Daron M. Standley

Daron M. Standley Professor standley [at] biken.osaka-u.ac.jp

Education

Ph.D. Chemistry, Columbia University, New York - 1998

BS Physics, Harvey Mudd College, Claremont, CA - 1993

Research & Career

Guest Associate Professor, Center for Advanced Medical Engineering and Informatics, Institute for Protein Research, Osaka University (April, 2006 to September, 2008)

Senior Researcher, Protein Data Bank Japan, Institute for Protein Research, Osaka University (April, 2003 to September, 2008)

Scientific Software Developer Schrödinger, Inc. (September, 1998 to March, 2003)

Awards

Prize for Outstanding Achievement in Education and Research at Osaka University in 2009

Publications

Year Authors Title Publication Cites
2011 A Kitamura, Y Maekawa, H Uehara, K Izumi, I Kawachi, M Nishizawa, ... A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans THE JOURNAL OF CLINICAL INVESTIGATION, 2011, 121, 4150-4160 216
2012 A Patil, S Teraguchi, H Dinh, K Nakai, DM Standley Functional annotation of intrinsically disordered domains by their amino acid content using IDD navigator BIOCOMPUTING, 2012, 2012, 164-175 7
2014 A Vandenbon, S Teraguchi, O Takeuchi, Y Suzuki, DM Standley Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation BMC GENOMICS 15 (S10), S, 2014, 4 2
2012 A Vandenbon, S Teraguchi, S Akira, K Takeda, DM Standley Systems biology approaches to toll‐like receptor signaling WILEY INTERDISCIPLINARY REVIEWS: SYSTEMS BIOLOGY AND MEDICINE, 2012, 4, 497-507 26
2012 A Vandenbon, Y Kumagai, S Akira, DM Standley A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription BMC GENOMICS 13 (S7), S, 2012, 11 11
2013 A Vandenbon, Y Kumagai, S Teraguchi, KM Amada, S Akira, DM Standley A Parzen window-based approach for the detection of locally enriched transcription factor binding sites BMC BIOINFORMATICS, 2013, 14, 26-26 3
2020 AA Koesoema, DM Standley, M Tamura, T Matsuda Access to both enantiomers of substituted 2-tetralol analogs by a highly enantioselective reductase TETRAHEDRON LETTERS, 2020, 151682 0
2020 AA Koesoema, DM Standley, S Ohshima, M Tamura, T Matsuda Control of enantioselectivity in the enzymatic reduction of halogenated acetophenone analogs by substituent positions and sizes TETRAHEDRON LETTERS, 2020, 151820 0
2020 AA Koesoema, DM Standley, T Senda, T Matsuda Impact and relevance of alcohol dehydrogenase enantioselectivities on biotechnological applications APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2020, 1-13 0
2019 AA Koesoema, Y Sugiyama, KT Sriwong, Z Xu, S Verina, DM Standley, ... Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 103 (23-24), 2019, 9529-9541 3
2019 AA Koesoema, Y Sugiyama, Z Xu, DM Standley, M Senda, T Senda, ... Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 103 (23-24), 2019, 9543-9553 4
2019 AA Koesoema, Y Sugiyama, Z Xu, DM Standley, M Senda, T Senda, ... Correction to: Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 103 (23-24), 2019, 9555 0
2013 AJ Hobro, DM Standley, S Ahmad, NI Smith Deconstructing RNA: optical measurement of composition and structure PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2013, 15, 13199-13208 17
2012 AR Kinjo, H Suzuki, R Yamashita, Y Ikegawa, T Kudou, R Igarashi, ... Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format NUCLEIC ACIDS RESEARCH 40 (D1), D453-D, 2012, 460 122
