS Computational Biology, 15(4):e1006969, (2019)
[156] [pdf] [Abstract] Melanie L'Enfant, Pricillia Kutudila, Catherine Rayon, Jean-Marc Domon, Woong-Hee Shin, Daisuke Kihara, Anne Wadouachi, Jerome Pelloux, Gwladys Pourceau, & Corinne Pau-Roblot, Lactose derivatives as potential inhibitors of pectin methylesterases. Int. J. Biological Macromolecules, 132: 1140-1146 (2019)
[155] [pdf] [Abstract] Mauricio Macossay-Casillo, Giulio Marvelli, Mainak Guharoy, Aashish Jain, Daisuke Kihara, Peter Tompa, & Shoshana Wodak, The balancing act of intrincically disordered proteins: enabling functional diversity while minimizing promiscuity. J. Mol. Biol., 431: 1650-1670 (2019)
[154] [pdf] [Abstract] Woong-Hee Shin & Daisuke Kihara, 55 years of the Rossmann fold. Methods in Mol. Biol., 1958: 1-13 (2019)
[153] [pdf] [Abstract] Charles W. Christoffer & Daisuke Kihara, Modeling protein-protein interactions with intrisically disordered proteins. Intrinsically Disordered Proteins, Nicola Salvi (ed.), pp. 189-206, Elsevier, (2019).
[152] [pdf] [Abstract] Xusi Han, Woong-Hee Shin, Charles W. Christoffer, Genki Terashi, Lyman Monroe, & Daisuke Kihara, Study of the variability of the native protein structure. Encyclopedia of Bioinformatics and Computational Biology, 3: 606-619 (2019)
[151] [pdf] [Abstract] Ishita K. Khan, Aashish Jain, Reda Rawi, Halima Bensmail, & Daisuke Kihara, Prediction of protein group function by iterative classification on functional relevance network. Bioinformatics, 35: 1388-1394 (2019) [iGFP Code]
[150] [pdf] [Abstract] Aashish Jain & Daisuke Kihara, Phylo-PFP: Improved automated protein function prediction using phylogenetic distance of distantly related sequences. Bioinformatics, 35: 753-759 (2019) [Phylo-PFP Server]
[149] [pdf] [Abstract] Yi Xiong, Yanhua Qiao, Daisuke Kihara, Hui-Yuan Zhang, Xiaolei Zhu, & Dong-Qing Wei, Survery of machine learning techniques for prediction of the isoform specificity of cytochrome P450 substrates. Current Drug Metabolism, 20: 229-235, (2019)
[148] Genki Terashi, & Daisuke Kihara Protein tertiary structure modeling from cryo-EM density maps by tree graph optimization. Jikken Igaku (Experimental Medicine), 36: 2767-2770 (in Japanese) (2018)
[147] [pdf] [Abstract] Aashish Jain, Hareesh Gali, & Daisuke Kihara Identification of moonlighting proteins in genomes using text mining techniques Proteomics, 18:e1800083, (2018)
[146] [pdf] [Abstract] Uma K. Aryal*, Ziyun Ding*,Victoria Hedrick, Tiago Jose Paschoal Sobreira, Daisuke Kihara, & Louis A. Sherman (* co-first authors) Analysis of protein complexes in the unicellular cyanobacterium Cyanothece ATCC 51142. J. Proteome Research, 17: 3628-3643 (2018) [MASQ_PPI Code for detecting PPIs from mass spec data]
[145] [pdf] [Abstract] Genki Terashi & Daisuke Kihara, De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge. J. Str. Biol., 204: 351-359, (2018) [MAINMAST]
[144] [pdf] [Abstract] Ziyun Ding & Daisuke Kihara, Recent computational methods for predicting protein-protein interactions using various protein features. Current Protocols in Protein Science, e62, (2017)
[143] [pdf] [Abstract] Genki Terashi & Daisuke Kihara, De novo main-chain modeling for EM maps using MAINMAST. Nature Communications, 9: 1618 (2018) [MAINMAST]
[142] [pdf] [Abstract] Lenna X. Peterson, Yoichiro Togawa, Juan Esquivel-Rodriguez, Genki Terashi, Charles Christoffer, Amitava Roy, Wooong-Hee Shin, & Daisuke Kihara, Modeling the assembly order of multimeric heteroprotein complexes. PLoS Comput. Biol., 14:e1005937 (2018)
[141] [pdf] [Abstract] Ziyun Ding, Qing Wei, & Daisuke Kihara, Computing and visualizing gene function similarity and coherence with NaviGO. Methods in Mol. Biol., 1807: 113-130, (2018)
[140] [pdf] [Abstract] Woong-Hee Shin & Daisuke Kihara, Virtual ligand screening using PL-PatchSurfer2, a molecular surface-based protein-ligand docking method. Methods in Mol. Biol., 1762: 105-121, (2018).
