Daisuke Kihara - Publications

Department of Biological Sciences Purdue University, West Lafayette, IN, United States 

204 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Broyles BK, Gutierrez AT, Maris TP, Coil DA, Wagner TM, Wang X, Kihara D, Class CA, Erkine AM. Activation of gene expression by detergent-like protein domains. Iscience. 24: 103017. PMID 34522860 DOI: 10.1016/j.isci.2021.103017  1
2021 Christoffer C, Bharadwaj V, Luu R, Kihara D. LZerD Protein-Protein Docking Webserver Enhanced With Structure Prediction. Frontiers in Molecular Biosciences. 8: 724947. PMID 34466411 DOI: 10.3389/fmolb.2021.724947  1
2021 Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, ... ... Kihara D, et al. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins. PMID 34453465 DOI: 10.1002/prot.26222  1
2021 Verburgt J, Kihara D. Benchmarking of structure refinement methods for protein complex models. Proteins. PMID 34309909 DOI: 10.1002/prot.26188  1
2021 Mori T, Terashi G, Matsuoka D, Kihara D, Sugita Y. Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps. Journal of Chemical Information and Modeling. PMID 34142833 DOI: 10.1021/acs.jcim.1c00230  1
2021 Wang X, Flannery ST, Kihara D. Protein Docking Model Evaluation by Graph Neural Networks. Frontiers in Molecular Biosciences. 8: 647915. PMID 34113650 DOI: 10.3389/fmolb.2021.647915  1
2021 Christoffer C, Chen S, Bharadwaj V, Aderinwale T, Kumar V, Hormati M, Kihara D. LZerD webserver for pairwise and multiple protein-protein docking. Nucleic Acids Research. PMID 33963854 DOI: 10.1093/nar/gkab336  1
2021 Sanyal A, Zbornik EA, Watson BG, Christoffer C, Ma J, Kihara D, Mattoo S. Kinetic and structural parameters governing Fic-mediated adenylylation/AMPylation of the Hsp70 chaperone, BiP/GRP78. Cell Stress & Chaperones. PMID 33942205 DOI: 10.1007/s12192-021-01208-2  1
2021 Wang X, Alnabati E, Aderinwale TW, Maddhuri Venkata Subramaniya SR, Terashi G, Kihara D. Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning. Nature Communications. 12: 2302. PMID 33863902 DOI: 10.1038/s41467-021-22577-3  1
2021 Ahsan N, Rao RSP, Wilson RS, Punyamurtula U, Salvato F, Petersen M, Ahmed MK, Abid MR, Verburgt JC, Kihara D, Yang Z, Fornelli L, Foster SB, Ramratnam B. Mass spectrometry-based proteomic platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches. Proteomics. e2000279. PMID 33860983 DOI: 10.1002/pmic.202000279  0.08
2021 Jain A, Terashi G, Kagaya Y, Maddhuri Venkata Subramaniya SR, Christoffer C, Kihara D. Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction. Scientific Reports. 11: 7574. PMID 33828153 DOI: 10.1038/s41598-021-87204-z  1
2021 Han X, Terashi G, Christoffer C, Chen S, Kihara D. VESPER: global and local cryo-EM map alignment using local density vectors. Nature Communications. 12: 2090. PMID 33828103 DOI: 10.1038/s41467-021-22401-y  1
2021 Maddhuri Venkata Subramaniya SR, Terashi G, Jain A, Kagaya Y, Kihara D. Protein Contact Map Refinement for Improving Structure Prediction Using Generative Adversarial Networks. Bioinformatics (Oxford, England). PMID 33787852 DOI: 10.1093/bioinformatics/btab220  1
2021 Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, ... ... Kihara D, et al. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods. PMID 33542514 DOI: 10.1038/s41592-020-01051-w  1
2021 Ramadesikan S, Skiba L, Lee J, Madhivanan K, Sarkar D, De La Fuente A, Hanna CB, Terashi G, Hazbun T, Kihara D, Aguilar RC. Genotype & Phenotype in Lowe Syndrome: Specific OCRL1 patient mutations differentially impact cellular phenotypes. Human Molecular Genetics. PMID 33517444 DOI: 10.1093/hmg/ddab025  1
2020 Wang X, Kihara D, Luo J, Qi GJ. EnAET: A Self-Trained framework for Semi-Supervised and Supervised Learning with Ensemble Transformations. Ieee Transactions On Image Processing : a Publication of the Ieee Signal Processing Society. PMID 33347409 DOI: 10.1109/TIP.2020.3044220  1
2020 Shin WH, Kumazawa K, Imai K, Hirokawa T, Kihara D. Current Challenges and Opportunities in Designing Protein-Protein Interaction Targeted Drugs. Advances and Applications in Bioinformatics and Chemistry : Aabc. 13: 11-25. PMID 33209039 DOI: 10.2147/AABC.S235542  1
2020 Terashi G, Zha Y, Kihara D. Protein Structure Modeling from Cryo-EM Map Using MAINMAST and MAINMAST-GUI Plugin. Methods in Molecular Biology (Clifton, N.J.). 2165: 317-336. PMID 32621234 DOI: 10.1007/978-1-0716-0708-4_19  1
2020 Christoffer C, Kihara D. IDP-LZerD: Software for Modeling Disordered Protein Interactions. Methods in Molecular Biology (Clifton, N.J.). 2165: 231-244. PMID 32621228 DOI: 10.1007/978-1-0716-0708-4_13  1
2020 Aderinwale T, Christoffer CW, Sarkar D, Alnabati E, Kihara D. Computational structure modeling for diverse categories of macromolecular interactions. Current Opinion in Structural Biology. 64: 1-8. PMID 32599506 DOI: 10.1016/J.Sbi.2020.05.017  1
2020 Gonzalez B, Monroe L, Li K, Yan R, Wright E, Walter T, Kihara D, Weintraub ST, Thomas JA, Serwer P, Jiang W. Phage G Structure at 6.1 Å Resolution, Condensed DNA, and Host Identity Revision to a Lysinibacillus. Journal of Molecular Biology. PMID 32454153 DOI: 10.1016/J.Jmb.2020.05.016  1
2020 Terashi G, Kagaya Y, Kihara D. MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. Journal of Chemical Information and Modeling. 60: 2634-2643. PMID 32197044 DOI: 10.1021/Acs.Jcim.9B01110  1
