UCSF Chimera—A visualization system for exploratory research and analysis
Abstract
The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real‐world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1605–1612, 2004
Citing Literature
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- Jan Schulz, Anika Kreienbrink, Peter Coburger, Benedikt Schwarze, Toni Grell, Peter Lönnecke and Evamarie Hey‐Hawkins, 12‐Vertex Zwitterionic Bis‐phosphonium‐nido‐carborates through Ring‐Opening Reactions of 1,2‐Diphosphetanes, Chemistry – A European Journal, 24, 23, (6208-6216), (2018).
- Lifeng Zhu, Qi Wu, Cao Deng, Mengjie Zhang, Chenglin Zhang, Hua Chen, Guoqing Lu and Fuwen Wei, Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes, Environmental Microbiology, 20, 5, (1711-1722), (2018).
- Marie Trévisan, Mathieu Fossépré, Delphine Paolantoni, Jenifer Rubio‐Magnieto, Pascal Dumy, Sébastien Ulrich and Mathieu Surin, Self‐assembly and chiroptical properties in supramolecular complexes of adenosine phosphates and guanidinium‐bispyrene, Chirality, 30, 6, (719-729), (2018).
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- Amandine Bovay, Vincent Zoete, Garry Dolton, Anna M. Bulek, David K. Cole, Pierre J. Rizkallah, Anna Fuller, Konrad Beck, Olivier Michielin, Daniel E. Speiser, Andrew K. Sewell and Silvia A. Fuertes Marraco, T cell receptor alpha variable 12‐2 bias in the immunodominant response to Yellow fever virus, European Journal of Immunology, 48, 2, (258-272), (2017).
- Annika Mae Lamb, Han Ming Gan, Chris Greening, Leo Joseph, Yin Peng Lee, Alejandra Morán‐Ordóñez, Paul Sunnucks and Alexandra Pavlova, Climate‐driven mitochondrial selection: A test in Australian songbirds, Molecular Ecology, 27, 4, (898-918), (2018).
- Umashri Kendur, Geeta H. Chimmalagi, Sunil M. Patil, Kalagouda B. Gudasi and Christopher S. Frampton, Synthesis, structural characterization and biological evaluation of mononuclear transition metal complexes of zwitterionic dehydroacetic acid N‐aroylhydrazone ligand, Applied Organometallic Chemistry, 32, 4, (2018).
- Alain Scaiola, Cohue Peña, Melanie Weisser, Daniel Böhringer, Marc Leibundgut, Purnima Klingauf‐Nerurkar, Stefan Gerhardy, Vikram Govind Panse and Nenad Ban, Structure of a eukaryotic cytoplasmic pre‐40S ribosomal subunit, The EMBO Journal, 37, 7, (2018).
- Poorna Manasa Bhamidimarri, Lakshmi Surekha Krishnapati, Surendra Ghaskadbi and Siva Kumar Nadimpalli, Mannose 6‐phosphate‐dependent lysosomal enzyme targeting in hydra: a biochemical, immunological and structural elucidation, FEBS Letters, 592, 8, (1366-1377), (2018).
- Muyang He, Weikang Li, Qingchuan Zheng and Hongxing Zhang, A molecular dynamics investigation into the mechanisms of alectinib resistance of three ALK mutants, Journal of Cellular Biochemistry, 119, 7, (5332-5342), (2018).
- Adam Pecina, Jiří Brynda, Lukáš Vrzal, Ramachandran Gnanasekaran, Magdalena Hořejší, Saltuk M. Eyrilmez, Jan Řezáč, Martin Lepšík, Pavlína Řezáčová, Pavel Hobza, Pavel Majer, Václav Veverka and Jindřich Fanfrlík, Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II–Inhibitor Complexes, ChemPhysChem, 19, 7, (873-879), (2018).
- Matthew L. Blank, Michelle L. Parker, Raghavendran Ramaswamy, Cameron J. Powell, Elizabeth D. English, Yaw Adomako‐Ankomah, Lena F. Pernas, Sean D. Workman, John C. Boothroyd, Martin J. Boulanger and Jon P. Boyle, A Toxoplasma gondii locus required for the direct manipulation of host mitochondria has maintained multiple ancestral functions, Molecular Microbiology, 108, 5, (519-535), (2018).
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- Paolo Ascenzi, Loris Leboffe, Daniele Toti, Fabio Polticelli and Viviana Trezza, Fipronil recognition by the FA1 site of human serum albumin, Journal of Molecular Recognition, 31, 8, (2018).
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- Seo‐Yeon Lee, Yun‐Seok Choi, Eun‐Hee Kim, Hae‐Kap Cheong, Yun‐Ju Lee, Jin‐Gu Lee, Yihong Ye and Kyoung‐Seok Ryu, Nonenzymatic acetylation of ubiquitin Lys side chains is modulated by their neighboring residues, The FEBS Journal, 285, 7, (1277-1289), (2018).
- Tae‐Gyu Lim, Yoon‐A Kim, Jong‐Eun Kim, Sohee Baek, Sung‐Young Lee, Charles C. Lee, Hanyong Chen, Jong Rhan Kim, Jung Yeon Kwon, Ann M. Bode, Chang Yong Lee, Zigang Dong, Deok‐Kun Oh, Jun Seong Park and Ki Won Lee, PKCι is a target of 7,8,4′‐trihydroxyisoflavone for the suppression of UVB‐induced MMP‐1 expression, Experimental Dermatology, 27, 5, (449-452), (2017).
- Cláudia S. Nóbrega and Sofia R. Pauleta, Interaction between Neisseria gonorrhoeae bacterial peroxidase and its electron donor, the lipid‐modified azurin, FEBS Letters, 592, 9, (1473-1483), (2018).
- Sofía M. García‐Mauriño, Antonio Díaz‐Quintana, Francisco Rivero‐Rodríguez, Isabel Cruz‐Gallardo, Christian Grüttner, Marian Hernández‐Vellisca and Irene Díaz‐Moreno, A putative RNA binding protein from Plasmodium vivax apicoplast, FEBS Open Bio, 8, 2, (177-188), (2017).
- Vincenzo Filippis, Laura Acquasaliente, Giulia Pontarollo and Daniele Peterle, Noncoded amino acids in protein engineering: Structure–activity relationship studies of hirudin–thrombin interaction, Biotechnology and Applied Biochemistry, 65, 1, (69-80), (2018).
- Beyza Bulutoglu, Jennifer Haghpanah, Elliot Campbell and Scott Banta, Engineered Biomolecular Recognition of RDX by Using a Thermostable Alcohol Dehydrogenase as a Protein Scaffold, ChemBioChem, 19, 3, (247-255), (2018).
- Dimas Suárez, Natalia Díaz, Evelio Francisco and Angel Martín Pendás, Application of the Interacting Quantum Atoms Approach to the S66 and Ionic‐Hydrogen‐Bond Datasets for Noncovalent Interactions, ChemPhysChem, 19, 8, (973-987), (2018).