[139] [pdf] [Abstract] Lenna X. Peterson, Woong-Hee Shin, Hyungrae Kim, & Daisuke Kihara, Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions. Proteins: Structure, Function, and Bioinformatics, 86 (Suppl 1): 311-320 (2018)
[138] [pdf] [Abstract] Genki Terashi & Daisuke Kihara, Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent. Proteins: Structure, Function, and Bioinformatics, 86 (Supppl 1): 189-201, (2018)
[137] [PDF] [Abstract] Satwica Yerneni, Ishita K Khan, Qing Wei, & Daisuke Kihara IAS: Interaction specific GO term associations for predicting protein-protein interaction networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15: 1247-1258(2018) [IAS score]
[136] [pdf] [Abstract] S. Chiba, T. Ishida, K. Ikeda, M. Mochizuki, R. Teramoto, Y.H. Taguchi, M. Iwadate, H. Umeyama, C. Ramakrishnan, A.M. Thangakani, D. Velmurugan, M.M. Gromiha, T.Okuno, K. Kato, S. Minami, G. Chikenji, S.D. Suzuki, K. Yanagisawa, Woong-Hee Shin, Daisuke Kihara, K.Z. Yamamoto, Y. Moriwaki, N. Yasuo, R. Yoshino, S. Zozulya, P. Borysko, R. Stavniichuk, T. Honma, T. Hirokawa, Y. Akiyama, & M. Sekijima, An interative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes. Scientific Reports, 7: 12038 (2017)
[135] [pdf] [Abstract] Xusi Han, Qing Wei, & Daisuke Kihara, Protein 3D structure and electron microscopy map retrieval using 3D-SURFER2.0 and EM_SURFER. Current Protocols, 60:3.14.1-3.14.15 (2017)
[134] [pdf] [Abstract] Woong-Hee Shin*, Charles Christoffer*, & Daisuke Kihara (*co-first author), In silico structure-based approaches to discover protein-protein interaction targeting drugs. Methods, 131: 22-32 (2017)
[133] [pdf] [Abstract] Ishita K. Khan, Mansurul Bhuiyan, & Daisuke Kihara, DextMP: deep dive into text for predicting moonlighting proteins. Bioinformatics, 33: i83-i91 (2017), Presented at ISMB2017. [DextMP]
[132] [pdf] [Abstract] Na Song, Daniela Craciun, Charles W. Christoffer, Xusi Han, Daisuke Kihara, Guillaume Levieux, Matthieu Montes, Hong Qin, Pranjal Sahu, Genki Terashi, & Haiguang Liu, SHREC'17 Track: Protein shape retrieval. Eurographics Workshop on 3D Object Retrieval, I. Pratikakis, F. Dupont, & M. Ovsjanikov (Eds.) (2017)
[131] [pdf] [Abstract] Lenna X. Peterson, Amitava Roy, Charles Christoffer, Genki Terashi, & Daisuke Kihara , Modeling disordered protein interactions from biophysical principles. PLoS Computational Biol., 13: e1005485, (2017)
[130] [pdf] [Abstract] Sayoni Das, Ishita Khan, Daisuke Kihara, & Christine Orengo Exploring structure-function relationships in moonlighting proteins. Moonlighting Proteins: Novel Virulence Factors in Bacterial Infections, B. Henderson (ed.) Chapter 2, pp. 21-44, Wiley-Blackwell (2017)
[129] [pdf] [Abstract] Qing Wei, Ishita Khan, Ziyun Ding, Satwica Yerneni, & Daisuke Kihara NaviGO: Interactive tool for visualization and funtional similarity and coherence analysis with gene ontology. BMC Bioinformatics, 18: 177 (2017) [NaviGO Server]
[128] [PDF] [Abstract] Lyman Monroe*, Genki Terashi*, & Daisuke Kihara (* co-first authors), Variability of protein structure models from electron microscopy. Structure, 25: 592-602 (2017)
[127] [pdf] [Abstract] Woong-Hee Shin, Xuejiao Kang, Jian Zhang, & Daisuke Kihara Prediction of local quality of protein structure models considering spatial neighbors in graphical models. Scientific Reports, 7: 40629 (2017) [GMQ program]
[126] [PDF] [Abstract] Qing Wei, David La, & Daisuke Kihara BindML/BindML+: Detecting protein-protein interface propensity from amino acid substitution patterns. Methods in Molecular Biology, 1529: 279-289 (2017) [BindML server]
[125] [PDF] [Abstract] Lenna X. Peterson, Michal Jamroz, Andrzej Kolinski, & Daisuke Kihara Predicting real-valued protein residue fluctuation using FlexPred. Methods in Mol. Biol., 1484: 175-186 (2017) [FlexPred Server]
[124] [PDF] [Abstract] Lingfei Zeng*, Woong-Hee Shin*, Xiaolei Zhu, Sung Hoon Park, Chiwook Park, W. Andy Tao, & Daisuke Kihara (* equal contribution), Dicovery of NAD-binding proteins inthe E.coli proteome using combined energetic-based and structural-bioinformatics-based approach. J. Proteome Res., 16: 470-480. (2017)
[123] [PDF] [Abstract] Lenna X. Peterson, Hyungrae Kim, Juan Esquivel-Rodriguez, Amitava Roy, Xusi Han, Woong-Hee Shin, Jian Zhang, Genki Terashi, Matt Lee, & Daisuke Kihara Human and server docking prediction for CAPRI Round 30-35 using LZerD with combined scoring functions. Proteins: Structure Function, and Bioinformatics, 85: 513-527 (2017)
[122] [PDF] [Abstract] Ishita K. Khan, Joshua McGraw, & Daisuke Kihara MPFit: Computational tool for predicting moonlighting proteins. Methods in Mol. Biol., 1611:45-47. (2017) [MPFit]
[121] [PDF] [Abstract] Qing Wei, Joshua McGraw, Ishita K. Khan, & Daisuke Kihara Using PFP and ESG protein function prediction webservers. Methods in Mol. Biol., 1611:1-14 (2017) [PFP] [ESG] [NaviGO]
[120] [PDF] [Abstract] Woong-Hee Shin, Charles Christoffer, Jibo Wang, & Daisuke Kihara PL-PatchSurfer2: Improved local surface matching-based virtual screening method that is tolerant to target and ligand structure variation. J. Chem. Inf. Model, 56: 1676-1691 (2016) [PL-PatchSurfer2]