2011 AR Kinjo, Y Kumagai, H Dinh, O Takeuchi, DM Standley Functional characterization of protein domains common to animal viruses and mouse BMC GENOMICS, 2011, 12, 1-10 2
2017 B Nosirov, J Billaud, A Vandenbon, D Diez, E Wijaya, KJ Ishii, ... Mapping circulating serum miRNAs to their immune-related target mRNAs ADVANCES AND APPLICATIONS IN BIOINFORMATICS AND CHEMISTRY: AABC, 2017, 10, 1-1 5
2020 C Ono, T Fukuhara, S Li, J Wang, A Sato, T Izumi, Y Fauzyah, ... Various miRNAs are involved in efficient HCV replication BIORXIV, 2020 0
2015 D Hall, S Li, K Yamashita, R Azuma, JA Carver, DM Standley RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure ANALYTICAL BIOCHEMISTRY, 2015, 472, 52-61 4
2014 D Hall, S Li, K Yamashita, R Azuma, JA Carver, DM Standley A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein BIOPHYSICAL CHEMISTRY, 2014, 190, 50-55 3
2009 D Kuroda, H Shirai, M Lis, A Kinjo, D Standley, H Nakamura Structural classification and modeling of antibody hypervariable loops: knowledge-based approaches: 242 PROTEIN SCIENCE, 2009, 18 0
2017 D Schritt, K Katoh, S Li, DM Standley Modeling Biocatalysts FUTURE DIRECTIONS IN BIOCATALYSIS, 2017, 385-398 0
2019 D Schritt, S Li, J Rozewicki, K Katoh, K Yamashita, W Volkmuth, G Cavet, ... Repertoire builder: high-throughput structural modeling of B and T cell receptors MOLECULAR SYSTEMS DESIGN & ENGINEERING, 2019, 4, 761-768 6
2019 D Yamasoba, K Sato, T Ichinose, T Imamura, L Koepke, S Joas, E Reith, ... N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation NATURE MICROBIOLOGY, 2019, 4, 1532-1544 7
1939 DC Koester, SI Awan, DB Werz, YH Lee, T Ikegami, DM Standley, ... Don’t risk missing out! Subscribe to ChemBioChem. Contact www. wileycustomerhelp. com CHEMBIOCHEM, 1939, 2011, 2011-2011 0
2002 DM STANDLEY AB 1N1T1O PROTE1N STRUCTURE PRED1CT1ON US1NG A S1ZE-DEPENDENT TERT1ARY FOLD1NG POTENT1AL COMPUTATIONAL METHODS FOR PROTEIN FOLDING, 2002, 223 0
2014 DM Standley 2SCP-07 Intrinsic disorder mediates cooperative signal transduction in STIM1 (構造バイオインフォマティクスによる蛋白質機能予測・解析, シンポジウム, 第 52 回日本生物物理学会年会 (2014 年度)) 生物物理 54 (1), S, 2014, 133 0
1999 DM Standley Protein tertiary structure prediction by constrained and unconstrained energy minimization. , 1999 0
2008 DM Standley, AR Kinjo, H Nakamura Functional annotation by sequence-weighted structural alignments ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 64, C460-C, 2008, 460 0
2008 DM Standley, AR Kinjo, K Kinoshita, H Nakamura Protein structure databases with new web services for structural biology and biomedical research BRIEFINGS IN BIOINFORMATICS, 2008, 9, 276-285 44
2008 DM Standley, AR Kinjo, M Lis, M van der Giezen, H Nakamura Structure-based functional annotation of protein sequences guided by comparative models THE SECOND INTERNATIONAL SYMPOSIUM ON OPTIMIZATION AND SYSTEMS BIOLOGY …, 2008 1
2008 DM Standley, H Nakamura From structures to functions: annotation by structural bioinformatics TANPAKUSHITSU KAKUSAN KOSO. PROTEIN, NUCLEIC ACID, ENZYME, 2008, 53, 638-638 0
2005 DM Standley, H Nakamura Beyond Text-based Queries at the Protein Data Bank, Japan ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 61, C482-C, 2005, 482 0