2020 DeVille JS, Kihara D, Sit A. 2DKD: a toolkit for content-based local image search. Source Code For Biology and Medicine. 15: 1. PMID 32064000 DOI: 10.1186/S13029-020-0077-1  1
2020 Terashi G, Christoffer C, Kihara D. Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes. Methods in Molecular Biology (Clifton, N.J.). 2074: 95-112. PMID 31583633 DOI: 10.1007/978-1-4939-9873-9_8  1
2020 Langenfeld F, Peng Y, Lai Y, Rosin PL, Aderinwale T, Terashi G, Christoffer C, Kihara D, Benhabiles H, Hammoudi K, Cabani A, Windal F, Melkemi M, Giachetti A, Mylonas S, et al. SHREC 2020: Multi-domain protein shape retrieval challenge Computers & Graphics. 91: 189-198. DOI: 10.1016/J.Cag.2020.07.013  1
2020 Gubins I, Chaillet ML, Schot Gvd, Veltkamp RC, Förster F, Hao Y, Wan X, Cui X, Zhang F, Moebel E, Wang X, Kihara D, Zeng X, Xu M, Nguyen NP, et al. SHREC 2020: Classification in cryo-electron tomograms Computers & Graphics. 91: 279-289. DOI: 10.1016/J.Cag.2020.07.010  1
2020 Terashi G, Kihara D. De Novo Protein Structure Modeling Tool MAINMAST Enhanced for Multiple Chain Complexes and Bound Ligands Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2667  1
2020 Kihara D, Terashi G, Subramaniya SRMV. De Novo Computational Protein Tertiary Structure Modeling Pipeline for Cryo-EM Maps of Intermediate Resolution Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.1657  1
2019 Sit A, Shin WH, Kihara D. Three-Dimensional Krawtchouk Descriptors for Protein Local Surface Shape Comparison. Pattern Recognition. 93: 534-545. PMID 32042209 DOI: 10.1016/J.Patcog.2019.05.019  1
2019 Alnabati E, Kihara D. Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps. Molecules (Basel, Switzerland). 25. PMID 31878333 DOI: 10.3390/Molecules25010082  1
2019 Chiba S, Ohue M, Gryniukova A, Borysko P, Zozulya S, Yasuo N, Yoshino R, Ikeda K, Shin WH, Kihara D, Iwadate M, Umeyama H, Ichikawa T, Teramoto R, Hsin KY, et al. A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Scientific Reports. 9: 19585. PMID 31863054 DOI: 10.1038/S41598-019-55069-Y  1
2019 Jain A, Kihara D. NNTox: Gene Ontology-Based Protein Toxicity Prediction Using Neural Network. Scientific Reports. 9: 17923. PMID 31784686 DOI: 10.1038/S41598-019-54405-6  1
2019 Wang X, Terashi G, Christoffer CW, Zhu M, Kihara D. Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks. Bioinformatics (Oxford, England). PMID 31746961 DOI: 10.1093/Bioinformatics/Btz870  1
2019 Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Kihara D, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/S13059-019-1835-8  1
2019 Ramanathan K, Shanthi V, Maiti S, Shin WH, Kihara D. Current progress and future perspectives of polypharmacology : From the view of non-small cell lung cancer. Seminars in Cancer Biology. PMID 31698087 DOI: 10.1016/J.Semcancer.2019.10.019  1
2019 Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Peterson L, Verburgt J, Kihara D. Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38-46. Proteins. PMID 31697428 DOI: 10.1002/Prot.25850  1
2019 Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, ... ... Kihara D, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838  1
2019 Shin WH, Kihara D. Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0. Journal of Computer-Aided Molecular Design. PMID 31506789 DOI: 10.1007/S10822-019-00222-Y  1
2019 Maddhuri Venkata Subramaniya SR, Terashi G, Kihara D. Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning. Nature Methods. 16: 911-917. PMID 31358979 DOI: 10.1016/J.Bpj.2019.11.417  1
2019 Ding Z, Kihara D. Computational identification of protein-protein interactions in model plant proteomes. Scientific Reports. 9: 8740. PMID 31217453 DOI: 10.1038/S41598-019-45072-8  1
2019 L'Enfant M, Kutudila P, Rayon C, Domon JM, Shin WH, Kihara D, Wadouachi A, Pelloux J, Pourceau G, Pau-Roblot C. Lactose derivatives as potential inhibitors of pectin methylesterases. International Journal of Biological Macromolecules. PMID 30978419 DOI: 10.1016/J.Ijbiomac.2019.04.049  1
2019 Han X, Sit A, Christoffer C, Chen S, Kihara D. A global map of the protein shape universe. Plos Computational Biology. 15: e1006969. PMID 30978181 DOI: 10.7490/F1000Research.1116715.1  1
2019 Shin WH, Kihara D. 55 Years of the Rossmann Fold. Methods in Molecular Biology (Clifton, N.J.). 1958: 1-13. PMID 30945211 DOI: 10.1007/978-1-4939-9161-7_1  1
2019 Macossay-Castillo M, Marvelli G, Guharoy M, Jain A, Kihara D, Tompa P, Wodak SJ. The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity. Journal of Molecular Biology. PMID 30878482 DOI: 10.1016/J.Jmb.2019.03.008  1
2019 Kihara D, Peterson L, Esquivel-Rodríguez J, Togawa Y, Christoffer C, Terashi G, Roy A, Shin W. Extending computational protein complex modeling: disordered protein interactions & assembly order of multimeric protein complexes F1000research. 8. DOI: 10.7490/F1000Research.1116546.1  1
2019 Jain A, Kihara D. Accelerating protein function discovery using computational tools F1000research. 8. DOI: 10.7490/F1000Research.1116456.1  1
2019 Terashi G, Zha Y, Kihara D. Enhancement for MAINMAST, De Novo Main-Chain Tracing Method: Symmetric Multi-Chain Modeling, Local Refinement, and Graphical User Interface Microscopy and Microanalysis. 25: 146-147. DOI: 10.1017/S1431927619001466  1
2019 Terashi G, Zha Y, Kihara D. Improved De Novo Main-Chain Tracing Method Mainmast for Multi-Chain Modeling, Local Refinement, and Graphical User Interface Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.3094  1