- Chao Shang, Yongkui Zhang, Xue You, Nihong Guo, Yang Wang, Yang Fan and Wenbin Liu, The effect of 7,8,4´‐trihydroxyflavone on tyrosinase activity and conformation: Spectroscopy and docking studies, Luminescence, 33, 4, (681-691), (2018).
- Oliver Buß, Delphine Muller, Sven Jager, Jens Rudat and Kersten S. Rabe, Improvement in the Thermostability of a β‐Amino Acid Converting ω‐Transaminase by Using FoldX, ChemBioChem, 19, 4, (379-387), (2017).
- Jill A. Chipman and John F. Berry, Extraordinarily Large Ferromagnetic Coupling (J≥150 cm−1) by Electron Delocalization in a Heterometallic Mo≣Mo−Ni Chain Complex, Chemistry – A European Journal, 24, 7, (1494-1499), (2017).
- Rohit Shukla, Harish Shukla, Parismita Kalita and Timir Tripathi, Structural insights into natural compounds as inhibitors of Fasciola gigantica thioredoxin glutathione reductase, Journal of Cellular Biochemistry, 119, 4, (3067-3080), (2017).
- Daniel Șterbuleac and Călin Lucian Maniu, Computer Simulations Reveal a Novel Blocking Mode of the hERG Ion Channel by the Antiarrhythmic Agent Clofilium, Molecular Informatics, 37, 6-7, (2018).
- Zeinab Saberi, Behzad Rezaei and Taghi Khayamian, A fluorescent aptasensor for analysis of adenosine triphosphate based on aptamer–magnetic nanoparticles and its single‐stranded complementary DNA labeled carbon dots, Luminescence, 33, 4, (640-646), (2018).
- David M. Engelhard, Lukas M. Stratmann and Guido H. Clever, Structure–Property Relationships in CuII‐Binding Tetramolecular G‐Quadruplex DNA, Chemistry – A European Journal, 24, 9, (2117-2125), (2017).
- Sauli Haataja, Priya Verma, Ou Fu, Anastassios C. Papageorgiou, Sakari Pöysti, Roland J. Pieters, Ulf J. Nilsson and Jukka Finne, Rationally Designed Chemically Modified Glycodendrimer Inhibits Streptococcus suis Adhesin SadP at Picomolar Concentrations, Chemistry – A European Journal, 24, 8, (1905-1912), (2018).
- Wei Zhao and Hongqi Ai, Effect of pH on Aβ42 Monomer and Fibril‐like Oligomers—Decoding in Silico of the Roles of pK Values of Charged Residues, ChemPhysChem, 19, 9, (1103-1116), (2018).
- Annalaura Sabatucci, Daniel Tortolani, Enrico Dainese and Mauro Maccarrone, In silico mapping of allosteric ligand binding sites in type‐1 cannabinoid receptor, Biotechnology and Applied Biochemistry, 65, 1, (21-28), (2018).
- Alessandro Coppe, Leonardo Nogara, Matteo Samuele Pizzuto, Alice Cani, Simone Cesaro, Riccardo Masetti, Franco Locatelli, Geertruy te Kronnie, Giuseppe Basso, Stefania Bortoluzzi and Silvia Bresolin, Somatic mutations activating Wiskott–Aldrich syndrome protein concomitant with RAS pathway mutations in juvenile myelomonocytic leukemia patients, Human Mutation, 39, 4, (579-587), (2018).
- Eva K. Regel, Tobias Weikert, Anna Niehues, Bruno M. Moerschbacher and Ratna Singh, Protein‐engineering of chitosanase from Bacillus sp. MN to alter its substrate specificity, Biotechnology and Bioengineering, 115, 4, (863-873), (2018).
- Jeffrey A. Lawton, Noelle A. Prescott and Ping X. Lawton, From gene to structure: Lactobacillus bulgaricus D‐lactate dehydrogenase from yogurt as an integrated curriculum model for undergraduate molecular biology and biochemistry laboratory courses, Biochemistry and Molecular Biology Education, 46, 3, (270-278), (2018).
- Ashutosh Srivastava, Tsuyoshi Hirota, Stephan Irle and Florence Tama, Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition, Proteins: Structure, Function, and Bioinformatics, 86, 3, (344-353), (2017).
- Shikshya Shrestha, Cheng Zhang, Calvin R. Jerde, Qian Nie, Hu Li, Steven M. Offer and Robert B. Diasio, Gene‐Specific Variant Classifier (DPYD‐Varifier) to Identify Deleterious Alleles of Dihydropyrimidine Dehydrogenase, Clinical Pharmacology & Therapeutics, 104, 4, (709-718), (2018).
- Shayon Bhattacharya, Liang Xu and Damien Thompson, Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment, Wiley Interdisciplinary Reviews: Computational Molecular Science, 8, 4, (2018).
- Glaucio R. Nagurniak, Giovanni F. Caramori, Alvaro Muñoz‐Castro, Renato L. T. Parreira and Éder H. da Silva, The ability of Ex2Box4+ to interact with guests containing π‐electron‐rich and π‐electron‐poor moieties, International Journal of Quantum Chemistry, 118, 15, (2018).
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- Feng Huang, Jingliang Chen, Junsong Zhang, Likai Tan, Gui Lu, Yongjie Luo, Ting Pan, Juanran Liang, Qianwen Li, Baohong Luo, Hui Zhang and Gen Lu, Identification of a novel compound targeting the nuclear export of influenza A virus nucleoprotein, Journal of Cellular and Molecular Medicine, 22, 3, (1826-1839), (2017).
- Maximilian Brackmann, Jing Wang and Marek Basler, Type VI secretion system sheath inter‐subunit interactions modulate its contraction, EMBO reports, 19, 2, (225-233), (2017).
- Priyadarsini Kadirvel and Sharmila Anishetty, Potential role of salt‐bridges in the hinge‐like movement of apicomplexa specific β‐hairpin of Plasmodium and Toxoplasma profilins: A molecular dynamics simulation study, Journal of Cellular Biochemistry, 119, 4, (3683-3696), (2018).
- Qifeng Bai, Horacio Pérez‐Sánchez, Zhuoyu Shi, Lanlan Li, Danfeng Shi, Huanxiang Liu and Xiaojun Yao, Computational studies on horseshoe shape pocket of human orexin receptor type 2 and boat conformation of suvorexant by molecular dynamics simulations, Chemical Biology & Drug Design, 92, 1, (1221-1231), (2018).
- Minh Khoa Nguyen, Léonard Jaillet and Stéphane Redon, ART‐RRT: As‐Rigid‐As‐Possible exploration of ligand unbinding pathways, Journal of Computational Chemistry, 39, 11, (665-678), (2018).
- Gokhan Zengin, Devina Lobine, Adriano Mollica, Marcello Locatelli, Simone Carradori and Mohamad Fawzi Mahomoodally, Multiple pharmacological approaches on Fibigia eriocarpa extracts by in vitro and computational assays, Fundamental & Clinical Pharmacology, 32, 4, (400-413), (2018).