[119] [PDF] [Abstract] Meghana Chitale, Ishita K. Khan, & Daisuke Kihara Missing gene identification using functional coherence scores. Scientific Reports, 6: 31725. (2016) [GO-MEP]
[118] [PDF] Abram Magner, Daisuke Kihara, & Wojciech Szpankowski A study of the Boltzmann sequence-structure channel. Proceedings of the IEEE, 105: 286-306 (2016)
[PDF] The Boltzmann sequence-structure channel. 2016 IEEE International Symposium on Information Theory (ISIT 2016), 255-259 (2016)
[117] [PDF] [Abstract] Yuxiang Jian,,,, Samuel Chapman, Dukka BKC, Ishita K Khan, Daisuke Kihara,,,, Iddo Friedberg, & Predrag Radivojac (147 authors) An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology, 17: 184 (2016)
[116] [PDF] [Abstract] Laura Kingsley, Juan Esquivel-Rodriguez, Ying Yang, Daisuke Kihara, Markus Lill Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations. J. Comp. Chem., 37: 1861-1865. (2016)
[115] [PDF] [Abstract] Michal Jamroz, Andrzej Kolinski, & Daisuke Kihara Ensemble-based evaluation for protein structure models. Bioinformatics, 32: i314-i321 (2016) Presented at ISMB 2016 [FlexScore]
[114] [PDF] [Abstract] Ishita K. Khan & Daisuke Kihara Genome-scale prediction of moonlighting proteins using diverse protein association information. Bioinformatics, 32: 2281-2288. (2016) [MPFit]
[113] [PDF] [Abstract] Nathan Gardner, Lyman Monroe, Daisuke Kihara, & Chiwook Park Energetic coupling between ligand binding and dimerization in E. coli phosphoglycerate mutase. Biochemistry, 55: 1711-1723. (2016)
[112] [PDF] [Abstract] MF Lensink, S Velankar, A Kryshtafovych, S-Y Huang, D Schneidman-Duhovny, A Sali, J Segura, N Fernandez-Fuentes, S Viswanath, R Elber, S Grudinin, P Popov, E Neveu, H Lee, M Baek, S Park, L Heo, GR Lee, C Seok, S Qin, H-X Zhou, DW Ritchie, B Maigret, M-D Devignes, A Ghoorah, M Torchala, RAG Chaleil, PA. Bates, E Ben-Zeev, M Eisenstein, SS Negi, Z Weng, T Vreven, BG Pierce, TM Borrman, J Yu, F Ochsenbein, R Guerois, A Vangone, JPGLM Rodrigues, G van Zundert, M Nellen, L Xue, E Karaca, ASJ Melquiond, K Visscher, PL Kastritis, AMJJ Bonvin, X Xu, L Qiu, C Yan, J Li, Z Ma, J Cheng, X Zou, Y Shen, LX Peterson, H-R Kim, A Roy, X Han, J Esquivel-Rodriguez, D Kihara, X Yu, NJ Bruce, JC Fuller, RC Wade, I Anishchenko, PJ Kundrotas, IA Vakser, K Imai, K Yamada, T Oda, T Nakamura, K Tomii, C Pallara, M Romero-Durana, B Jiménez-García, IH Moal, J Férnandez-Recio, JY Joung, JY Kim, K Joo, J Lee, D Kozakov, S Vajda, S Mottarella, DR Hall, D Beglov, A Mamonov, B Xia, T Bohnuud, CA Del Carpio, E Ichiishi, N Marze, D Kuroda, SSR Burman, JJ Gray, E Chermak, L Cavallo, R Oliva, A Tovchigrechko, & SJ Wodak Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment Proteins: Structure, Function, and Bioinformatics, 84 Suppl 1: 323-348 (2016)
[---] [PDF] [Abstract] Daisuke Kihara Computational protein function predictions. Methods, 93: 1-2, (2016)
[111] [PDF] [Abstract] Woong-Hee Shin, Mark G. Bures, & Daisuke Kihara PatchSurfers: Two methods for local molecular property-based binding ligand prediction. Methods, 93: 41-50, (2016)
[110] [PDF] [Abstract] Xiaolei Zhu, Woong-Hee Shin, Hyungrae Kim, & Daisuke Kihara Combined approach of Patch-Surfer and PL-PatchSurfer for protein-ligand binding prediction in CSAR 2013 and 2014. J. Chem. Info. Model., 56: 1088-1099 (2015)
[109] [PDF] [Abstract] Hyung-Rae Kim, & Daisuke Kihara Protein structure prediction using residue- and fragment-environment potentials in CASP11. Proteins: Structure, Function, and Bioinformatics, 84 Suppl 1: 105-117(2016)
[108] [PDF] [Abstract] Ishita K Khan*, Qing Wei*, Samuel Chapman, Dukka BKC, & Daisuke Kihara (* equal contribution) The PFP and ESG protein function prediction methods in 2014: Effect of database updates and ensemble approaches. GigaScience, 4: 43 (2015)
[107] [PDF] [Abstract] Fabien Senechal, Melanie L'Enfant, Jean-Marc Domon, Emeline Rosiau, Marie-Jeanne Crepeau, Ogier Surcouf, Juan Esquivel-Rodriguez, Paulo Marcelo, Alain Mareck, Francois Guerineau, Hyung-Rae Kim, Jozef Mravec, Estelle Bonnin, Elisabeth Jamet, Daisuke Kihara, Patrice Lerouge, Marie-Christine Ralet, Jerome Pelloux, & Catherine Rayon Tuning of pectine methylesterification: PECTIN METHYLESTERASE INHIBITOR 7 modulates the processive activity of co-expressed PME3 in a pH-dependent manner. J. Biol. Chem, 290: 23320-23335 (2015)
[106] [PDF] [Abstract] Woong-Hee Shin, Xiaolei Zhu, Mark Gregory Bures, & Daisuke Kihara Three-dimensional compound comparison methods and their application in drug discovery. Molecules, 20: 12841-12862 (2015)
[105] [PDF] [Abstract] Juan Esquivel-Rodriguez, Yi Xiong, Xusi Han, Shuomeng Gang, Charles Christoffer, & Daisuke Kihara Navigating 3D Electron Microscopy Maps with EM-SURFER. BMC Bioinformatics, 16:181 (2015)[EM-SURFER server]
[104] [PDF] [Abstract] Abram Magner, Wojciech Szpankowski, & Daisuke Kihara On the origin of protein superfamilies and superfolds. Scientific Reports 5: 8166 (2015)