2019 Ramanathan K, Maiti S, Shanthi V, Shin W, Kihara D. Implementation of pharmacophore-based 3D QSAR model and scaffold analysis in order to excavate pristine ALK inhibitors Medicinal Chemistry Research. 28: 1726-1739. DOI: 10.1007/S00044-019-02410-9  1
2018 Xiong Y, Qiao Y, Kihara D, Zhang HY, Zhu X, Wei DQ. Survey of Machine Learning Techniques for Prediction of the Isoform Specificity of Cytochrome P450 Substrates. Current Drug Metabolism. PMID 30338736 DOI: 10.2174/1389200219666181019094526  1
2018 Jain A, Gali H, Kihara D. Identification of Moonlighting Proteins in Genomes Using Text Mining Techniques. Proteomics. e1800083. PMID 30260564 DOI: 10.1002/Pmic.201800083  1
2018 Aryal UK, Ding Z, Hedrick V, Paschoal Sobreira TJ, Kihara D, Sherman LA. Analysis of protein complexes in the unicellular cyanobacterium Cyanothece ATCC 51142. Journal of Proteome Research. PMID 30216071 DOI: 10.1021/Acs.Jproteome.8B00170  1
2018 Khan IK, Jain A, Rawi R, Besmail H, Kihara D. Prediction of protein group function by iterative classification on functional relevance network. Bioinformatics (Oxford, England). PMID 30192921 DOI: 10.1093/Bioinformatics/Bty787  1
2018 Jain A, Kihara D. Phylo-PFP: Improved automated protein function prediction using phylogenetic distance of distantly related sequences. Bioinformatics (Oxford, England). PMID 30165572 DOI: 10.1093/Bioinformatics/Bty704  1
2018 Terashi G, Kihara D. De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge. Journal of Structural Biology. 204: 351-359. PMID 30075190 DOI: 10.1016/J.Jsb.2018.07.013  1
2018 Ding Z, Wei Q, Kihara D. Computing and Visualizing Gene Function Similarity and Coherence with NaviGO. Methods in Molecular Biology (Clifton, N.J.). 1807: 113-130. PMID 30030807 DOI: 10.1007/978-1-4939-8561-6_9  1
2018 Ding Z, Kihara D. Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. Current Protocols in Protein Science. e62. PMID 29927082 DOI: 10.1002/Cpps.62  1
2018 Terashi G, Kihara D. De novo main-chain modeling for EM maps using MAINMAST. Nature Communications. 9: 1618. PMID 29691408 DOI: 10.1038/S41467-018-04053-7  1
2018 Shin WH, Kihara D. Virtual Ligand Screening Using PL-PatchSurfer2, a Molecular Surface-Based Protein-Ligand Docking Method. Methods in Molecular Biology (Clifton, N.J.). 1762: 105-121. PMID 29594770 DOI: 10.1007/978-1-4939-7756-7_7  1
2018 Peterson LX, Togawa Y, Esquivel-Rodriguez J, Terashi G, Christoffer C, Roy A, Shin WH, Kihara D. Modeling the assembly order of multimeric heteroprotein complexes. Plos Computational Biology. 14: e1005937. PMID 29329283 DOI: 10.1016/J.Bpj.2018.11.1078  1
2018 Terashi G, Kihara D. Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent. Proteins. 86: 189-201. PMID 28833585 DOI: 10.1002/Prot.25373  1
2018 Peterson LX, Roy A, Christoffer C, Terashi G, Kihara D. Structure modeling of disordered protein interactions F1000research. 7. DOI: 10.7490/F1000Research.1115294.1  1
2018 Jamroz M, Kolinski A, Kihara D. Prediction of real-value fluctuations of globular proteins F1000research. 7. DOI: 10.7490/F1000Research.1115246.1  1
2018 Kihara D, Sael L, Xiong Y, Zhu X, Esquivel-Rodriguez J. Next generation molecular surface representation for rapid global/local protein shape comparison, docking, and low-resolution data F1000research. 7. DOI: 10.7490/F1000Research.1115240.1  1
2018 Chitale M, Hawkins T, Park C, Kihara D. ESG: Extended Similarity Group method for automated protein function prediction F1000research. 7. DOI: 10.7490/F1000Research.1115239.1  1
2018 Sael L, Kihara D. Local protein surface patch method for protein-ligand binding prediction F1000research. 7. DOI: 10.7490/F1000Research.1115190.1  1
2018 Kihara D, Venkatraman V, La D, Yang YD, Sael L, Juan E, Li B. A unified protein docking procedure with a shape complementarity screening using 3D Zernike descriptors F1000research. 7. DOI: 10.7490/F1000Research.1115189.1  1
2018 Yang YD, Park C, Kihara D. Protein structure prediction without optimizing weighting factors for scoring function F1000research. 7. DOI: 10.7490/F1000Research.1115188.1  1
2018 Lee S, Li B, La D, Rustamov R, Kihara D. A fast methodology for high throughput comparison of tertiary structure and physicochemical properties of proteins F1000research. 7. DOI: 10.7490/F1000Research.1115187.1  1
2018 Monroe L, Terashi G, Kihara D. Reliability of Electron Microscopy Atomic Model Refinement Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.905  1
2018 Terashi G, Kihara D. Mainmast: De Novo Main-Chain Model Tracing for EM Maps using Tree-Graph Optimization Method Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.243  1
2017 Han X, Wei Q, Kihara D. Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER. Current Protocols in Bioinformatics. 60: 3.14.1-3.14.15. PMID 29220075 DOI: 10.1002/Cpbi.37  1
2017 Magner A, Kihara D, Szpankowski W. A Study of the Boltzmann Sequence-Structure Channel. Proceedings of the Ieee. Institute of Electrical and Electronics Engineers. 105: 286-305. PMID 28943650 DOI: 10.1109/JPROC.2016.2608797  1
2017 Chiba S, Ishida T, Ikeda K, Mochizuki M, Teramoto R, Taguchi YH, Iwadate M, Umeyama H, Ramakrishnan C, Thangakani AM, Velmurugan D, Gromiha MM, Okuno T, Kato K, Minami S, ... ... Kihara D, et al. An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes. Scientific Reports. 7: 12038. PMID 28931921 DOI: 10.1038/S41598-017-10275-4  1