- Kristyna Bousova, Petr Herman, Jaroslav Vecer, Lucie Bednarova, Lenka Monincova, Pavel Majer, Ladislav Vyklicky, Jiri Vondrasek and Jan Teisinger, Shared CaM‐ and S100A1‐binding epitopes in the distal TRPM4 N terminus, The FEBS Journal, 285, 3, (599-613), (2017).
- Christina Brandstaedter, Karin Fritz‐Wolf, Stine Weder, Marina Fischer, Beate Hecker, Stefan Rahlfs and Katja Becker, Kinetic characterization of wild‐type and mutant human thioredoxin glutathione reductase defines its reaction and regulatory mechanisms, The FEBS Journal, 285, 3, (542-558), (2017).
- Hao Tan, Renyun Miao, Tianhai Liu, Lufang Yang, Yumin Yang, Chunxiu Chen, Jianrong Lei, Yuhui Li, Jiabei He, Qun Sun, Weihong Peng, Bingcheng Gan and Zhongqian Huang, A bifunctional cellulase–xylanase of a new Chryseobacterium strain isolated from the dung of a straw‐fed cattle, Microbial Biotechnology, 11, 2, (381-398), (2017).
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- Sho Amatsu, Takuhiro Matsumura, Masahiro Yutani and Yukako Fujinaga, Multivalency effects of hemagglutinin component of type B botulinum neurotoxin complex on epithelial barrier disruption, Microbiology and Immunology, 62, 2, (80-89), (2018).
- Andreas Schaller, Annick Stintzi, Susana Rivas, Irene Serrano, Nina V. Chichkova, Andrey B. Vartapetian, Dana Martínez, Juan J. Guiamét, Daniela J. Sueldo, Renier A. L. Hoorn, Vicente Ramírez and Pablo Vera, From structure to function – a family portrait of plant subtilases, New Phytologist, 218, 3, (901-915), (2017).
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- Joanna Sliwiak, Michal Sikorski and Mariusz Jaskolski, PR‐10 proteins as potential mediators of melatonin‐cytokinin cross‐talk in plants: crystallographic studies of LlPR‐10.2B isoform from yellow lupine, The FEBS Journal, 285, 10, (1907-1922), (2018).
- Zheng Qu, Setsuko Fujita‐Becker, Edda Ballweber, Semra Ince, Christian Herrmann, Rasmus R. Schröder and Hans Georg Mannherz, Interaction of isolated cross‐linked short actin oligomers with the skeletal muscle myosin motor domain, The FEBS Journal, 285, 9, (1715-1729), (2018).
- Syeda Abida Ejaz, Aamer Saeed, Syed Jawad Ali Shah, Abdul Hameed, Joanna Lecka, Jean Sévigny and Jamshed Iqbal, Distinctive inhibition of alkaline phosphatase isozymes by thiazol‐2‐ylidene‐benzamide derivatives: Functional insights into their anticancer role, Journal of Cellular Biochemistry, 119, 8, (6501-6513), (2018).
- Abdul Rehman Phull, Mubshir Hassan, Qamar Abbas, Hussain Raza, Ihsan ul Haq, Sung Yum Seo and Song Ja Kim, In Vitro, In Silico Elucidation of Antiurease Activity, Kinetic Mechanism and COX‐2 Inhibitory Efficacy of Coagulansin A of Withania coagulans, Chemistry & Biodiversity, 15, 1, (2018).
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- Arun B. Gurung and Atanu Bhattacharjee, Impact of a non‐synonymous Q281R polymorphism on structure of human Lipoprotein‐Associated Phospholipase A2 (Lp‐PLA2), Journal of Cellular Biochemistry, 119, 8, (7009-7021), (2018).
- Pankaj Gupta, Adeel H. Zaidi and Sunil K. Manna, Suppression of IKK, but not activation of p53 is responsible for cell death mediated by naturally occurring oxidized tetranortriterpenoid, Journal of Cellular Biochemistry, 119, 8, (6828-6841), (2018).
- Marina Cvetkovska, Beth Szyszka‐Mroz, Marc Possmayer, Paula Pittock, Gilles Lajoie, David R. Smith and Norman P. A. Hüner, Characterization of photosynthetic ferredoxin from the Antarctic alga Chlamydomonas sp. UWO241 reveals novel features of cold adaptation, New Phytologist, 219, 2, (588-604), (2018).
- Joydeep Chakraborty, Natalia S. Nemeria, Edgardo Farinas and Frank Jordan, Catalysis of transthiolacylation in the active centers of dihydrolipoamide acyltransacetylase components of 2‐oxo acid dehydrogenase complexes, FEBS Open Bio, 8, 6, (880-896), (2018).
- Rolf Boelens, Dmitri Svergun, Jan Ellenberg, Stephen Cusack, Martin A. Walsh, Harald Schwalbe, Anastassis Perrakis, Vladimír Sklenář, Jose Maria Carazo Garcia, Hartmut Oschkinat, Andrew Thompson, Marjolein Thunnissen, Bram Koster, Gordon Leonard, Bernhard Brutscher, David I. Stuart, Poul Nissen, Hanna Wacklin, András Perczel, Margarida Archer, Rik Wierenga, Georgios A. Spyroulias and Joel Sussman, iNEXT: a European facility network to stimulate translational structural biology, FEBS Letters, 592, 12, (1909-1917), (2018).
- Ádria P. B. Saraiva, Ricardo M. Miranda, Renan P. P. Valente, Jéssica O. Araújo, Rutelene N. B. Souza, Clauber H. S. Costa, Amanda R. S. Oliveira, Michell O. Almeida, Antonio F. Figueiredo, João E. V. Ferreira, Cláudio Nahum Alves and Kathia M. Honorio, Molecular description of α‐keto‐based inhibitors of cruzain with activity against Chagas disease combining 3D‐QSAR studies and molecular dynamics, Chemical Biology & Drug Design, 92, 2, (1475-1487), (2018).
- Phillip A. Morin, Andrew D. Foote, Charles Scott Baker, Brittany L. Hancock‐Hanser, Kristin Kaschner, Bruce R. Mate, Sarah L. Mesnick, Victoria L. Pease, Patricia E. Rosel and Alana Alexander, Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses, Molecular Ecology, 27, 11, (2604-2619), (2018).
- Li‐Na Pan, Feng‐Zhu Wang, Xin‐Yue Zhang, Yan‐Ni Zhao, Geng‐Ping Zhu and Min Li, Identification and characterization of heat shock proteins in a parasitic wasp Chouioia cuneae (Hymenoptera: Eulophidae), Entomological Research, 48, 3, (145-155), (2017).
- Bérénice Jahn, Arjan Pol, Henning Lumpe, Thomas R. M. Barends, Andreas Dietl, Carmen Hogendoorn, Huub J. M. Op den Camp and Lena J. Daumann, Similar but Not the Same: First Kinetic and Structural Analyses of a Methanol Dehydrogenase Containing a Europium Ion in the Active Site, ChemBioChem, 19, 11, (1147-1153), (2018).