2007 DM Standley, H Toh, H Nakamura ASH structure alignment package: sensitivity and selectivity in domain classification BMC BIOINFORMATICS, 2007, 8, 116-116 47
2004 DM Standley, H Toh, H Nakamura Detecting local structural similarity in proteins by maximizing number of equivalent residues PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2004, 57, 381-391 35
2005 DM Standley, H Toh, H Nakamura GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures BMC BIOINFORMATICS, 2005, 6, 221-221 32
2008 DM Standley, H Toh, H Nakamura Functional annotation by sequence‐weighted structure alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2008, 72, 1333-1351 9
2007 DM Standley, H Toh, H Nakamura S08I2 Functional Annotation Sequence-weighted Structure Alignments (Bioinformatics in the Era of Structural Proteomics) SEIBUTSU BUTSURI 47 (SUPPLEMENT), S, 2007, 11 0
2006 DM Standley, H Toh, H Nakamura 1P481 Real-time Structure Based Queries at the Protein Data Bank japan (23. Bioinformatics, genomics and proteomics (I), Poster Session, Abstract, Meeting Program of EABS & BSJ … SEIBUTSU BUTSURI 46 (SUPPLEMENT2), S, 2006, 267 0
2019 DM Standley, JDO Nieri, S Li, D Schritt, K Yamashita Immunological entity clustering software US PATENT APP. 16/333,875, 2019 0
1998 DM Standley, JR Gunn, RA Friesner, AE McDermott Tertiary structure prediction of mixed α/β proteins via energy minimization PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 1998, 33, 240-252 30
2009 DM Standley, M Lis, AR Kinjo, H Nakamura Protein Function Annotation from Sequences and Structures with Tools at PDBj 亚洲晶体学联合大会摘要集, 2009 0
2012 DM Standley, M van der Giezen Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly RES. REP. BIOCHEM, 2012, 2, 1-8 5
2010 DM Standley, R Yamashita, AR Kinjo, H Toh, H Nakamura SeSAW: balancing sequence and structural information in protein functional mapping BIOINFORMATICS, 2010, 26, 1258-1259 12
2006 DM Standley, R Yamashita, K Ichikawa, K Kinoshita, N Ito, H Nakamura New Web Services for Structural Genomics at PDBj: Development of POBML and its Applications ABSTRACT BOOK OF THE 4TH ISGO INTERNATIONAL CONFERENCE ON STRUCTURAL GENOMICS, 2006 0
1999 DM Standley, VA Eyrich, AK Felts, RA Friesner, AE McDermott A branch and bound algorithm for protein structure refinement from sparse NMR data sets JOURNAL OF MOLECULAR BIOLOGY, 1999, 285, 1691-1710 43
2001 DM Standley, VA Eyrich, Y An, DL Pincus, JR Gunn, RA Friesner Protein structure prediction using a combination of sequence‐based alignment, constrained energy minimization, and structural alignment PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS 45 (S5), 2001, 133-139 21
2001 DM Standley, VA Eyrich, Y An, DL Pincus, JR Gunn, RA Friesner Ab Initio: Prediction Reports-Protein Structure Prediction Using a Combination of Sequence-Based Alignment, Constrained Energy Minimization, and Structural Alignment Published … PROTEINS-STRUCTURE FUNCTION AND GENETICS, 2001, 133-139 0
2006 DM Standley, Y Yonezawa, Y Goto, H Nakamura Flexible docking of an amyloid-forming peptide from β2-microglobulin FEBS LETTERS, 2006, 580, 6199-6205 8
2013 E KANAMORI, Y MURAKAMI, JOY SARMIENTO, S LIANG, ... PREDICTION OF PROTEIN-PROTEIN COMPLEX STRUCTURES BIOMOLECULAR FORMS AND FUNCTIONS: A CELEBRATION OF 50 YEARS OF THE …, 2013 1