2017 Khan IK, Bhuiyan M, Kihara D. DextMP: deep dive into text for predicting moonlighting proteins. Bioinformatics (Oxford, England). 33: i83-i91. PMID 28881966 DOI: 10.1093/Bioinformatics/Btx231  1
2017 Peterson LX, Shin WH, Kim H, Kihara D. Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions. Proteins. PMID 28845596 DOI: 10.1002/Prot.25376  1
2017 Shin WH, Christoffer CW, Kihara D. In Silico Structure-Based Approaches to Discover Protein-Protein Interaction-Targeting Drugs. Methods (San Diego, Calif.). PMID 28802714 DOI: 10.1016/J.Ymeth.2017.08.006  1
2017 Khan I, McGraw J, Kihara D. MPFit: Computational Tool for Predicting Moonlighting Proteins. Methods in Molecular Biology (Clifton, N.J.). 1611: 45-57. PMID 28451971 DOI: 10.1007/978-1-4939-7015-5_5  1
2017 Wei Q, McGraw J, Khan I, Kihara D. Using PFP and ESG Protein Function Prediction Web Servers. Methods in Molecular Biology (Clifton, N.J.). 1611: 1-14. PMID 28451967 DOI: 10.1007/978-1-4939-7015-5_1  1
2017 Peterson LX, Roy A, Christoffer C, Terashi G, Kihara D. Modeling disordered protein interactions from biophysical principles. Plos Computational Biology. 13: e1005485. PMID 28394890 DOI: 10.1371/Journal.Pcbi.1005485  1
2017 Alkam T, Mamiya T, Kimura N, Yoshida A, Kihara D, Tsunoda Y, Aoyama Y, Hiramatsu M, Kim HC, Nabeshima T. Prenatal nicotine exposure decreases the release of dopamine in the medial frontal cortex and induces atomoxetine-responsive neurobehavioral deficits in mice. Psychopharmacology. PMID 28332006 DOI: 10.1007/s00213-017-4591-z  0.01
2017 Wei Q, Khan IK, Ding Z, Yerneni S, Kihara D. NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. Bmc Bioinformatics. 18: 177. PMID 28320317 DOI: 10.1186/S12859-017-1600-5  1
2017 Monroe L, Terashi G, Kihara D. Variability of Protein Structure Models from Electron Microscopy. Structure (London, England : 1993). 25: 592-602.e2. PMID 28262392 DOI: 10.7490/F1000Research.1114548.1  1
2017 Zeng L, Shin WH, Zhu X, Park SH, Park C, Tao WA, Kihara D. Discovery of Nicotinamide Adenine Dinucleotide Binding Proteins in the Escherichia coli Proteome Using a Combined Energetic- and Structural-Bioinformatics-Based Approach. Journal of Proteome Research. 16: 470-480. PMID 28152599 DOI: 10.1021/Acs.Jproteome.6B00624  1
2017 Shin WH, Kang X, Zhang J, Kihara D. Prediction of Local Quality of Protein Structure Models Considering Spatial Neighbors in Graphical Models. Scientific Reports. 7: 40629. PMID 28074879 DOI: 10.1038/Srep40629  1
2017 Wei Q, La D, Kihara D. BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns. Methods in Molecular Biology (Clifton, N.J.). 1529: 279-289. PMID 27914057 DOI: 10.1007/978-1-4939-6637-0_14  1
2017 Peterson L, Jamroz M, Kolinski A, Kihara D. Predicting Real-Valued Protein Residue Fluctuation Using FlexPred. Methods in Molecular Biology (Clifton, N.J.). 1484: 175-186. PMID 27787827 DOI: 10.1007/978-1-4939-6406-2_13  1
2017 Monroe L, Terashi G, Kihara D. How reliable are protein structures determined by electron microscopy F1000research. 6. DOI: 10.7490/F1000Research.1114549.1  1
2017 Shin W, Zeng L, Park C, Tao WA, Kihara D. Molecular surface-based screening methods for repurposing drugs: application to find novel NAD binders in the E. Coli proteome F1000research. 6. DOI: 10.7490/F1000Research.1114212.1  1
2017 Shin W, Kihara D. PL-PatchSurfer2: a virtual screening method tolerant to receptor structure variation using surface-patch matching F1000research. 6. DOI: 10.7490/F1000Research.1114211.1  1
2016 Peterson LX, Kim H, Esquivel-Rodriguez J, Roy A, Han X, Shin WH, Zhang J, Terashi G, Lee M, Kihara D. Human and Server Docking Prediction for CAPRI Round 30-35 Using LZerD with Combined Scoring Functions. Proteins. PMID 27654025 DOI: 10.1002/Prot.25165  1
2016 Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, ... ... Kihara D, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6  1
2016 Chitale M, Khan IK, Kihara D. Missing gene identification using functional coherence scores. Scientific Reports. 6: 31725. PMID 27552989 DOI: 10.1038/Srep31725  1
2016 Shin WH, Christoffer CW, Wang J, Kihara D. PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method that is Tolerant to Target and Ligand Structure Variation. Journal of Chemical Information and Modeling. PMID 27500657 DOI: 10.1021/Acs.Jcim.6B00163  1
2016 Jamroz M, Kolinski A, Kihara D. Ensemble-based evaluation for protein structure models. Bioinformatics (Oxford, England). 32: i314-i321. PMID 27307633 DOI: 10.1093/Bioinformatics/Btw262  1
2016 Kingsley LJ, Esquivel-Rodríguez J, Yang Y, Kihara D, Lill MA. Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations. Journal of Computational Chemistry. PMID 27232548 DOI: 10.1002/Jcc.24412  1
2016 Khan IK, Kihara D. Genome-scale prediction of moonlighting proteins using diverse protein association information. Bioinformatics (Oxford, England). PMID 27153604 DOI: 10.1093/Bioinformatics/Btw166  1
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Kihara D, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  1
2016 Gardner NW, Monroe LK, Kihara D, Park C. Energetic Coupling between Ligand Binding and Dimerization in E. coli Phosphoglycerate Mutase. Biochemistry. PMID 26919584 DOI: 10.1021/Acs.Biochem.5B00980  1