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- Anne‐Mieke J. W. Haasnoot, Marco W. Schilham, Sylvia Kamphuis, Petra C. E. Hissink Muller, Arnd Heiligenhaus, Dirk Foell, Kirsten Minden, Roel A. Ophoff, Timothy R. D. J. Radstake, Anneke I. Den Hollander, Tjitske H. C. M. Reinards, Sanne Hiddingh, Nicoline E. Schalij‐Delfos, Esther P. A. H. Hoppenreijs, Marion A. J. Rossum, Carine Wouters, Rotraud K. Saurenmann, J. Merlijn Berg, Nico M. Wulffraat, Rebecca Cate, Joke H. Boer, Sara L. Pulit, Jonas J. W. Kuiper, Tilmann Kallinich, Angelika Thon, Jasmin Kümmerle‐Deschner, Hans‐Iko Huppertz, Gerd Horneff, Anton Hospach, Kirsten Mönkemöller, Johannes‐Peter Haas, Gerd Ganser, Ivan Foeldvari and Jens Klotsche, Identification of an Amino Acid Motif in HLA–DRβ1 That Distinguishes Uveitis in Patients With Juvenile Idiopathic Arthritis, Arthritis & Rheumatology, 70, 7, (1155-1165), (2018).
- Dongxiao Hao, Zhiwei Yang, Teng Gao, Zhiqi Tian, Lei Zhang and Shengli Zhang, Role of glycans in cholesteryl ester transfer protein revealed by molecular dynamics simulation, Proteins: Structure, Function, and Bioinformatics, 86, 8, (882-891), (2018).
- Srinivas Kumar Ponna, Salla Ruskamo, Matti Myllykoski, Corinna Keller, Tobias M. Boeckers and Petri Kursula, Structural basis for PDZ domain interactions in the post‐synaptic density scaffolding protein Shank3, Journal of Neurochemistry, 145, 6, (449-463), (2018).
- Shuwen Yin, Xuanxuan Zhang, Fangyuan Lai, Taizhen Liang, Jiayong Wen, Wanying Lin, Jiayin Qiu, Shuwen Liu and Lin Li, Trilobatin as an HIV‐1 entry inhibitor targeting the HIV‐1 Gp41 envelope, FEBS Letters, 592, 13, (2361-2377), (2018).
- Tereza Králová, Tomáš Albrecht, Josef Bryja, David Hořák, Arild Johnsen, Jan T. Lifjeld, Marian Novotný, Ondřej Sedláček, Hana Velová and Michal Vinkler, Signatures of diversifying selection and convergence acting on passerine Toll‐like receptor 4 in an evolutionary context, Molecular Ecology, 27, 13, (2871-2883), (2018).
- Kaitlin A. Phillips, Thomas M. Stonelake, Kepeng Chen, Yuqi Hou, Jianzhang Zhao, Simon J. Coles, Peter N. Horton, Shannon J. Keane, Emily C. Stokes, Ian A. Fallis, Andrew J. Hallett, Sean P. O'Kell, Joseph M. Beames and Simon J. A. Pope, Ligand‐Tuneable, Red‐Emitting Iridium(III) Complexes for Efficient Triplet–Triplet Annihilation Upconversion Performance, Chemistry – A European Journal, 24, 34, (8577-8588), (2018).
- Masaki Ikeda, Kazuhiro Satomura, Tsuyoshi Sekizuka, Kentaro Hanada, Toshinori Endo and Naoki Osada, Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys, American Journal of Primatology, 80, 7, (2018).
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- Aleksandra J. Wierzba, Aleksandra Wincenciuk, Maksymilian Karczewski, Valentine I. Vullev and Dorota Gryko, meso‐Modified Cobalamins: Synthesis, Structure, and Properties, Chemistry – A European Journal, 24, 41, (10344-10356), (2018).
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- Görkem Sarıkaya, Güneş Çoban, Sülünay Parlar, Ayse H. Tarikogullari, Güliz Armagan, Mümin A. Erdoğan, Vildan Alptüzün and Ayşe S. Alpan, Multifunctional cholinesterase inhibitors for Alzheimer's disease: Synthesis, biological evaluations, and docking studies of o/p‐propoxyphenylsubstituted‐1H‐benzimidazole derivatives, Archiv der Pharmazie, 351, 8, (2018).
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- Mohammad H. Bohari, Xing Yu, Chandan Kishor, Brijesh Patel, Rob Marc Go, Hadieh A. Eslampanah Seyedi, Yaron Vinik, I. Darren Grice, Yehiel Zick and Helen Blanchard, Structure‐Based Design of a Monosaccharide Ligand Targeting Galectin‐8, ChemMedChem, 13, 16, (1664-1672), (2018).
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- Nathalie Clement, Nicolas Renault, Jean‐Luc Guillaume, Erika Cecon, Anne‐Sophie Journé, Xavier Laurent, Kenjiro Tadagaki, Francis Cogé, Arnaud Gohier, Philippe Delagrange, Philippe Chavatte and Ralf Jockers, Importance of the second extracellular loop for melatonin MT1 receptor function and absence of melatonin binding in GPR50, British Journal of Pharmacology, 175, 16, (3281-3297), (2017).
- Luca Rizzi, Cecilia Gotti, Marco De Amici, Clelia Dallanoce and Carlo Matera, A Small Library of 1,2,3‐Triazole Analogs of CAP‐55: Synthesis and Binding Affinity at Nicotinic Acetylcholine Receptors, Chemistry & Biodiversity, 15, 9, (2018).
- Nevenka Dudvarski Stanković, Frank Bicker, Stefanie Keller, David TW Jones, Patrick N Harter, Arne Kienzle, Clarissa Gillmann, Philipp Arnold, Anna Golebiewska, Olivier Keunen, Alf Giese, Andreas Deimling, Tobias Bäuerle, Simone P Niclou, Michel Mittelbronn, Weilan Ye, Stefan M Pfister and Mirko HH Schmidt, EGFL7 enhances surface expression of integrin α5β1 to promote angiogenesis in malignant brain tumors, EMBO Molecular Medicine, 10, 9, (2018).
- Sushant Kumar and Kaza Suguna, Crystal structure of the retroviral protease‐like domain of a protozoal DNA damage‐inducible 1 protein, FEBS Open Bio, 8, 9, (1379-1394), (2018).
- Alessio Bocedi, Giada Cattani, Lorenzo Stella, Renato Massoud and Giorgio Ricci, Thiol disulfide exchange reactions in human serum albumin: the apparent paradox of the redox transitions of Cys34, The FEBS Journal, 285, 17, (3225-3237), (2018).
- Anne‐Hélène Jan Deniau, Maeva Subileau and Eric Dubreucq, Characterization and Reshaping of a Large and Hydrophobic Nucleophile Pocket in Lipases/Acyltransferases, ChemBioChem, 19, 17, (1839-1844), (2018).
- Tim Efthymiou, Jesse Gavette, Matthias Stoop, Francesco De Riccardis, Mathy Froeyen, Piet Herdewijn and Ramanarayanan Krishnamurthy, Chimeric XNA: An Unconventional Design for Orthogonal Informational Systems, Chemistry – A European Journal, 24, 49, (12811-12819), (2018).