[103] [PDF] [Abstract] Yue Liu, Ju Sheng, Andrei Fokine, Geng, Meng, Woong-Hee Shin, Feng, Long, Richard J. Kuhn, Daisuke Kihara, & Michael G. Rossmann Structure and inhibition of EV-D68, a virus that causes respiratory illness in children. Science 347: 71-74 (2015)
[102] [PDF] [Abstract] Xiaolei Zhu, Yi Xiong, & Daisuke Kihara Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. Bioinformatics 31: 707-713 (2015)[Parch-Surfer2.0 server]
[101] [PDF] [Abstract] Ishita K. Khan*, Qing Wei*, & Daisuke Kihara (* equal contribution), PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualizatoin tool. Bioinformatics 31: 271-272 (2015)[PFP server][ESG server]
[100] [PDF] [Abstract] Yuka Otsuka, Ai Muto, Rikiya Takeuchi, Chihiro Okada, Motokazu Ishikawa, Koichiro Nakamura, Natsuko Yamamoto, Hitomi Dose, Kenji Nakahigashi, Shigeki Tanishima, Sivasundaram Suharnan, Wataru Nomura, Toru Nakayashiki, Walid G. Aref, Barry R. Bocher, Tyrell Conway, Michael Gribskov, Daisuke Kihara, Kenneth E. Rudd, Yukako Tohsato, Barry L. Wanner, & Hirotada Mori, GenoBase: comprehensive resource database of Escherichia coli K-12. Nuc. Acid Research, 43: D606-D617 (2015)[GenoBase]
[99] [PDF] [Abstract] Ishita K. Khan, Yuqian Chen, Tiange Dong, Xioawei Hong, Rikiya Takeuchi, Hirotada Mori, & Daisuke Kihara, Genome-scale identification and characterization of moonlighting proteins. Biology Direct. 9: 30 (2014)
[98] [PDF] [Abstract] Ishita K. Khan & Daisuke Kihara, Computational characterization of moonlighting proteins. Biochem. Soc. Trans. 42: 1780-1785 (2014)
[97] [PDF] [Abstract] Uma K Aryal, Yi Xiong, Zachary McBride, Daisuke Kihara, Jun Xie, Mark C. Hall, & Daniel B. Szymanski, A proteomic strategy for global analysis of plant protein complexes. Plant Cell, 26: 3867-3882 (2014)
[96] [PDF] [Abstract] Bingjie Hu, Xiaolei Zhu, Lyman Monroe, Mark G. Bures, & Daisuke Kihara, PL-PatchSurfer: A novel molecular local surface-based method for exploring protein-ligand interactions. Int. J. Molecular Science, 15: 15122-15145 (2014)
[95] [PDF] [Abstract] Hyung-Rae Kim & Daisuke Kihara, Detecting local residue environment similarity for recognizing near-native structure models. Proteins: Structure, Function, and Bioinformatics, 82: 3255-3272 (2014)
[94] [PDF] [Abstract] Anna T. Olek, Catherine Rayon, Lee Makowski, Hyung Rae Kim, Peter Ciesielski, John Badger, Lake N. Paul, Subhangi Ghosh, Daisuke Kihara, Michael Crowley, Michael E. Himmel, Jeffrey T. Bolin, & Nicholas C. Carpita, The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers. Plant Cell, 26: 2996-3009 (2014)
[93] [PDF] [Abstract] Atilla Sit & Daisuke Kihara, Comparison of Image Patches Using Local Moment Invariants. IEEE Transactions on Image Processing, 23: 2369-2379 (2014)
[92] [PDF] [Abstract] Lenna X. Peterson, Xuejiao Kang, & Daisuke Kihara, Assessment of protein side-chain conformation prediction accuracy in different residue environments. Proteins: Structure, Function, and Bioinformatics, 82: 1971-1984 (2014)
[---] [PDF] [Abstract] Jim Cavalcoli, Lonnie Welch, Bruce Aronow, Sorin Draghici, & Daisuke Kihara, The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio. Bioinformatics, 30: 148-149 (2014)
[91] [PDF] [Abstract] Sungho Won, Min-Seok Kwon, Manuel Mattheisen, Suyeon Park, Changsoon Park, Daisuke Kihara, Sven Cichon, Roel Ophoff, Markus M. Nothen, Marcella Rietschel, Max Baur, & Christoph Lange, Efficient strategy for detecting gene x gene joint action and its application in schizophrenia. Genetic Epidemiology, 38: 60-71 (2014)
[90] [PDF] [Abstract] Juan Esquivel-Rodriguez, Vianney Filos-Gonzalez, Bin Li, & Daisuke Kihara, Pairwise and multimeric protein-protein docking using the LZerD program suite. Methods in Molecular Biology, 1137: 209-234 (2014)
[89] [PDF] [Abstract] Yi Xiong, Juan Esquivel-Rodriguez, Lee Sael, & Daisuke Kihara, 3D-SURFER 2.0. Web platform for real-time search and characterization of protein surfaces. Methods in Molecular Biology, 1137: 105-117 (2014)
[88] [PDF] [Abstract] Yi Xiong, Dan Syzmanski, & Daisuke Kihara, Characterization and prediction of human protein-protein interactions. Biological Data Mining and Its Applications in Healthcare, X.-L. Li, S.-K. Ng, & J.T.L. Wang (eds), Chapter 9, pp.237-261, World Scientific, New Jersey, USA (2014)
[87] [PDF] [Abstract] Victor Padilla-Sanchez, Song Gao, Hyung Rae Kim, Daisuke Kihara, Lei Sun, Michael G Rossmann, & Venigalla B Rao, Structure-Function Analysis of the DNA Translocating Portal of the Bacteriophage T4 Packaging Machine. J. Mol. Biology, 426: 1019-1038(2013)
[86] [PDF] [Abstract] Juan Esquivel-Rodriguez & Daisuke Kihara, Computational methods for constructing protein structure models from 3D electron microscopy maps. J. Structural Biology, 184: 93-102 (2013)
[85] [PDF] [Abstract] Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Kilambi KP, Gray JJ, Popov P, Grudinin S, Esquivel-Rodriguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D., Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions, Proteins, 81: 1980-1987 (2013)