2007 E Kanamori, Y Murakami, Y Tsuchiya, DM Standley, H Nakamura, ... Docking of protein molecular surfaces with evolutionary trace analysis PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2007, 69, 832-838 29
2012 E Kanamori, Y Tsuchiya, Y Murakami, J Sarmiento, S Liang, D Standley, ... Prediction of Protein-Protein Complex Structures Using a Docking Server, surFit: 317 PROTEIN SCIENCE, 2012, 21 0
2019 H Fukuda, S Li, L Sardo, JL Smith, K Yamashita, AD Sarca, K Shirakawa, ... Structural Determinants of the APOBEC3G N-terminal domain for HIV-1 RNA association FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 2019, 9, 129-129 2
2018 H Hanieh, K Masuda, H Metwally, JP Chalise, M Mohamed, KK Nyati, ... Arid5a stabilizes OX40 mRNA in murine CD4+ T cells by recognizing a stem‐loop structure in its 3′UTR EUROPEAN JOURNAL OF IMMUNOLOGY, 2018, 48, 593-604 14
2011 H Iwasaki, O Takeuchi, S Teraguchi, K Matsushita, T Uehata, K Kuniyoshi, ... The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR–IL-1R by controlling degradation of regnase-1 NATURE IMMUNOLOGY, 2011, 12, 1167-1175 188
2020 H Metwally, T Tanaka, S Li, G Parajuli, S Kang, H Hanieh, S Hashimoto, ... Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production SCIENCE SIGNALING, 2020, 13 0
2014 H Morikawa, N Ohkura, A Vandenbon, M Itoh, S Nagao-Sato, H Kawaji, ... Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, 2014, 111, 5289-5294 93
2005 H Nakamura, N Ito, R Yamashita, D Standley, A Paehler, A Yoshihara PDBML: the XML-based Database and its Applications ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 61, C128-C, 2005, 128 0
2014 H Shirai, K Ikeda, K Yamashita, Y Tsuchiya, J Sarmiento, S Liang, ... High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2014, 82, 1624-1635 42
2006 HM Berman, SK Burley, W Chiu, A Sali, A Adzhubei, PE Bourne, ... Outcome of a workshop on archiving structural models of biological macromolecules STRUCTURE, 2006, 14, 1211-1217 51
2017 J Hirano, T Okamoto, Y Sugiyama, T Suzuki, S Kusakabe, M Tokunaga, ... Characterization of SPP inhibitors suppressing propagation of HCV and protozoa PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES 114 (50), E10782-, 2017, 10791 5
2011 J Ikebe, DM Standley, H Nakamura, J Higo Ab initio simulation of a 57‐residue protein in explicit solvent reproduces the native conformation in the lowest free‐energy cluster PROTEIN SCIENCE, 2011, 20, 187-196 24
2007 J Liao, K Zhuo, S Yu, X Li, D Li Bursaphelenchus uncispicularis n. sp.(Nematoda: Parasitaphelenchidae) from Pinus yunnanensis in China NEMATOLOGY, 2007, 9, 237-242 12
2015 J Ohshima, M Sasai, J Liu, K Yamashita, JS Ma, Y Lee, H Bando, ... RabGDIα is a negative regulator of interferon-γ–inducible GTPase-dependent cell-autonomous immunity to Toxoplasma gondii PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES 112 (33), E4581-, 2015, 4590 20
2019 J Rozewicki, S Li, KM Amada, DM Standley, K Katoh MAFFT-DASH: integrated protein sequence and structural alignment NUCLEIC ACIDS RESEARCH 47 (W1), W5-W, 2019, 10 36
2020 K Fukushima, T Satoh, F Sugihara, Y Sato, T Okamoto, Y Mitsui, S Yoshio, ... Dysregulated Expression of the Nuclear Exosome Targeting Complex Component Rbm7 in Nonhematopoietic Cells Licenses the Development of Fibrosis IMMUNITY 52 (3), 542-556., 2020, 13 1