- Johanna Kondelin, Kari Salokas, Lilli Saarinen, Kristian Ovaska, Heli Rauanheimo, Roosa‐Maria Plaketti, Jiri Hamberg, Xiaonan Liu, Leena Yadav, Alexandra E Gylfe, Tatiana Cajuso, Ulrika A Hänninen, Kimmo Palin, Heikki Ristolainen, Riku Katainen, Eevi Kaasinen, Tomas Tanskanen, Mervi Aavikko, Minna Taipale, Jussi Taipale, Laura Renkonen‐Sinisalo, Anna Lepistö, Selja Koskensalo, Jan Böhm, Jukka‐Pekka Mecklin, Halit Ongen, Emmanouil T Dermitzakis, Outi Kilpivaara, Pia Vahteristo, Mikko Turunen, Sampsa Hautaniemi, Sari Tuupanen, Auli Karhu, Niko Välimäki, Markku Varjosalo, Esa Pitkänen and Lauri A Aaltonen, Comprehensive evaluation of coding region point mutations in microsatellite‐unstable colorectal cancer, EMBO Molecular Medicine, 10, 9, (2018).
- Vipul Solanki, Srajan Kapoor and Krishan Gopal Thakur, Structural insights into the mechanism of Type IVa pilus extension and retraction ATPase motors, The FEBS Journal, 285, 18, (3402-3421), (2018).
- Mauro Lapelosa, Oscar Burrone and Walter Rocchia, Specific Residue Interactions Regulate the Binding of Dengue Antigens to Broadly Neutralizing EDE Antibodies, ChemistryOpen, 7, 8, (604-610), (2018).
- Perry Caviness, Ryan Bauer, Keisuke Tanaka, Katarzyna Janowska, Jeffrey Randall Roeser, Dawn Harter, Jes Sanders, Christopher Ruth, Osamu Matsushita and Joshua Sakon, Ca2+‐induced orientation of tandem collagen binding domains from clostridial collagenase ColG permits two opposing functions of collagen fibril formation and retardation, The FEBS Journal, 285, 17, (3254-3269), (2018).
- Reaz Uddin and Kevin M. Downard, Molecular basis of benzimidazole inhibitors to hepatitis C virus envelope glycoprotein, Chemical Biology & Drug Design, 92, 3, (1638-1646), (2018).
- Rajan Kumar Pandey, Rupal Ojha, Amit Mishra and Vijay Kumar Prajapati, Designing B‐ and T‐cell multi‐epitope based subunit vaccine using immunoinformatics approach to control Zika virus infection, Journal of Cellular Biochemistry, 119, 9, (7631-7642), (2018).
- Michaela Nekardová, Ladislava Vymětalová, Prashant Khirsariya, Silvia Kováčová, Michaela Hylsová, Radek Jorda, Vladimír Kryštof, Jindřich Fanfrlík, Pavel Hobza and Kamil Paruch, Structural Basis of the Interaction of Cyclin‐Dependent Kinase 2 with Roscovitine and Its Analogues Having Bioisosteric Central Heterocycles, ChemPhysChem, 18, 7, (785-795), (2017).
- Anne‐Hélène Jan, Éric Dubreucq and Maeva Subileau, Revealing the Roles of Subdomains in the Catalytic Behavior of Lipases/Acyltransferases Homologous to CpLIP2 through Rational Design of Chimeric Enzymes, ChemBioChem, 18, 10, (941-950), (2017).
- Thomas Driant, Florian Nachon, Cyril Ollivier, Pierre‐Yves Renard and Etienne Derat, On the Influence of the Protonation States of Active Site Residues on AChE Reactivation: A QM/MM Approach, ChemBioChem, 18, 7, (666-675), (2017).
- Hendrik Hähl, Jose Nabor Vargas, Alessandra Griffo, Päivi Laaksonen, Géza Szilvay, Michael Lienemann, Karin Jacobs, Ralf Seemann and Jean‐Baptiste Fleury, Pure Protein Bilayers and Vesicles from Native Fungal Hydrophobins, Advanced Materials, 29, 1, (2016).
- Rubin Dasgupta, Himal K. Ganguly, E. K. Modugula and Gautam Basu, Type VIa β‐turn‐fused helix N‐termini: A novel helix N‐cap motif containing cis proline, Peptide Science, 108, 1, (2017).
- Mrinmoy Saha, Michael T. Scerba, Nathaniel I. Shank, Tracy L. Hartman, Caitlin A. Buchholz, Robert W. Buckheit, Stewart R. Durell and Daniel H. Appella, Probing Mercaptobenzamides as HIV Inactivators via Nucleocapsid Protein 7, ChemMedChem, 12, 10, (714-721), (2017).
- Souvik Pandey, Menyhárt B. Sárosi, Peter Lönnecke and Evamarie Hey‐Hawkins, Planar‐Chiral Secondary Ferrocenylphosphanes, European Journal of Inorganic Chemistry, 2017, 2, (256-262), (2016).
- Christoph Alexander Bauer, Andreas Hansen and Stefan Grimme, The Fractional Occupation Number Weighted Density as a Versatile Analysis Tool for Molecules with a Complicated Electronic Structure, Chemistry – A European Journal, 23, 25, (6150-6164), (2017).
- Arianna Bertolani, Andrea Pizzi, Lisa Pirrie, Lara Gazzera, Giulia Morra, Massimiliano Meli, Giorgio Colombo, Alessandro Genoni, Gabriella Cavallo, Giancarlo Terraneo and Pierangelo Metrangolo, Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines, Chemistry – A European Journal, 23, 9, (2051-2058), (2016).
- Mohammad Fahimul Hassan and Abdul Rauf, Synthesis and study on the binding of thiazol‐2(3H)‐ylidine derivative with human serum albumin using spectroscopic and molecular docking methods, Luminescence, 32, 4, (602-611), (2016).
- Matthaia Ieronymaki, Francesca Nuti, Diego Brancaccio, Giada Rossi, Feliciana Real‐Fernández, Yihong Cao, Olivier Monasson, Maud Larregola, Elisa Peroni, Jacques Uziel, Giuseppina Sabatino, Ettore Novellino, Alfonso Carotenuto, Anna Maria Papini and Paolo Rovero, Structure–Activity Relationship Studies, SPR Affinity Characterization, and Conformational Analysis of Peptides That Mimic the HNK‐1 Carbohydrate Epitope, ChemMedChem, 12, 10, (751-759), (2017).
- Michael Dreifke, Felix J. Brieler and Michael Fröba, Immobilization of Alcohol Dehydrogenase from E. coli onto Mesoporous Silica for Application as a Cofactor Recycling System, ChemCatChem, 9, 7, (1197-1210), (2017).
- Duc D. Nguyen, Bao Wang and Guo‐Wei Wei, Accurate, robust, and reliable calculations of Poisson–Boltzmann binding energies, Journal of Computational Chemistry, 38, 13, (941-948), (2017).