2016 Kihara D. Computational protein function predictions. Methods (San Diego, Calif.). 93: 1-2. PMID 26778120 DOI: 10.1016/J.Ymeth.2016.01.001  0.01
2016 Kim H, Kihara D. Protein structure prediction using residue- and fragment-environment potentials in CASP11. Proteins. 84: 105-17. PMID 26344195 DOI: 10.1002/Prot.24920  1
2016 Shin W, Kihara D. Pl-Patchsurfer: A Fast, Surface-Patch-Based Virtual Screening Program using Three-Dimensional Zernike Descriptors Biophysical Journal. 110: 1-7. DOI: 10.1016/J.Bpj.2015.11.1044  1
2015 Zhu X, Shin WH, Kim H, Kihara D. Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014. Journal of Chemical Information and Modeling. PMID 26691286 DOI: 10.1021/Acs.Jcim.5B00625  1
2015 Shin WH, Bures MG, Kihara D. PatchSurfers: Two methods for local molecular property-based binding ligand prediction. Methods (San Diego, Calif.). PMID 26427548 DOI: 10.1016/J.Ymeth.2015.09.026  1
2015 Yerneni S, Khan I, Wei Q, Kihara D. IAS: Interaction specific GO term associations for predicting protein-protein interaction networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 26415209 DOI: 10.1109/Tcbb.2015.2476809  1
2015 Khan IK, Wei Q, Chapman S, Kc DB, Kihara D. The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches. Gigascience. 4: 43. PMID 26380077 DOI: 10.1186/S13742-015-0083-4  1
2015 Shin WH, Zhu X, Bures MG, Kihara D. Three-Dimensional Compound Comparison Methods and Their Application in Drug Discovery. Molecules (Basel, Switzerland). 20: 12841-62. PMID 26193243 DOI: 10.3390/Molecules200712841  1
2015 Sénéchal F, L'Enfant M, Domon JM, Rosiau E, Crépeau MJ, Surcouf O, Esquivel-Rodriguez J, Marcelo P, Mareck A, Guérineau F, Kim HR, Mravec J, Bonnin E, Jamet E, Kihara D, et al. Tuning of Pectin Methylesterification: PECTIN METHYLESTERASE INHIBITOR 7 MODULATES THE PROCESSIVE ACTIVITY OF CO-EXPRESSED PECTIN METHYLESTERASE 3 IN A pH-DEPENDENT MANNER. The Journal of Biological Chemistry. 290: 23320-35. PMID 26183897 DOI: 10.1074/Jbc.M115.639534  1
2015 Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D. Navigating 3D electron microscopy maps with EM-SURFER. Bmc Bioinformatics. 16: 181. PMID 26025554 DOI: 10.1186/S12859-015-0580-6  1
2015 Magner A, Szpankowski W, Kihara D. On the origin of protein superfamilies and superfolds. Scientific Reports. 5: 8166. PMID 25703447 DOI: 10.1038/Srep08166  1
2015 Liu Y, Sheng J, Fokine A, Meng G, Shin WH, Long F, Kuhn RJ, Kihara D, Rossmann MG. Structure and inhibition of EV-D68, a virus that causes respiratory illness in children. Science (New York, N.Y.). 347: 71-4. PMID 25554786 DOI: 10.1126/Science.1261962  1
2015 Otsuka Y, Muto A, Takeuchi R, Okada C, Ishikawa M, Nakamura K, Yamamoto N, Dose H, Nakahigashi K, Tanishima S, Suharnan S, Nomura W, Nakayashiki T, Aref WG, Bochner BR, ... ... Kihara D, et al. GenoBase: comprehensive resource database of Escherichia coli K-12. Nucleic Acids Research. 43: D606-17. PMID 25399415 DOI: 10.1093/Nar/Gku1164  1
2015 Zhu X, Xiong Y, Kihara D. Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. Bioinformatics (Oxford, England). 31: 707-13. PMID 25359888 DOI: 10.1093/Bioinformatics/Btu724  1
2015 Khan IK, Wei Q, Chitale M, Kihara D. PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool. Bioinformatics (Oxford, England). 31: 271-2. PMID 25273111 DOI: 10.1093/Bioinformatics/Btu646  1
2015 Liu Y, Sheng J, Fokine A, Meng G, Shin WH, Long F, Kuhn RJ, Kihara D, Rossmann MG. Virus structure. Structure and inhibition of EV-D68, a virus that causes respiratory illness in children. Science. 347: 71-74. DOI: 10.2210/Pdb4Wm7/Pdb  1
2015 Magner A, Kihara D, Szpankowski W. Phase transitions in a sequence-structure channel 2015 Information Theory and Applications Workshop, Ita 2015 - Conference Proceedings. 235-239. DOI: 10.1109/ITA.2015.7308994  1
2015 Esquivel-Rodriguez J, Han X, Christoffer C, Kang X, Monroe L, Kihara D. Fast Shape-Based Global and Local Electron Density Map Search Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.1050  1
2014 Khan I, Chen Y, Dong T, Hong X, Takeuchi R, Mori H, Kihara D. Genome-scale identification and characterization of moonlighting proteins. Biology Direct. 9: 30. PMID 25497125 DOI: 10.1186/S13062-014-0030-9  1
2014 Khan IK, Kihara D. Computational characterization of moonlighting proteins. Biochemical Society Transactions. 42: 1780-5. PMID 25399606 DOI: 10.1042/Bst20140214  1
2014 Aryal UK, Xiong Y, McBride Z, Kihara D, Xie J, Hall MC, Szymanski DB. A proteomic strategy for global analysis of plant protein complexes. The Plant Cell. 26: 3867-82. PMID 25293756 DOI: 10.1105/Tpc.114.127563  1
2014 Hu B, Zhu X, Monroe L, Bures MG, Kihara D. PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions. International Journal of Molecular Sciences. 15: 15122-45. PMID 25167137 DOI: 10.3390/Ijms150915122  1
2014 Kim H, Kihara D. Detecting local residue environment similarity for recognizing near-native structure models. Proteins. 82: 3255-72. PMID 25132526 DOI: 10.1002/Prot.24658  1
2014 Olek AT, Rayon C, Makowski L, Kim HR, Ciesielski P, Badger J, Paul LN, Ghosh S, Kihara D, Crowley M, Himmel ME, Bolin JT, Carpita NC. The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers. The Plant Cell. 26: 2996-3009. PMID 25012190 DOI: 10.1105/Tpc.114.126862  1
2014 Sit A, Kihara D. Comparison of image patches using local moment invariants. Ieee Transactions On Image Processing : a Publication of the Ieee Signal Processing Society. 23: 2369-79. PMID 24718574 DOI: 10.1109/Tip.2014.2315923  1