2008 K Hamblin, DM Standley, MB Rogers, A Stechmann, AJ Roger, R Maytum, ... Localization and nucleotide specificity of Blastocystis succinyl‐CoA synthetase MOLECULAR MICROBIOLOGY, 2008, 68, 1395-1405 24
2013 K Katoh, DM Standley MAFFT multiple sequence alignment software version 7: improvements in performance and usability MOLECULAR BIOLOGY AND EVOLUTION, 2013, 30, 772-780 14121
2014 K Katoh, DM Standley MAFFT: iterative refinement and additional methods MULTIPLE SEQUENCE ALIGNMENT METHODS, 2014, 131-146 255
2016 K Katoh, DM Standley A simple method to control over-alignment in the MAFFT multiple sequence alignment program BIOINFORMATICS, 2016, 32, 1933-1942 194
2012 K Maruyama, M Fukasaka, A Vandenbon, T Saitoh, T Kawasaki, T Kondo, ... The transcription factor Jdp2 controls bone homeostasis and antibacterial immunity by regulating osteoclast and neutrophil differentiation IMMUNITY, 2012, 37, 1024-1036 55
2016 K Masuda, B Ripley, KK Nyati, PK Dubey, MMU Zaman, H Hanieh, M Higa, ... Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA JOURNAL OF EXPERIMENTAL MEDICINE, 2016, 213, 605-619 41
2009 K Matsushita, O Takeuchi, DM Standley, Y Kumagai, T Kawagoe, ... Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay NATURE, 2009, 458, 1185-1190 446
2010 K Oshima, D Standley, E Kanamori, Y Murakami, T Oroguchi, M Ikeguchi, ... 3P294 Structural modeling for protein complexes using small angle x-ray scattering (Bioinformatics: Structural genomics, The 48th Annual Meeting of the Biophysical Society of … SEIBUTSU BUTSURI 50 (SUPPLEMENT2), S, 2010, 197 0
2010 K Oshima, D Standley, E Kanamori, Y Murakami, T Oroguchi, M Ikeguchi, ... 3P294 X 線小角散乱を用いたタンパク質複合体の構造モデリング (生命情報科学-構造ゲノミクス, 第 48 回日本生物物理学会年会) 生物物理 50 (2), S, 2010, 197 0
2016 K Takeda, S Sakakibara, D Motooka, S Nakamura, K Yamashita, ... Identification of Nasal Resident Bacteria as Causative Allergens in Eosinophilic Chronic Rhinosinusitis EUROPEAN JOURNAL OF IMMUNOLOGY, 2016, 46, 1114-1114 0
2019 K Takeda, S Sakakibara, K Yamashita, D Motooka, S Nakamura, ... Allergic conversion of protective mucosal immunity against nasal bacteria in patients with chronic rhinosinusitis with nasal polyposis JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY 143 (3), 1163-1175., 2019, 15 14
2014 K Yamashita, K Ikeda, K Amada, S Liang, Y Tsuchiya, H Nakamura, ... Kotai Antibody Builder: automated high-resolution structural modeling of antibodies BIOINFORMATICS, 2014, 30, 3279-3280 37
2010 K Zhuo, R Cui, WM Ye, M Luo, H Wang, X Hu, J Liao Morphological and molecular characterization of Aphelenchoides fujianensis n. sp.(Nematoda: Aphelenchoididae) from Pinus massoniana in China ZOOTAXA, 2010, 2509, 39-52 35
2017 KK Nyati, K Masuda, MMU Zaman, PK Dubey, D Millrine, JP Chalise, ... TLR4-induced NF-κB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a NUCLEIC ACIDS RESEARCH, 2017, 45, 2687-2703 49
2011 M Fernandez, Y Kumagai, DM Standley, A Sarai, K Mizuguchi, S Ahmad Prediction of dinucleotide-specific RNA-binding sites in proteins BMC BIOINFORMATICS 12 (S13), S, 2011, 5 34