- Travis Johnston, Boyu Zhang, Adam Liwo, Silvia Crivelli and Michela Taufer, In situ data analytics and indexing of protein trajectories, Journal of Computational Chemistry, 38, 16, (1419-1430), (2017).
- Tamara Papp, László Kollár and Tamás Kégl, Theoretical insights into the nature of PtSn bond: Reevaluating the bonding/back‐bonding properties of trichlorostannate with comparison to the cyano ligand, Journal of Computational Chemistry, 38, 19, (1712-1726), (2017).
- Beata Podkościelna, Oihana Gordobil, Anastasia V. Riazanova, Galina Dobele, Jalel Labidi, Mikael E. Lindström, Vladimir M. Gun'ko and Olena Sevastyanova, Novel Porous Materials Obtained from Technical Lignins and Their Methacrylate Derivatives Copolymerized with Styrene and Divinylbenzene, ChemistrySelect, 2, 7, (2257-2264), (2017).
- Jonathan Catazaro, Austin J. Lowe, Ronald L. Cerny and Robert Powers, The NMR solution structure and function of RPA3313: a putative ribosomal transport protein from Rhodopseudomonas palustris, Proteins: Structure, Function, and Bioinformatics, 85, 1, (93-102), (2016).
- K. V. Abhinav, Kaushal Sharma, A. Surolia and Mamannamana Vijayan, Distortion of the ligand molecule as a strategy for modulating binding affinity: Further studies involving complexes of jacalin with β‐substituted disaccharides, IUBMB Life, 69, 2, (72-78), (2017).
- Tae‐Joon Kim, Soon‐Tae Lee, Jangsup Moon, Jun‐Sang Sunwoo, Jung‐Ick Byun, Jung‐Ah Lim, Yong‐Won Shin, Jin‐Sun Jun, Han Sang Lee, Woo‐Jin Lee, Ah Reaum Yang, Yunhee Choi, Kyung‐Il Park, Keun‐Hwa Jung, Ki‐Young Jung, Manho Kim, Sang Kun Lee and Kon Chu, Anti‐LGI1 encephalitis is associated with unique HLA subtypes, Annals of Neurology, 81, 2, (183-192), (2017).
- Marisa I Mendes, Desirée EC Smith, Ana Pop, Pascal Lennertz, Matilde R Fernandez Ojeda, Warsha A Kanhai, Silvy JM Dooren, Yair Anikster, Ivo Barić, Caroline Boelen, Jaime Campistol, Lonneke Boer, Ariana Kariminejad, Hulya Kayserili, Agathe Roubertie, Krijn T Verbruggen, Christine Vianey‐Saban, Monique Williams and Gajja S Salomons, Clinically Distinct Phenotypes of Canavan Disease Correlate with Residual Aspartoacylase Enzyme Activity, Human Mutation, 38, 5, (524-531), (2017).
- Junhui Li, Yue Zhang, Yanzhai Song, Hui Zhang, Jiangbo Fan, Qun Li, Dongfen Zhang and Yongbiao Xue, Electrostatic potentials of the S‐locus F‐box proteins contribute to the pollen S specificity in self‐incompatibility in Petunia hybrida, The Plant Journal, 89, 1, (45-57), (2016).
- Zheng Liu, Cristina Gutierrez‐Vargas, Jia Wei, Robert A. Grassucci, Ming Sun, Noel Espina, Susan Madison‐Antenucci, Liang Tong and Joachim Frank, Determination of the ribosome structure to a resolution of 2.5 Å by single‐particle cryo‐EM, Protein Science, 26, 1, (82-92), (2016).
- Luca Pannone, Gianfranco Bocchinfuso, Elisabetta Flex, Cesare Rossi, Giuseppina Baldassarre, Christina Lissewski, Francesca Pantaleoni, Federica Consoli, Francesca Lepri, Monia Magliozzi, Massimiliano Anselmi, Silvia Delle Vigne, Giovanni Sorge, Kadri Karaer, Goran Cuturilo, Alessandro Sartorio, Sigrid Tinschert, Maria Accadia, Maria C. Digilio, Giuseppe Zampino, Alessandro Luca, Hélène Cavé, Martin Zenker, Bruce D. Gelb, Bruno Dallapiccola, Lorenzo Stella, Giovanni B. Ferrero, Simone Martinelli and Marco Tartaglia, Structural, Functional, and Clinical Characterization of a Novel PTPN11 Mutation Cluster Underlying Noonan Syndrome, Human Mutation, 38, 4, (451-459), (2017).
- Birgit Unterweger, Nyssa Drinkwater, Priscilla Johanesen, Dena Lyras, Geoffrey J. Dumsday and Sheena McGowan, X‐ray crystal structure of cytochrome P450 monooxygenase CYP101J2 from Sphingobium yanoikuyae strain B2, Proteins: Structure, Function, and Bioinformatics, 85, 5, (945-950), (2017).
- Alexandra Plácido, Andreia Coelho, Lucas Abreu Nascimento, Andreanne Gomes Vasconcelos, Maria Fátima Barroso, Joilson Ramos‐Jesus, Vladimir Costa, Francisco das Chagas Alves Lima, Cristina Delerue‐Matos, Ricardo Martins Ramos, Mariela M. Marani and José Roberto de Souza de Almeida Leite, Cry1A(b)16 toxin from Bacillus thuringiensis: Theoretical refinement of three‐dimensional structure and prediction of peptides as molecular markers for detection of genetically modified organisms, Proteins: Structure, Function, and Bioinformatics, 85, 7, (1248-1257), (2017).
- Bartlomiej Fedorczyk, Piotr F. J. Lipiński, Dagmara Tymecka, Anna K. Puszko, Beata Wilenska, Gerard Y. Perret and Aleksandra Misicka, Conformational latitude – activity relationship of KPPR tetrapeptide analogues toward their ability to inhibit binding of vascular endothelial growth factor 165 to neuropilin‐1, Journal of Peptide Science, 23, 6, (445-454), (2017).
- Burcu Kaplan‐Türköz, A putative Toll/interleukin‐1 receptor domain protein from Helicobacter pylori is dimeric in solution and interacts with human Toll‐like receptor adaptor myeloid differentiation primary response 88, Microbiology and Immunology, 61, 2, (85-91), (2017).
- Ann‐Maree Catanzariti, Huong T. T. Do, Pierrick Bru, Mara Sain, Louise F. Thatcher, Martijn Rep and David A. Jones, The tomato I gene for Fusarium wilt resistance encodes an atypical leucine‐rich repeat receptor‐like protein whose function is nevertheless dependent on SOBIR1 and SERK3/BAK1, The Plant Journal, 89, 6, (1195-1209), (2017).
- Nicolas Coudray, Sean L. Seyler, Ralph Lasala, Zhening Zhang, Kathy M. Clark, Mark E. Dumont, Alexis Rohou, Oliver Beckstein and David L. Stokes, Structure of the SLC4 transporter Bor1p in an inward‐facing conformation, Protein Science, 26, 1, (130-145), (2016).