[84] [PDF] [Abstract] Yi Xiong*, Xiaolei Zhu*, & Daisuke Kihara (* equal contribution), Ligand binding site identification. In silico Drug Discovery and Design Techniques. M. Lill (eds), Future Science, London, UK, Chapter 16, pp. 204-220 (2013)
[83] [PDF] [Abstract] Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Toronen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kassner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Honigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Bjorne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Skunca N, Supek F, Bosnjak M, Panov P, Dzeroski S, Smuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I , A large-scale evaluation of computational protein function prediction. Nature Methods, 10: 221-227(2013)
[82] [PDF] [Abstract] Meghana Chitale*, Ishita K. Khan*, & Daisuke Kihara (* equal contribution), In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. BMC Bioinformatics, 14 Suppl 3: S2 (2013)
[81] [PDF] [Abstract] David La, Misun Kong, William Hoffman, YounIm Choi & Daisuke Kihara, Predicting permanent and transient protein-protein interfaces. Proteins: Structure, Function, and Bioinformatics, 81: 805-818 (2013) [BindML+ server]
[80] [PDF] [Abstract] Mingjie Tang*, Kean Ming Tan*, Xin Lu Tan, Lee Sael, Meghana Chitale, Juan Esquivel-Rodriguez, & Daisuke Kihara (* equal contribution), Graphical models for protein function and structure predictions., Handbook of Biological Knowledge Discovery, Mourad Elloumi & Albert Y. Zomaya(eds.), Chapter 9, pp.191-222, Wiley (2013)
[79] [PDF] [Abstract] Chao Yuan, Hao Chen, & Daisuke Kihara, Effective inter-residue contact definitions for accurate protein fold recognition. BMC Bioinformatics, 13: 292 (2012)
[78] [PDF] [Abstract] Juan Esquivel-Rodriguez, & Daisuke Kihara, Effect of conformation sampling strategies in genetic algorithm for multiple protein docking. BMC Proceedings, 6 Suppl 7: S4 (2012)
[77] [PDF] [Abstract] Ishita Khan, Meghana Chitale, Catherine Rayon, & Daisuke Kihara, Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins. BMC Proceedings, 6 Suppl 7: S5 (2012)
[76] [PDF] [Abstract] Mario Abdel Messih, Meghana Chitale, Vladimir B. Bajic, Daisuke Kihara*, & Xin Gao* (* co-corresponding authors), Protein domain recurrence and order can enhance prediction of protein functions. Bioinformatics, 28: i440-i450 (2012)
[75] [PDF] [Abstract] Juan Esquivel-Rodriguez, Yifeng D. Yang, & Daisuke Kihara , Multi-LZerD: Multiple protein docking for asymmetric complexes. Proteins: Structure, Function, and Bioinformatics, 80: 1818-1833 (2012)
[74] [PDF] [Abstract] Juan Esquivel-Rodriguez & Daisuke Kihara , Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors. J Phys Chem B, 116: 6854-6861 (2012)
[73] [PDF] [Abstract] Elwood A. Mullins,Courtney M. Starks, Julie A. Francois, Lee Sael, Daisuke Kihara, & T. Joseph Kappock, Formyl-coenzyme A (CoA):oxalate CoA-transferase from the acidophile Acetobacter aceti has a distinctive electrostatic surface and inherent acid stability. Protein Science, 21: 686-696(2012)
[72] [PDF] [Abstract] Michal Jamroz, Andrzej Kolinski, & Daisuke Kihara , Structural features that predict real-value fluctuations of globular proteins. Proteins: Structure, Function, and Bioinformatics, 80: 1425-1435 (2012) [flexPred server]
[71] [PDF] [Abstract] Lee Sael*, Meghana Chitale*, & Daisuke Kihara (* equal contribution), Structure- and sequence-based function prediction for non-homologous proteins. Journal of Structural and Functional Genomics, 13: 111-123 (2012)
[70] [PDF] [Abstract] Bin Li & Daisuke Kihara , Protein Docking Prediction Using Predicted Protein-Protein Interface . BMC Bioinformatics, 13:7 (2012) [PI-LZerD software]
[69] [PDF] [Abstract] Lee Sael & Daisuke Kihara , Detecting Local Ligand-Binding Site Similarity in Non-Homologous Proteins by Surface Patch Comparison , Proteins: Str. Funct. Bioinformatics, 80: 1177-1195 (2012)
[68] [PDF] [Abstract] Juan Esquivel-Rodriguez & Daisuke Kihara , Evaluation of multiple protein docking structures using correctly predicted pairwise subunits , BMC Bioinformatics, 13:S6 (2012) (Best paper award at GLBIO 2011, ISMB )
[67] [PDF] [Abstract] Lee Sael & Daisuke Kihara , Constructing patch-based ligand-binding pocket database for predicting function of proteins, BMC Bioinformatics, 13:S7(2012)
[66] [PDF] [Abstract] David La & Daisuke Kihara, A novel method for protein-protein interaction site prediction using phylogenetic substitution models., Proteins: Structure, Function, and Bioinformatics, 80: 126-141 (2012) [BindML server]
[65] [PDF] [Abstract] Zhonglian Huang, Priyanka Surana, Daisuke Kihara, Richard Meilan, & Keith Woeste, JnCML-like, an EF-hand motif-containing gene seasonally upregulated in the transition zone of black walnut (Juglans nigra L.)., American Journal of Molecular Biology, 1: 140-155 (2011)