2017 M Hayashi, T Aoshi, Y Haseda, K Kobiyama, E Wijaya, N Nakatsu, ... Advax, a delta inulin microparticle, potentiates in-built adjuvant property of co-administered vaccines EBIOMEDICINE, 2017, 15, 127-136 14
2011 M Lis, T Kim, JJ Sarmiento, D Kuroda, HV Dinh, AR Kinjo, K Amada, ... Bridging the gap between single-template and fragment based protein structure modeling using Spanner IMMUNOME RESEARCH, 2011, 7, 1-1 17
2015 M Onishi, K Ozasa, K Kobiyama, K Ohata, M Kitano, K Taniguchi, ... Hydroxypropyl-β-cyclodextrin spikes local inflammation that induces Th2 cell and T follicular helper cell responses to the coadministered antigen THE JOURNAL OF IMMUNOLOGY, 2015, 194, 2673-2682 39
2017 M Sasai, N Sakaguchi, JS Ma, S Nakamura, T Kawabata, H Bando, Y Lee, ... Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense NATURE IMMUNOLOGY, 2017, 18, 899-899 34
2009 M Yamamoto, DM Standley, S Takashima, H Saiga, M Okuyama, ... A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3 JOURNAL OF EXPERIMENTAL MEDICINE, 2009, 206, 2747-2760 217
2016 M Yokogawa, T Tsushima, NN Noda, H Kumeta, Y Enokizono, ... Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions SCIENTIFIC REPORTS, 2016, 6, 1-10 24
2014 MF Lensink, IH Moal, PA Bates, PL Kastritis, ASJ Melquiond, E Karaca, ... Blind prediction of interfacial water positions in CAPRI PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2014, 82, 620-632 44
2014 N Takemura, T Kawasaki, J Kunisawa, S Sato, A Lamichhane, ... Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome NATURE COMMUNICATIONS, 2014, 5, 1-15 91
2006 P Gou, GT Hanke, Y Kimata-Ariga, DM Standley, A Kubo, I Taniguchi, ... Higher order structure contributes to specific differences in redox potential and electron transfer efficiency of root and leaf ferredoxins BIOCHEMISTRY, 2006, 45, 14389-14396 26
2009 R Apostolov, Y Yonezawa, DM Standley, G Kikugawa, Y Takano, ... Membrane attachment facilitates ligand access to the active site in monoamine oxidase A BIOCHEMISTRY, 2009, 48, 5864-5873 13
2013 R Moretti, SJ Fleishman, R Agius, M Torchala, PA Bates, PL Kastritis, ... Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2013, 81, 1980-1987 92
2017 R Yonehara, S Nada, T Nakai, M Nakai, A Kitamura, A Ogawa, ... Structural basis for the assembly of the Ragulator-Rag GTPase complex NATURE COMMUNICATIONS, 2017, 8, 1-11 26
2010 RJ Milewski, Y Kumagai, K Fujita, DM Standley, NI Smith Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis IMMUNOME RESEARCH, 2010, 6, 1-10 7
2019 S Li, J Wilamowski, S Teraguchi, FJ van Eerden, J Rozewicki, A Davila, ... Structural modeling of lymphocyte receptors and their antigens IN VITRO DIFFERENTIATION OF T-CELLS, 2019, 207-229 1
2014 S Li, K Yamashita, KM Amada, DM Standley Quantifying sequence and structural features of protein–RNA interactions NUCLEIC ACIDS RESEARCH, 2014, 42, 10086-10098 31
2011 S Liang, C Zhang, DM Standley Protein loop selection using orientation‐dependent force fields derived by parameter optimization PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2011, 79, 2260-2267 7
2012 S Liang, C Zhang, J Sarmiento, DM Standley Protein loop modeling with optimized backbone potential functions JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8, 1820-1827 11
2011 S Liang, D Zheng, C Zhang, DM Standley Fast and accurate prediction of protein side-chain conformations BIOINFORMATICS, 2011, 27, 2913-2914 37