- Hong‐Wei Wang and Jia‐Wei Wang, How cryo‐electron microscopy and X‐ray crystallography complement each other, Protein Science, 26, 1, (32-39), (2016).
- Cassandra Terry, Shuo Jiang, David S. Radford, Qiang Wan, Svetomir Tzokov, Anne Moir and Per A. Bullough, Molecular tiling on the surface of a bacterial spore – the exosporium of the Bacillus anthracis/cereus/thuringiensis group, Molecular Microbiology, 104, 4, (539-552), (2017).
- Sebastián D'Ippólito, Leonardo Agustín Arias, Claudia Anahí Casalongué, Gabriela Carolina Pagnussat and Diego Fernando Fiol, The DC1‐domain protein VACUOLELESS GAMETOPHYTES is essential for development of female and male gametophytes in Arabidopsis, The Plant Journal, 90, 2, (261-275), (2017).
- Han‐Yi Chen and Xu Li, Identification of a residue responsible for UDP‐sugar donor selectivity of a dihydroxybenzoic acid glycosyltransferase from Arabidopsis natural accessions, The Plant Journal, 89, 2, (195-203), (2016).
- Yumeng Yan, Zeyu Wen, Xinxiang Wang and Sheng‐You Huang, Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking, Proteins: Structure, Function, and Bioinformatics, 85, 3, (497-512), (2017).
- N. C. Leksa, P.‐L. Chiu, G. M. Bou‐Assaf, C. Quan, Z. Liu, A. B. Goodman, M. G. Chambers, S. E. Tsutakawa, M. Hammel, R. T. Peters, T. Walz and J. D. Kulman, The structural basis for the functional comparability of factor VIII and the long‐acting variant recombinant factor VIII Fc fusion protein, Journal of Thrombosis and Haemostasis, 15, 6, (1167-1179), (2017).
- T. Matsui, A. Hori, J. Hamako, F. Matsushita, Y. Ozeki, Y. Sakurai, M. Hayakawa, M. Matsumoto and Y. Fujimura, Mutant botrocetin‐2 inhibits von Willebrand factor‐induced platelet agglutination, Journal of Thrombosis and Haemostasis, 15, 3, (538-548), (2017).
- Ayeman Amanullah, Arun Upadhyay, Deepak Chhangani, Vibhuti Joshi, Ribhav Mishra, Koji Yamanaka and Amit Mishra, Proteasomal Dysfunction Induced By Diclofenac Engenders Apoptosis Through Mitochondrial Pathway, Journal of Cellular Biochemistry, 118, 5, (1014-1027), (2017).
- Sneha P, Kumar Thirumal D, Himani Tanwar, Siva R, George Priya Doss C and Hatem Zayed, Structural Analysis of G1691S Variant in the Human Filamin B Gene Responsible for Larsen Syndrome: A Comparative Computational Approach, Journal of Cellular Biochemistry, 118, 7, (1900-1910), (2017).
- Corinne Portioli, Michele Bovi, Donatella Benati, Marta Donini, Massimiliano Perduca, Alessandro Romeo, Stefano Dusi, Hugo L. Monaco and Marina Bentivoglio, Novel functionalization strategies of polymeric nanoparticles as carriers for brain medications, Journal of Biomedical Materials Research Part A, 105, 3, (847-858), (2016).
- Sarah Schulz, Martin Wilkes, Deryck J Mills, Werner Kühlbrandt and Thomas Meier, Molecular architecture of the N‐type ATPase rotor ring from Burkholderia pseudomallei, EMBO reports, 18, 4, (526-535), (2017).
- Eduard Baquero, Aurélie A Albertini, Hélène Raux, Abbas Abou‐Hamdan, Elisabetta Boeri‐Erba, Malika Ouldali, Linda Buonocore, John K Rose, Jean Lepault, Stéphane Bressanelli and Yves Gaudin, Structural intermediates in the fusion‐associated transition of vesiculovirus glycoprotein, The EMBO Journal, 36, 5, (679-692), (2017).
- Shan Wu, Dan Tan, John L. Woolford, Meng‐Qiu Dong and Ning Gao, Atomic modeling of the ITS2 ribosome assembly subcomplex from cryo‐EM together with mass spectrometry‐identified protein–protein crosslinks, Protein Science, 26, 1, (103-112), (2016).
- Clay A. Foster and Ann H. West, Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two‐component signaling systems, Proteins: Structure, Function, and Bioinformatics, 85, 1, (155-176), (2016).
- Philipp Bieri, Marc Leibundgut, Martin Saurer, Daniel Boehringer and Nenad Ban, The complete structure of the chloroplast 70S ribosome in complex with translation factor pY, The EMBO Journal, 36, 4, (475-486), (2016).
- Kwang‐Hyun Park, Yan An, Tae‐Yang Jung, In‐Young Baek, Haemin Noh, Woo‐Chan Ahn, Hans Hebert, Ji‐Joon Song, Jeong‐Hoon Kim, Byung‐Ha Oh and Eui‐Jeon Woo, RNA activation‐independent DNA targeting of the Type III CRISPR‐Cas system by a Csm complex, EMBO reports, 18, 5, (826-840), (2017).
- Chandran Nithin, Sunandan Mukherjee and Ranjit Prasad Bahadur, A non‐redundant protein–RNA docking benchmark version 2.0, Proteins: Structure, Function, and Bioinformatics, 85, 2, (256-267), (2016).
- Maria‐Eugenia Dieterle, Silvia Spinelli, Irina Sadovskaya, Mariana Piuri and Christian Cambillau, Evolved distal tail carbohydrate binding modules of actobacillus phage J‐1: a novel type of anti‐receptor widespread among lactic acid bacteria phages, Molecular Microbiology, 104, 4, (608-620), (2017).
- Sarah G. Nowakowski, Michael Regnier and Valerie Daggett, Molecular mechanisms underlying deoxy‐ADP.Pi activation of pre‐powerstroke myosin, Protein Science, 26, 4, (749-762), (2017).
- Andrey G Malyutin, Sharmishtha Musalgaonkar, Stephanie Patchett, Joachim Frank and Arlen W Johnson, Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis, The EMBO Journal, 36, 7, (854-868), (2017).
- Dheva T Setiaputra, Derrick TH Cheng, Shan Lu, Jesse M Hansen, Udit Dalwadi, Cindy HY Lam, Jeffrey L To, Meng‐Qiu Dong and Calvin K Yip, Molecular architecture of the yeast Elongator complex reveals an unexpected asymmetric subunit arrangement, EMBO reports, 18, 2, (280-291), (2016).
- Manas Ranjan Sahoo, Swati Gaikwad, Deepak Khuperkar, Maitreyi Ashok, Mary Helen, Santosh Kumar Yadav, Aditi Singh, Indrasen Magre, Prachi Deshmukh, Supriya Dhanvijay, Pabitra Kumar Sahoo, Yogendra Ramtirtha, Mallur Srivatsan Madhusudhan, Pananghat Gayathri, Vasudevan Seshadri and Jomon Joseph, Nup358 binds to AGO proteins through its SUMO‐interacting motifs and promotes the association of target mRNA with miRISC, EMBO reports, 18, 2, (241-263), (2016).