[64] [PDF] [Abstract] Meghana Chitale, Shriphani Palakodety & Daisuke Kihara, Quantification of protein group coherence and pathway assignment using functional association., BMC Bioinformatics, 12:373 (2011)
[63] [PDF] [Abstract] SJ Fleishman, TA Whitehead, E-M Strauch, JE Corn, S Qin, H-X Zhou, JC Mitchell, ONA Demerdash, M Takeda-Shitaka, G Terashi, IH Moal, X Li, PA Bates, M Zacharias, H Park, J-S Ko, H Lee, C Seok, T Bourquard, J Bernauer, A Poupon, J Aze, S Soner, SK Ovali, P Ozbek, NB Tal, T Haliloglu, H Hwang, T Vreven, BG Pierce, Z Weng, L Perez-Cano, C Pons, J Fernandez-Recio, F Jiang, CH Robert, M Guharoy, S Liu, Y Huang, L Li, D Guo, Y Chen, Y Xiao, N London, Z Itzhaki, O Schueler-Furman, Y Inbar, V Patapov, M Cohen, G Schreiber, Y Tsuchiya, E Kanamori, DM Standley,H Nakamura, K Kinoshita, CM Driggers, RG Hall, JL Morgan, VL Hsu, J Zhan, Y Yang, Y Zhou, PL Kastritis, AMJJ Bonvin, W Zhang, CJ Camacho, KP Kilambi, B Weitzner, J Porter, A Sircar, JJ Gray, M Ohue, N Uchikoga, Y Matsuzaki, T Ishida, Y Akiyama, R Khashan, S Bush, D Fouches, A Tropsha, J Esquivel-Rodriguez, D Kihara, PB Stranges, R Jacak, B Kuhlman, SJ Wodak, J Janin, & D Baker, Community wide asssessment of protein-interface modeling using a protein design based benchmark., J. Mol. Biol, 414: 289-302(2011)
[62] [PDF] [Abstract] Daisuke Kihara, Lee Sael, Rayan Chikhi, & Juan Esquivel-Rodriguez, Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking., Curr. Protein and Peptide Science, 12: 520-530 (2011)
[61] [PDF] [Abstract] Greta L. Lundgaard, Natae E. Daniels, Slovenie Pyndiah, Erica K. Cassimere, Kazi M. Ahmed, Amelie Rodrigue, Daisuke Kihara, Carol Post, & Daitoku Sakamuro, Identification of a novel effector domain of BIN1 for cancer suppression., J. Cellular Biochemistry, 112: 2992-3001 (2011)
[60] [PDF] [Abstract] Balamurugan Jagadeesan, Amy E. Fleishman Littlejohn, Mary Anne Amalaradjou, Atul K. Singh, Krishna K. Mishra, David La, Daisuke Kihara, & Arun K. Bhunia, N-terminal Gly224-Gly411 Domain in Listeria Adhesion Protein Interacts with Host Receptor Hsp60., PLoS ONE, 6:e20694 (2011)
[59] [PDF] [Abstract] Pei-Fen Liu, Daisuke Kihara, & Chiwook Park, Energetics-based discovery of protein-ligand interactions on a proteomics scale., J. Mol. Biol., 408: 147-162 (2011)
[58] [PDF] [Abstract] Meghana Chitale & Daisuke Kihara , Computational protein function prediction: Framework and challenges., Protein function prediction for omics era, D. Kihara ed., Chapter 1, pp. 1-17, Springer. (2011)
[57] [PDF] [Abstract] Meghana Chitale & Daisuke Kihara , Enhanced sequence-based function prediction methods and application to functional similairty networks., Protein function prediction for omics era, D. Kihara ed., Chapter 2, pp. 19-34, Springer.(2011)
[56] [PDF] [Abstract] Rayan Chikhi, Lee Sael, & Daisuke Kihara , Protein binding ligand prediction using moment-based methods., Protein function prediction for omics era, D. Kihara ed., Chapter 8, pp. 145-163, Springer. (2011)
[55] [PDF] [Abstract] Hao Chen & Daisuke Kihara , Effect of using suboptimal alignments in template-based protein structure prediction., Proteins: Str. Funct. Bioinformatics, 79: 315-334. (2011) SUPRB threading program
[54] [PDF] [Abstract] Lee Sael & Daisuke Kihara , Binding ligand prediction for proteins using partial matching of local surface patches., International Journal of Molecular Sciences, 11:5009-5026. (2010)
[53] [PDF] [Abstract] Lee Sael & Daisuke Kihara, Protein surface representation for application to comparing low-resolution protein structure data., BMC Bioinformatics 11:S2. (2010) (Best Paper Award at GIW2010 )
[---] [PDF] Daisuke Kihara, Letter from Abroad: Research activity in Kihara Lab at Purdue University, Seibutsu Butsuri (Biophysics), (in Japanese) 50: 258-259, (2010).
[52] [PDF] [Abstract] Yifeng D Yang, Preston Spratt, Hao Chen, Changsoon Park & Daisuke Kihara, Sub-AQUA: Real-Value Quality Assessment of Protein Structure Models., PEDS Protein Engineering Design & Selection, 23: 617-632.(2010). [Sub-AQUA server]
[51] [PDF] [Abstract] Troy Hawkins*, Meghana Chitale* & Daisuke Kihara (* equal contribution), Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP., BMC Bioinformatics, 11:265.(2010).
[50] [PDF] [Abstract] Rayan Chikhi, Lee Sael & Daisuke Kihara, Real-time ligand binding pocket database search using local surface descriptors., Proteins: Structure, Function, and Bioinformatics, 78:2007-2028.(2010).
[49] [PDF] [Abstract] Daisuke Kihara, Yifeng D Yang, & Hao Chen, Error estimation of template-based protein structure models. , Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies. Andrzej Kolinski (ed.) , Springer-Verlag, Chapter 13, pp.295-314. (2010).
[48] [PDF] [Abstract] Lee Sael & Daisuke Kihara, Characterization and classification of local protein surfaces using self-organizing map, International Journal of Knowledge Discovery in Bioinformatics, 1, 32-47.(2010).
[47] [PDF] [Abstract] Vishwesh Venkatraman, Padmasini R Chakravarthy & Daisuke Kihara, Application of 3D Zernike descriptors to shape-based ligand similarity searching, J. Cheminformatics, 1:19(2009).