2010 S Liang, D Zheng, DM Standley, B Yao, M Zacharias, C Zhang EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results BMC BIOINFORMATICS, 2010, 11, 1-6 111
2013 S Liang, D Zheng, DM Standley, H Guo, C Zhang A novel function prediction approach using protein overlap networks BMC SYSTEMS BIOLOGY, 2013, 7, 61-61 17
2011 S Liang, Y Zhou, N Grishin, DM Standley Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions JOURNAL OF COMPUTATIONAL CHEMISTRY, 2011, 32, 1680-1686 30
2017 S Sakakibara, T Arimori, K Yamashita, H Jinzai, D Motooka, S Nakamura, ... Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus SCIENTIFIC REPORTS, 2017, 7, 1-14 10
2016 S Sakakibara, T Arimori, K Yamashita, H Jinzai, D Motooka, S Nakamura, ... Antigen-specific maturation of autoantibodies in systemic lupus erythematosus EUROPEAN JOURNAL OF IMMUNOLOGY, 2016, 46, 313-314 0
2014 S Tartey, K Matsushita, A Vandenbon, D Ori, T Imamura, T Mino, ... Akirin2 is critical for inducing inflammatory genes by bridging IκB‐ζ and the SWI/SNF complex THE EMBO JOURNAL, 2014, 33, 2332-2348 56
2010 S Teraguchi, A Patil, DM Standley Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins BMC BIOINFORMATICS 11 (S7), S, 2010, 7 9
2011 S Teraguchi, Y Kumagai, A Vandenbon, S Akira, DM Standley Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations PHYSICAL REVIEW E, 2011, 84, 62903-62903 9
2011 SJ Fleishman, TA Whitehead, EM Strauch, JE Corn, S Qin, HX Zhou, ... Community-wide assessment of protein-interface modeling suggests improvements to design methodology JOURNAL OF MOLECULAR BIOLOGY, 2011, 414, 289-302 132
2014 T Hirano, Y Iesato, Y Toriyama, A Imai, T Murata Detection of fovea-threatening diabetic macular edema by optical coherence tomography to maintain good vision by prophylactic treatment OPHTHALMIC RESEARCH, 2014, 52, 65-73 14
2010 T Katayama, K Arakawa, M Nakao, K Ono, KF Aoki-Kinoshita, ... The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows JOURNAL OF BIOMEDICAL SEMANTICS, 2010, 1, 8-8 48
2013 T Kawasaki, N Takemura, DM Standley, S Akira, T Kawai The second messenger phosphatidylinositol-5-phosphate facilitates antiviral innate immune signaling CELL HOST & MICROBE, 2013, 14, 148-158 35
2016 T Kouwaki, T Okamoto, A Ito, Y Sugiyama, K Yamashita, T Suzuki, ... Hepatocyte factor JMJD5 regulates hepatitis B virus replication through interaction with HBx JOURNAL OF VIROLOGY, 2016, 90, 3530-3542 17
2019 T Mino, N Iwai, M Endo, K Inoue, K Akaki, F Hia, T Uehata, T Emura, ... Translation-dependent unwinding of stem–loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs NUCLEIC ACIDS RESEARCH, 2019, 47, 8838-8859 1
2015 T Mino, Y Murakawa, A Fukao, A Vandenbon, HH Wessels, D Ori, ... Regnase-1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms CELL, 2015, 161, 1058-1073 180
2010 T Satoh, O Takeuchi, A Vandenbon, K Yasuda, Y Tanaka, Y Kumagai, ... The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection NATURE IMMUNOLOGY, 2010, 11, 936-944 845
2009 T Schwede, A Sali, B Honig, M Levitt, HM Berman, D Jones, SE Brenner, ... Outcome of a workshop on applications of protein models in biomedical research STRUCTURE, 2009, 17, 151-159 119