2014 Peterson LX, Kang X, Kihara D. Assessment of protein side-chain conformation prediction methods in different residue environments. Proteins. 82: 1971-84. PMID 24619909 DOI: 10.1002/Prot.24552  1
2014 Esquivel-Rodriguez J, Filos-Gonzalez V, Li B, Kihara D. Pairwise and multimeric protein-protein docking using the LZerD program suite. Methods in Molecular Biology (Clifton, N.J.). 1137: 209-34. PMID 24573484 DOI: 10.1007/978-1-4939-0366-5_15  1
2014 Xiong Y, Esquivel-Rodriguez J, Sael L, Kihara D. 3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces. Methods in Molecular Biology (Clifton, N.J.). 1137: 105-17. PMID 24573477 DOI: 10.1007/978-1-4939-0366-5_8  1
2014 Won S, Kwon MS, Mattheisen M, Park S, Park C, Kihara D, Cichon S, Ophoff R, Nöthen MM, Rietschel M, Baur M, Uitterlinden AG, Hofmann A, Lange C. Efficient strategy for detecting gene × gene joint action and its application in schizophrenia. Genetic Epidemiology. 38: 60-71. PMID 24272960 DOI: 10.1002/Gepi.21779  1
2014 Padilla-Sanchez V, Gao S, Kim HR, Kihara D, Sun L, Rossmann MG, Rao VB. Structure-function analysis of the DNA translocating portal of the bacteriophage T4 packaging machine. Journal of Molecular Biology. 426: 1019-38. PMID 24126213 DOI: 10.1016/J.Jmb.2013.10.011  1
2014 Cavalcoli J, Welch L, Aronow B, Draghici S, Kihara D. The international society of computational biology presents: The great lakes bioinformatics conference, may 16-18, 2014, Cincinnati, Ohio Bioinformatics. 30: 148-149. DOI: 10.1093/Bioinformatics/Btt673  1
2013 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, ... ... Kihara D, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  1
2013 Esquivel-Rodríguez J, Kihara D. Computational methods for constructing protein structure models from 3D electron microscopy maps. Journal of Structural Biology. 184: 93-102. PMID 23796504 DOI: 10.1016/J.Jsb.2013.06.008  1
2013 Chitale M, Khan IK, Kihara D. In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. Bmc Bioinformatics. 14: S2. PMID 23514353 DOI: 10.1186/1471-2105-14-S3-S2  1
2013 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, ... ... Kihara D, et al. A large-scale evaluation of computational protein function prediction. Nature Methods. 10: 221-7. PMID 23353650 DOI: 10.1038/Nmeth.2340  1
2013 La D, Kong M, Hoffman W, Choi YI, Kihara D. Predicting permanent and transient protein–protein interfaces Proteins. 81: 805-818. PMID 23239312 DOI: 10.1002/Prot.24235  1
2013 Kihara D, Esquivel-Rodriguez J. Macromolecular Structure Modeling and Electron Microscopy Fitting using 3D Zernike Descriptors Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.1956  1
2012 Khan I, Chitale M, Rayon C, Kihara D. Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins. Bmc Proceedings. 6: S5. PMID 23173871 DOI: 10.1186/1753-6561-6-S7-S5  1
2012 Esquivel-Rodríguez J, Kihara D. Effect of conformation sampling strategies in genetic algorithm for multiple protein docking Bmc Proceedings. 6: 1-6. PMID 23173833 DOI: 10.1186/1753-6561-6-S7-S4  1
2012 Yuan C, Chen H, Kihara D. Effective inter-residue contact definitions for accurate protein fold recognition. Bmc Bioinformatics. 13: 292. PMID 23140471 DOI: 10.1186/1471-2105-13-292  1
2012 Sael L, Kihara D. Constructing patch-based ligand-binding pocket database for predicting function of proteins Bmc Bioinformatics. 13: 1-5. PMID 22536870 DOI: 10.1186/1471-2105-13-S2-S7  1
2012 Esquivel-Rodríguez J, Kihara D. Evaluation of multiple protein docking structures using correctly predicted pairwise subunits Bmc Bioinformatics. 13: 1-4. PMID 22536869 DOI: 10.1186/1471-2105-13-S2-S6  1
2012 Esquivel-Rodríguez J, Yang YD, Kihara D. Multi-LZerD: multiple protein docking for asymmetric complexes. Proteins. 80: 1818-33. PMID 22488467 DOI: 10.1002/Prot.24079  1
2012 Esquivel-Rodríguez J, Kihara D. Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors. Journal of Physical Chemistry B. 116: 6854-6861. PMID 22417139 DOI: 10.1021/Jp212612T  1
2012 Mullins EA, Starks CM, Francois JA, Sael L, Kihara D, Kappock TJ. Formyl-coenzyme A (CoA):oxalate CoA-transferase from the acidophile Acetobacter aceti has a distinctive electrostatic surface and inherent acid stability. Protein Science : a Publication of the Protein Society. 21: 686-96. PMID 22374910 DOI: 10.1002/Pro.2054  1
2012 Jamroz M, Kolinski A, Kihara D. Structural features that predict real‐value fluctuations of globular proteins Proteins. 80: 1425-1435. PMID 22328193 DOI: 10.1002/Prot.24040  1
2012 Sael L, Kihara D. Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison. Proteins. 80: 1177-1195. PMID 22275074 DOI: 10.1002/Prot.24018  1
2012 Sael L, Chitale M, Kihara D. Structure- and sequence-based function prediction for non-homologous proteins. Journal of Structural and Functional Genomics. 13: 111-123. PMID 22270458 DOI: 10.1007/S10969-012-9126-6  1
2012 Li B, Kihara D. Protein docking prediction using predicted protein-protein interface Bmc Bioinformatics. 13: 7-7. PMID 22233443 DOI: 10.1186/1471-2105-13-7  1
2012 La D, Kihara D. A novel method for protein-protein interaction site prediction using phylogenetic substitution models Proteins. 80: 126-141. PMID 21989996 DOI: 10.1002/Prot.23169  1
2012 Esquivel-Rodriguez J, Kihara D. Computational Methods for Multiple Protein Docking for Asymmetric Complexes Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.1431  1