[46] [PDF] [Abstract] Vishwesh Venkatraman, Yifeng D Yang, Lee Sael & Daisuke Kihara, Protein-protein docking using region-based 3D Zernike descriptors, BMC Bioinformatics, 10:407(2009). [Suppl. Data]
[45] [PDF] [Abstract] David La*, Juan Esquivel-Rodriguez*, Vishwesh Venkatraman, Bin Li, Lee Sael, Steven Ueng, Steven Ahrendt & Daisuke Kihara (* equal contribution), 3D-SURFER: software for high throughput surface comparison and analysis, Bioinformatics, 25: 2843-2844 (2009).
[44] [PDF] [Abstract] Vishwesh Venkatraman, Lee Sael & Daisuke Kihara, Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors, Cell Biochemistry and Biophysics 54: 23-32 (2009).
[43] [PDF] [Abstract] Meghana Chitale, Troy Hawkins, Changsoon Park, & Daisuke Kihara, ESG: Extended similarity group method for automated protein function prediction, Bioinformatics, 25: 1739-1745(2009).
[42] [PDF] [Abstract] Lee Sael & Daisuke Kihara, Protein surface representation and comparison: New approaches in structural proteomics , Biological Data Mining, J. Chen, S. Lonardi, (eds), Chapman & Hall/CRC Press, USA, Chapter 3, pp. 89-109. (2009).
[41] [PDF] [Abstract] Daisuke Kihara, Hao Chen & Yifeng Yang, Quality assessment of computational protein models, Current Protein and Peptide Science, 10: 216-228, (2009).
[40] [PDF] [Abstract] Troy Hawkins, Meghana Chitale, Stan Luban & Daisuke Kihara, PFP: Automated prediction of gene ontology functional annotations with confidence scores, Proteins: Structure, Function, and Bioinformatics, 74: 566-582, (2009).
[39] [PDF] [Abstract] Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Daisuke Kihara, Knight TF Jr, Pico AR, Siegele DA, Wanner BL, Welch RD, The emerging world of wikis, Science, 320: 1289-1290 (2008).
[38] [Abstract] David La & Daisuke Kihara, Predicting binding interfaces of protein-protein interactions, (a book chapter in) Biological Data Mining in Protein Interaction Networks, X-L Li, S.K.Ng, (eds), Chapter 5, pp. 64-79, IGI-Global, Hershey, Philadelphia, USA. (2008).
[37] [PDF] [Abstract] Lee Sael, David La, Bin Li, Raif Rustamov & Daisuke Kihara, Rapid comparison of properties on protein surface, Proteins: Structure, Function, and Bioinformatics, 73: 1-10(2008).
[36] [PDF] [Abstract] Meghana Chitale, Troy Hawkins & Daisuke Kihara, Automated prediction of protein function from sequence, In Prediction of Protein Structure, Functions and Interactions, Janusz Bujnicki (ed.), Chapter 3, pp. 64-86, John Wiley & Sons, Ltd. (2008).
[35] [PDF] [Abstract] Yifeng D. Yang, Changsoon Park & Daisuke Kihara, Threading without optimizing weighting factors for scoring function, Proteins: Structure, Function, and Bioinformatics, 73: 581-596.(2008).
[34] [PDF] [Abstract] Lee Sael, Bin Li, David La, Yi Fang, Karthik Ramani, Raif Rustamov & Daisuke Kihara, Fast protein tertiary structure retrieval based on global surface shape similarity, Proteins: Structure, Function, and Bioinformatics, 72: 1259-1273. (2008).
[33] [PDF] Luo Si, Danni Yu, Daisuke Kihara, & Yi Fang, Combining gene sequence similarity and textual information for gene function annotation in the literature., Information Retrieval, 11: 389-404(2008).
[32] [PDF] [ABSTRACT] Troy Hawkins, Meghana Chitale & Daisuke Kihara, New paradigm in protein function prediction for large scale omics analysis., Molecular BioSystems, 4: 223-231 (2008).
[31] [PDF] [ABSTRACT] Hao Chen & Daisuke Kihara, Estimating quality of template-based protein models by alignment stability., Proteins: Struct. Funct. Bioinformatics, 71: 1255-1274 (2008).
[30] [PDF] [ABSTRACT] Bin Li, Srinivasan Turuvekere, Manish Agrawal, David La, Karthik Ramani & Daisuke Kihara, Characterization of local geometry of protein surfaces with the visibility criterion, Proteins: Struct. Funct. Bioinformatics, 71: 670-683 (2008).
[29] [PDF] Mingwu Zhang, Daisuke Kihara & Sunil Prabhakar, Tracing lineage in multi-version scientific databases., IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE), 440-447 (2007).
[28] [PDF] Yu-Shen Liu, Min Liu, Daisuke Kihara & Karthik Ramani, Salient critical points for meshes. , Proceedings of the 2007 ACM Solid and Physical Modeling, 277-282 (2007).
[27] [PDF] [ABSTRACT] Stan Luban & Daisuke Kihara, Comparative genomics of small RNAs in bacterial genomes, Omics, 11: 58-73 (2007).
[26] [PDF] [ABSTRACT] Troy Hawkins & Daisuke Kihara, Function prediction of uncharacterized proteins, J. Bioinformatics and Computational Biology, 5:1-30 (2007).
[25] [PDF] Daisuke Kihara, Troy Hawkins, Stan Luban Bin Li, Karthik Ramani, & Manish Agrawal, Protein function prediction in Proteomics Era" , Proceedings of the International Symposium on Frontiers of Computational Science, Y Kaneda et al. eds., pp. 143-148, Springer-Verlag, Berlin, Heidelberg. (2007).
[24] [PDF] [ABSTRACT] Jianjun Hu, Yifeng David Yang & Daisuke Kihara, EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences, BMC Bioinformatics, 7:342. (2006).
[23] [PDF] [ABSTRACT] Yen Hock Tan, He Huang & Daisuke Kihara, Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences, Proteins: Structure Funct, Bioinformatics, 64: 587-600. (2006).