2013 T Uehata, H Iwasaki, A Vandenbon, K Matsushita, E Hernandez-Cuellar, ... Malt1-Induced Cleavage of Regnase-1 in CD4+ Helper T Cells Regulates Immune Activation CELL, 2013, 153, 1036-1049 202
1999 VA Eyrich, DM Standley, AK Felts, RA Friesner Protein tertiary structure prediction using a branch and bound algorithm PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 1999, 35, 41-57 70
1999 VA Eyrich, DM Standley, RA Friesner Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set JOURNAL OF MOLECULAR BIOLOGY, 1999, 288, 725-742 72
2002 VA Eyrich, DM Standley, RA Friesner Ab initio protein structure prediction using a size-dependent tertiary folding potential ADVANCES IN CHEMICAL PHYSICS, 2002, 120, 223-264 6
2000 VA Eyrich, DM Standley, RA Friesner Global Optimization and Sampling in the Context of Tertiary Structure Prediction: A Comparison of Two Algorithms OPTIMIZATION IN COMPUTATIONAL CHEMISTRY AND MOLECULAR BIOLOGY, 2000, 57-71 0
2013 Y Enokizono, H Kumeta, K Funami, M Horiuchi, J Sarmiento, K Yamashita, ... Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, 2013, 110, 19908-19913 47
2014 Y Furukawa, S Teraguchi, T Ikegami, O Dagliyan, L Jin, D Hall, ... Intrinsic disorder mediates cooperative signal transduction in STIM1 JOURNAL OF MOLECULAR BIOLOGY, 2014, 426, 2082-2097 23
2013 Y Furukawa, S Teraguchi, T Ikegami, Y Suenari, O Dagliyan, L Jin, D Hall, ... Calcium-dependent Unfolding of the STIM1 EF-SAM Domain Drives Cooperative Calcium Influx: 362 PROTEIN SCIENCE, 2013, 22, 141-142 0
2016 Y Kamikawa, Y Hori, K Yamashita, L Jin, S Hirayama, DM Standley, ... Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins CHEMICAL SCIENCE, 2016, 7, 308-314 18
2020 Y Lee, H Yamada, A Pradipta, JS Ma, M Okamoto, H Nagaoka, ... Initial phospholipid-dependent Irgb6 targeting to Toxoplasma gondii vacuoles mediates host defense LIFE SCIENCE ALLIANCE, 2020, 3 1
2008 Y Tsuchiya, E Kanamori, DM Standley, H Nakamura, K Kinoshita Development of a scoring method for predicting protein complex structures ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 64, C227-C, 2008, 227 0
2011 Y YONEZAWA, DM STANDLEY, H SHIMOYAMA, H NAKAMURA A QM/MM Molecular Dynamics Simulation Study of the Cis-Trans Isomerization Process of N-Methylacetamide PEPTIDE SCIENCE: PROCEEDINGS OF THE... JAPANESE PEPTIDE SYMPOSIUM, 2011, 2010, 151-151 0
2011 Y Yonezawa, DM Standley, H Nakamura Degree of pyramidality governs the height and peak position of the free-energy-barrier for the cis–trans isomerization of N-Methylacetamide CHEMICAL PHYSICS LETTERS 503 (1-3), 2011, 139-144 3
2011 YH Lee, T Ikegami, DM Standley, K Sakurai, T Hase, Y Goto Binding Energetics of Ferredoxin‐NADP+ Reductase with Ferredoxin and Its Relation to Function CHEMBIOCHEM, 2011, 12, 2062-2070 21
2001 YL An, D Standley, D Pincus, V Eyrich, RA Friesner Fold recognition using composite structural templates followed by constrained global minimization. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 222, U411-U, 2001, 411 0
2019 Z Xu, S Li, J Rozewicki, K Yamashita, S Teraguchi, T Inoue, R Shinnakasu, ... Functional clustering of B cell receptors using sequence and structural features MOLECULAR SYSTEMS DESIGN & ENGINEERING, 2019, 4, 769-778 1
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