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Kihara D, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031  1
2011 Chitale M, Palakodety S, Kihara D. Quantification of protein group coherence and pathway assignment using functional association Bmc Bioinformatics. 12: 373-373. PMID 21929787 DOI: 10.1186/1471-2105-12-373  1
2011 Kihara D, Sael L, Chikhi R, Esquivel-Rodriguez J. Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking. Current Protein & Peptide Science. 12: 520-30. PMID 21787306 DOI: 10.2174/138920311796957612  1
2011 Jagadeesan B, Fleishman Littlejohn AE, Amalaradjou MA, Singh AK, Mishra KK, La D, Kihara D, Bhunia AK. N-terminal Gly(224)-Gly(411) domain in Listeria adhesion protein interacts with host receptor Hsp60. Plos One. 6: e20694. PMID 21738582 DOI: 10.1371/Journal.Pone.0020694  1
2011 Lundgaard GL, Daniels NE, Pyndiah S, Cassimere EK, Ahmed KM, Rodrigue A, Kihara D, Post CB, Sakamuro D. Identification of a novel effector domain of BIN1 for cancer suppression. Journal of Cellular Biochemistry. 112: 2992-3001. PMID 21678469 DOI: 10.1002/Jcb.23222  1
2011 Liu PF, Kihara D, Park C. Energetics-based discovery of protein-ligand interactions on a proteomic scale. Journal of Molecular Biology. 408: 147-62. PMID 21338610 DOI: 10.1016/J.Jmb.2011.02.026  1
2011 Chen H, Kihara D. Effect of using suboptimal alignments in template‐based protein structure prediction Proteins. 79: 315-334. PMID 21058297 DOI: 10.1002/Prot.22885  1
2011 Huang Z, Surana P, Kihara D, Meilan R, Woeste K. 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. DOI: 10.4236/Ajmb.2011.13015  0.01
2011 Sael L, Kihara D. Local Protein Surface Patch Method for Protein-Ligand Binding Prediction Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.2343  1
2011 Sael L, Esquivel-Rodriguez J, Kihara D. Novel Methods for Rapid Comparison and Multimeric Protein Complex Fitting for Low-Resolution Electron Microscopy Data Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.1962  1
2010 Sael L, Kihara D. Binding ligand prediction for proteins using partial matching of local surface patches. International Journal of Molecular Sciences. 11: 5009-5026. PMID 21614188 DOI: 10.3390/Ijms11125009  1
2010 Sael L, Kihara D. Improved protein surface comparison and application to low-resolution protein structure data Bmc Bioinformatics. 11: 1-12. PMID 21172052 DOI: 10.1186/1471-2105-11-S11-S2  1
2010 Yang YD, Spratt P, Chen H, Park C, Kihara D. Sub-AQUA: real-value quality assessment of protein structure models. Protein Engineering, Design & Selection : Peds. 23: 617-32. PMID 20525730 DOI: 10.1093/Protein/Gzq030  1
2010 Hawkins T, Chitale M, Kihara D. Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP Bmc Bioinformatics. 11: 265-265. PMID 20482861 DOI: 10.1186/1471-2105-11-265  1
2010 Chikhi R, Sael L, Kihara D. Real-time ligand binding pocket database search using local surface descriptors. Proteins. 78: 2007-28. PMID 20455259 DOI: 10.1002/Prot.22715  1
2010 Sael L, Kihara D. Characterization and Classification of Local Protein Surfaces Using Self-Organizing Map International Journal of Knowledge Discovery in Bioinformatics. 1: 32-47. DOI: 10.4018/Jkdb.2010100203  1
2010 Kihara D, Venkatraman V, Yang YD, Sael L. A Unified Protein Docking Procedure with a Shape Complementarity Screening using 3D Zernike Descriptors Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.2514  1
2009 Venkatraman V, Chakravarthy PR, Kihara D. Application of 3D Zernike descriptors to shape-based ligand similarity searching. Journal of Cheminformatics. 1: 19. PMID 20150998 DOI: 10.1186/1758-2946-1-19  1
2009 Venkatraman V, Yang YD, Sael L, Kihara D. Protein-protein docking using region-based 3D Zernike descriptors. Bmc Bioinformatics. 10: 407. PMID 20003235 DOI: 10.1186/1471-2105-10-407  1
2009 La D, Esquivel-Rodríguez J, Venkatraman V, Li B, Sael L, Ueng S, Ahrendt S, Kihara D. 3D-SURFER: software for high-throughput protein surface comparison and analysis. Bioinformatics (Oxford, England). 25: 2843-4. PMID 19759195 DOI: 10.1093/Bioinformatics/Btp542  1
2009 Venkatraman V, Sael L, Kihara D. Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors. Cell Biochemistry and Biophysics. 54: 23-32. PMID 19521674 DOI: 10.1007/S12013-009-9051-X  1
2009 Kihara D, Chen H, Yang YD. Quality assessment of protein structure models. Current Protein & Peptide Science. 10: 216-28. PMID 19519452 DOI: 10.2174/138920309788452173  1
2009 Chitale M, Hawkins T, Park C, Kihara D. ESG: extended similarity group method for automated protein function prediction Bioinformatics. 25: 1739-1745. PMID 19435743 DOI: 10.1093/Bioinformatics/Btp309  1
2009 Hawkins T, Chitale M, Luban S, Kihara D. PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data Proteins. 74: 566-582. PMID 18655063 DOI: 10.1002/Prot.22172  1
2009 Yang Y, Park C, Kihara D. Protein Structure Prediction Without Optimizing Weighting Factors For Scoring Function Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.3448  1
2009 Kihara D, Sael L, Chikhi R. Local surface shape-based protein function prediction using Zernike descriptors Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.3435  1
2008 Sael L, La D, Li B, Rustamov R, Kihara D. Rapid comparison of properties on protein surface. Proteins. 73: 1-10. PMID 18618695 DOI: 10.1002/Prot.22141  1