- Olga Jasnovidova, Magdalena Krejcikova, Karel Kubicek and Richard Stefl, Structural insight into recognition of phosphorylated threonine‐4 of RNA polymerase II C‐terminal domain by Rtt103p, EMBO reports, 18, 6, (906-913), (2017).
- Maria I Dauden, Jan Kosinski, Olga Kolaj‐Robin, Ambroise Desfosses, Alessandro Ori, Celine Faux, Niklas A Hoffmann, Osita F Onuma, Karin D Breunig, Martin Beck, Carsten Sachse, Bertrand Séraphin, Sebastian Glatt and Christoph W Müller, Architecture of the yeast Elongator complex, EMBO reports, 18, 2, (264-279), (2016).
- Kathiresan Natarajan, Sudarshan Gadadhar, Judith Souphron, Maria M Magiera and Carsten Janke, Molecular interactions between tubulin tails and glutamylases reveal determinants of glutamylation patterns, EMBO reports, 18, 6, (1013-1026), (2017).
- Simon S. Terzyan, Paul F. Cook, Annie Heroux and Marie H. Hanigan, Structure of 6‐diazo‐5‐oxo‐norleucine‐bound human gamma‐glutamyl transpeptidase 1, a novel mechanism of inactivation, Protein Science, 26, 6, (1196-1205), (2017).
- Marcus Wingen, Karl‐Erich Jaeger, Thomas Gensch and Thomas Drepper, Novel Thermostable Flavin‐binding Fluorescent Proteins from Thermophilic Organisms, Photochemistry and Photobiology, 93, 3, (849-856), (2017).
- K. Wei and X. Liu, Phylogenetic Analysis and Functional Characterization of the Influenza A H5N1 PB2 Gene, Transboundary and Emerging Diseases, 64, 2, (374-388), (2015).
- Madhavan Narayanan, Vijay R. Singh, Goutham Kodali, Katarina Moravcevic and Robert J. Stanley, An Ethenoadenine FAD Analog Accelerates UV Dimer Repair by DNA Photolyase, Photochemistry and Photobiology, 93, 1, (343-354), (2017).
- Francesco Pietra, On Dioxygen and Substrate Access to Soluble Methane Monooxygenases: An all‐Atom Molecular Dynamics Investigation in Water Solution, Chemistry & Biodiversity, 14, 1, (2016).
- John R. Srouji, Anting Xu, Annsea Park, Jack F. Kirsch and Steven E. Brenner, The evolution of function within the Nudix homology clan, Proteins: Structure, Function, and Bioinformatics, 85, 5, (775-811), (2017).
- Marie Wiechert and Eric Beitz, Mechanism of formate–nitrite transporters by dielectric shift of substrate acidity, The EMBO Journal, 36, 7, (949-958), (2017).
- Jari Kämäräinen, Tuomas Huokko, Sanna Kreula, Patrik R. Jones, Eva‐Mari Aro and Pauli Kallio, Pyridine nucleotide transhydrogenase PntAB is essential for optimal growth and photosynthetic integrity under low‐light mixotrophic conditions in Synechocystis sp. PCC 6803, New Phytologist, 214, 1, (194-204), (2016).
- Gerard C. P. Schaafsma and Mauno Vihinen, Large differences in proportions of harmful and benign amino acid substitutions between proteins and diseases, Human Mutation, 38, 7, (839-848), (2017).
- Navin Kumar, Mohd Shariq, Amarjeet Kumar, Rajesh Kumari, Naidu Subbarao, Rakesh K. Tyagi and Gauranga Mukhopadhyay, Analyzing the role of CagV, a VirB8 homolog of the type IV secretion system of Helicobacter pylori, FEBS Open Bio, 7, 7, (915-933), (2017).
- Sumera Perveen, Naeem Rashid, Xiao‐Feng Tang, Tadayuki Imanaka and Anastassios C. Papageorgiou, Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis shows maximum activity with zinc and forms a unique dimeric structure, FEBS Open Bio, 7, 8, (1217-1230), (2017).
- Vivian H. Tang, Geoffrey A. Stewart and Barbara J. Chang, Dermatophagoides pteronyssinus lyt encoding an NlpC/P60 endopeptidase is also present in mite‐associated bacteria that express LytFM variants, FEBS Open Bio, 7, 9, (1267-1280), (2017).
- Stefanie Wedepohl, Jens Dernedde, Ardeschir Vahedi‐Faridi, Rudolf Tauber, Wolfram Saenger and Haydar Bulut, Reducing Macro‐ and Microheterogeneity of N‐Glycans Enables the Crystal Structure of the Lectin and EGF‐Like Domains of Human L‐Selectin To Be Solved at 1.9 Å Resolution, ChemBioChem, 18, 13, (1338-1345), (2017).
- Bertrand Beckert, Maha Abdelshahid, Heinrich Schäfer, Wieland Steinchen, Stefan Arenz, Otto Berninghausen, Roland Beckmann, Gert Bange, Kürşad Turgay and Daniel N Wilson, Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization, The EMBO Journal, 36, 14, (2061-2072), (2017).
- Iskander Khusainov, Quentin Vicens, Rustam Ayupov, Konstantin Usachev, Alexander Myasnikov, Angelita Simonetti, Shamil Validov, Bruno Kieffer, Gulnara Yusupova, Marat Yusupov and Yaser Hashem, Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF, The EMBO Journal, 36, 14, (2073-2087), (2017).
- Geoffrey Masuyer, Julian Conrad and Pål Stenmark, The structure of the tetanus toxin reveals pH‐mediated domain dynamics, EMBO reports, 18, 8, (1306-1317), (2017).
- Eva Novotná, Karel Waisser, Jiří Kuneš, Karel Palát, Lenka Skálová, Barbora Szotáková, Vladimír Buchta, Jiřina Stolaříková, Vít Ulmann, Marcela Pávová, Jan Weber, Jitka Komrsková, Pavlína Hašková, Ivan Vokřál and Vladimír Wsól, Design, Synthesis, and Biological Evaluation of Isothiosemicarbazones with Antimycobacterial Activity, Archiv der Pharmazie, 350, 8, (2017).
- Cassidy R. Terrell and Laura L. Listenberger, Using molecular visualization to explore protein structure and function and enhance student facility with computational tools, Biochemistry and Molecular Biology Education, 45, 4, (318-328), (2017).
- Aamer Saeed, Parvez Ali Mahesar, Pervaiz Ali Channar, Fayaz Ali Larik, Qamar Abbas, Mubashir Hassan, Hussain Raza and Sung‐Yum Seo, Hybrid Pharmacophoric Approach in the Design and Synthesis of Coumarin Linked Pyrazolinyl as Urease Inhibitors, Kinetic Mechanism and Molecular Docking, Chemistry & Biodiversity, 14, 8, (2017).
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Al Nasr, Desh Ranjan, Mohammad
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Jing He, Solving the Secondary Structure Matching Problem in Cryo-EM
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