[22] [PDF] [ABSTRACT] Troy Hawkins, Stan Luban & Daisuke Kihara, Enhanced automated function prediction using distantly related sequences and contextual association by PFP." , Protein Sci, 15:1550-1556 (2006).
[21] [PDF] [ABSTRACT] Daisuke Kihara, Yifeng D. Yang & & Troy Hawkins, "Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools." , Cancer Informatics, 2:25-35. (2006).
[20] [PDF] [ABSTRACT] Jianjun Hu, Bin Li & Daisuke Kihara, "Limitations and potentials of current motif discovery algorithms." , Nucleic Acid Res. 33: 4899-4913. (2005).
[19] [PDF] [ABSTRACT] Daisuke Kihara., "On the effect of long-range interactions on the secondary structure formation of proteins." , Protein Science. 14: 1955-1963. (2005).
[18] [ABSTRACT] Daisuke Kihara., "Biomolecular Structure Databases." , Genome Function Research Handbook, Chapter 2. pp. 73-81. Yodosha Publishers, Tokyo, Japan. (2004).
[17] [PDF] [ABSTRACT] Jeffrey Skolnick, Daisuke Kihara and Yang Zhang., " Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm." , Proteins: Structure, Funct. Bioinformatics 56:502-518. (2004)
[16] [PDF] [ABSTRACT] Daisuke Kihara and Jeffrey Skolnick., " Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q." , Proteins: Structure, Funct. Bioinformatics 55: 464-473 (2004)
[15] [PDF] [ABSTRACT] Daisuke Kihara and Jeffrey Skolnick., " The PDB is a covering set of small protein structures." , J. Mol. Biol. 334: 793-802 (2003)
[14] [PDF] [ABSTRACT] Jeffrey Skolnick, Yang Zhang, Adrian Arakaki, Andrzej Kolinski, Michael Boniecki, Andras Szilagyi and Daisuke Kihara., " TOUCHSTONE: a unified approach to protein structure prediction." , Proteins: Structure, Funct. Genet. 53: Suppl.6: 469-479 (2003)
[13] [PDF] [ABSTRACT] Wei Li, Yang Zhang, Daisuke Kihara, Yuanpeng J. Huang, Deyou Zheng, Gaetano T. Montelione, Andrzej Kolinski, and Jeffrey Skolnick, " TOUCHSTONEX: Protein Structure Prediction Using Sparse NMR Data." , Proteins: Structure, Funct. Genet. 53: 290-306 (2003)
[12] [PDF] [ABSTRACT] Yang, Zhang, Daisuke Kihara and Jeffrey Skolnick, " Local Energy Landscape Flattening: Parallel Hyperbolic Monte Carlo Sampling of Protein Folding." , Proteins: Structure, Funct. Genet. 48: 192-201 (2002)
[11] [PDF] [ABSTRACT] Daisuke Kihara, Yang Zhang, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick, " Ab initio Protein Structure Prediction on a Genomic Scale: Application to the Mycoplasma genitalium Genome." , Proc. Natl. Acad. Sci. USA, 99: 5993-5998 (2002)
[10] [PDF] [ABSTRACT] Jeffrey Skolnick, Andrzej Kolinski, Daisuke Kihara, Marcos Betancourt, Piotr Rotkiewicz and Michael Boniecki, " Ab initio Protein Structure Prediction via a Combination of Threading, Lattice Folding, Clustering, and Structure Refinement." , Proteins: Structure, Funct. Genet. 45 (Suppl 5): 149-156 (2001)
[9] [ABSTRACT] Daisuke Kihara, " Genome Databases on the Internet." , Tanpakushitsu Kakusan Koso (Protein, Nucleic Acid and Enzyme) 46 (16 Suppl): 2639-2645 (2001)
[8] [PDF] Daisuke Kihara and Minoru Kanehisa, " Prediction of Membrane Proteins in Post-Genomic Era." , Recent Res. Developments in Protein Engng. 1: 179-196 (2001)
[7] [PDF] [ABSTRACT] Daisuke Kihara, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick, " TOUCHSTONE: An ab initio Protein Structure Prediction Method that Uses Threading-based Tertiary Restraints." , Proc. Natl. Acad. Sci. USA 98: 10125-10130 (2001)
[6] [PDF] [ABSTRACT] Andrzej Kolinski, Marcos Betancourt, Daisuke Kihara, Piotr Rotkiewicz and Jeffrey Skolnick, " Generalized Comparative Modeling (GENCOMP): A Combination of Sequence Comparison, Threading, and Lattice Modeling for Protein Structure Prediction and Refinement." , Proteins: Structure, Funct. Genet. 44: 133-149 (2001)
[5] [PDF] [ABSTRACT] Jeffrey Skolnick and Daisuke Kihara, " Defrosting the Frozen Approximation: PROSPECTOR - A New Approach to Threading." , Proteins: Structure, Funct. Genet. 42: 319-331 (2001)
[4] [PDF] [ABSTRACT] Daisuke Kihara and Minoru Kanehisa, " Tandem Cluster of Membrane Proteins in Complete Genome Sequences." , Genome Res. 10: 731-743 (2000)
[3] [ABSTRACT] Daisuke Kihara and Minoru Kanehisa., " The Genome Projects and Bioinformatics." , Iwanami Kouza (Iwanami Lecture Series): Gendai Igaku no Kiso (The Basis of Modern Medical Science), vol.1, Chap.11, pp: 215-235, Iwanami Shoten Publishers, Tokyo Japan (1998)
[2] [PDF] [ABSTRACT] Daisuke Kihara, Toshio Shimizu and Minoru Kanehisa, " Prediction of Membrane Proteins Based on Classification of Transmembrane Segments." , Protein Engng., 11: 961-970 (1998)
[1] [ABSTRACT] Daisuke Kihara, Minoru Kanehisa and Toshihisa Takagi., " Internet Resources for Genome Research." , Tanpakushitsu Kakusan Koso (Protein, Nucleic Acid and Enzyme), 42(17 Suppl): 3090-3099 (1997)

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