2008 Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Kihara D, Knight TF, Pico AR, Siegele DA, Wanner BL, Welch RD. The emerging world of wikis. Science (New York, N.Y.). 320: 1289-90. PMID 18535227 DOI: 10.1126/Science.320.5881.1289B  1
2008 Yang YD, Park C, Kihara D. Threading without optimizing weighting factors for scoring function. Proteins. 73: 581-96. PMID 18473394 DOI: 10.1002/Prot.22082  1
2008 Hawkins T, Chitale M, Kihara D. New paradigm in protein function prediction for large scale omics analysis Molecular Biosystems. 4: 223-231. PMID 18437265 DOI: 10.1039/B718229E  1
2008 Sael L, Li B, La D, Fang Y, Ramani K, Rustamov R, Kihara D. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins. 72: 1259-73. PMID 18361455 DOI: 10.1002/Prot.22030  1
2008 Li B, Turuvekere S, Agrawal M, La D, Ramani K, Kihara D. Characterization of local geometry of protein surfaces with the visibility criterion Proteins. 71: 670-683. PMID 17975834 DOI: 10.1002/Prot.21732  1
2008 Chitale M, Hawkins T, Park C, Kihara D. ESG: Extended Similarity Group method for automated protein function prediction Nature Precedings. DOI: 10.1038/Npre.2008.2193.1  1
2007 Chen H, Kihara D. Estimating quality of template-based protein models by alignment stability. Proteins. 71: 1255-1274. PMID 18041762 DOI: 10.1002/Prot.21819  1
2007 Hawkins T, Kihara D. Function prediction of uncharacterized proteins. Journal of Bioinformatics and Computational Biology. 5: 1-30. PMID 17477489 DOI: 10.1142/S0219720007002503  1
2007 Luban S, Kihara D. Comparative genomics of small RNAs in bacterial genomes Omics a Journal of Integrative Biology. 11: 58-73. PMID 17411396 DOI: 10.1089/Omi.2006.0005  1
2006 Hu J, Yang YD, Kihara D. EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences. Bmc Bioinformatics. 7: 342. PMID 16839417 DOI: 10.1186/1471-2105-7-342  1
2006 Hawkins T, Luban S, Kihara D. Enhanced automated function prediction using distantly related sequences and contextual association by PFP Protein Science. 15: 1550-1556. PMID 16672240 DOI: 10.1110/Ps.062153506  1
2005 Hu J, Li B, Kihara D. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Research. 33: 4899-913. PMID 16284194 DOI: 10.1093/Nar/Gki791  1
2005 Kihara D. The effect of long‐range interactions on the secondary structure formation of proteins Protein Science. 14: 1955-1963. PMID 15987894 DOI: 10.1110/Ps.051479505  0.01
2004 Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm Proteins: Structure, Function and Genetics. 56: 502-518. PMID 15229883 DOI: 10.1002/Prot.20106  1
2004 Kihara D, Skolnick J. Microbial Genomes Have over 72% Structure Assignment by the Threading Algorithm PROSPECTOR_Q Proteins: Structure, Function and Genetics. 55: 464-473. PMID 15048836 DOI: 10.1002/Prot.20044  1
2003 Kihara D, Skolnick J. The PDB is a covering set of small protein structures Journal of Molecular Biology. 334: 793-802. PMID 14636603 DOI: 10.1016/J.Jmb.2003.10.027  1
2003 Skolnick J, Zhang Y, Arakaki AK, Kolinski A, Boniecki M, Szilágyi A, Kihara D. TOUCHSTONE: a unified approach to protein structure prediction. Proteins. 53: 469-79. PMID 14579335 DOI: 10.1002/Prot.10551  1
2003 Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione GT, Kolinski A, Skolnick J. TOUCHSTONEX: Protein structure prediction with sparse NMR data Proteins: Structure, Function and Genetics. 53: 290-306. PMID 14517980 DOI: 10.1002/Prot.10499  1
2002 Zhang Y, Kihara D, Skolnick J. Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding Proteins: Structure, Function and Genetics. 48: 192-201. PMID 12112688 DOI: 10.1002/Prot.10141  1
2002 Kihara D, Zhang Y, Lu H, Kolinski A, Skolnick J. Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome Proceedings of the National Academy of Sciences of the United States of America. 99: 5993-5998. PMID 11959918 DOI: 10.1073/Pnas.092135699  1
2001 Skolnick J, Kolinski A, Kihara D, Betancourt M, Rotkiewicz P, Boniecki M. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement Proteins: Structure, Function and Genetics. 45: 149-156. PMID 11835492 DOI: 10.1002/Prot.1172  1
2001 Kihara D, Lu H, Kolinski A, Skolnick J. TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints Proceedings of the National Academy of Sciences of the United States of America. 98: 10125-10130. PMID 11504922 DOI: 10.1073/Pnas.181328398  1
2001 Kolinski A, Betancourt MR, Kihara D, Rotkiewicz P, Skolnick J. Generalized comparative modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement Proteins: Structure, Function and Genetics. 44: 133-149. PMID 11391776 DOI: 10.1002/Prot.1080  1
2001 Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR - A new approach to threading Proteins: Structure, Function and Genetics. 42: 319-331. PMID 11151004 DOI: 10.1002/1097-0134(20010215)42:3<319::Aid-Prot30>3.0.Co;2-A  1
2000 Igarashi Y, Kihara D, Kanehisa M. Classification and Analysis of Eukaryotic ABC Transporters in Complete Eukarya Genomes Genome Informatics. 11: 274-275. DOI: 10.11234/Gi1990.11.274  1
1997 Kihara D, Kanehisa M. Detection of Membrane Proteins in the Whole Genome Sequences Genome Informatics. 8: 300-301. DOI: 10.11234/Gi1990.8.300  1
1996 Kihara D, Shimizu T, Kanehisa M. A Prediction Method for Transmembrane Segments in Proteins Utilizing Multiple Discrimination Functions Genome Informatics. 7: 244-245. DOI: 10.11234/Gi1990.7.244  1
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