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1. Full Text Automated protein structure modeling with swiss-model workspace and the protein model portal
by Bordoli, Lorenza and Schwede, Torsten
Methods in Molecular Biology, ISSN 1064-3745, 2012, Volume 857, pp. 107 - 136
Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of... 
SWISS-MODEL | Comparative modeling | Automation | Homology modeling | Protein Model Portal | Molecular models | Protein structure prediction | Quality estimation | QMEAN | Models, Molecular | Molecular Sequence Data | Amino Acid Sequence | Structural Homology, Protein | Proteins - chemistry | Databases, Protein | Index Medicus | quality estimation | PMP | automation | homology modeling | comparative modeling | molecular models | protein structure prediction
Conference Proceeding
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2. Full Text OpenStructure: A flexible software framework for computational structural biology
by Biasini, Marco and Mariani, Valerio and Haas, Jürgen and Scheuber, Stefan and Schenk, Andreas D and Schwede, Torsten and Philippsen, Ansgar
Bioinformatics, ISSN 1367-4803, 08/2010, Volume 26, Issue 20, pp. 2626 - 2628
Motivation: Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and... 
SWISS-MODEL | PROTEIN | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MODEL QUALITY ESTIMATION | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | WORKSPACE | Computational Biology - methods | Software | Algorithms | Databases, Factual | Index Medicus | Applications Note
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3. Full Text Mapping the H-NOX/HK Binding Interface in &ITVibrio cholerae&IT by Hydrogen/Deuterium Exchange Mass Spectrometry
by Guo, YR and Iavarone, AT and Cooper, MM and Marletta, MA
BIOCHEMISTRY, ISSN 0006-2960, 03/2018, Volume 57, Issue 11, pp. 1779 - 1789
Heme-nitric oxide/oxygen binding (H-NOX) proteins are a group of hemoproteins that bind diatomic gas ligands such as nitric oxide (NO) and oxygen (O-2 ). H-NOX... 
ACTIVATION | SWISS-MODEL WORKSPACE | SHEWANELLA-ONEIDENSIS | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | NITRIC-OXIDE | FULL-LENGTH STRUCTURE | PROTEINS | SOLUBLE GUANYLATE-CYCLASE | HISTIDINE KINASE | VIBRIO-CHOLERAE
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4. Full Text Differential Contribution of Subunit Interfaces to alpha 9 alpha 10 Nicotinic Acetylcholine Receptor Function
by Boffi, JC and Marcovich, I and Gill-Thind, JK and Corradi, J and Collins, T and Lipovsek, MM and Moglie, M and Plazas, PV and Craig, PO and Millar, NS and Bouzat, C and Elgoyhen, AB
MOLECULAR PHARMACOLOGY, ISSN 0026-895X, 03/2017, Volume 91, Issue 3, pp. 250 - 262
Nicotinic acetylcholine receptors can be assembled from either homomeric or heteromeric pentameric subunit combinations. At the interface of the extracellular... 
CHOLINERGIC-RECEPTOR | HAIR-CELLS | SWISS-MODEL WORKSPACE | CALCIUM PERMEABILITY | CYS-LOOP RECEPTORS | EXTRACELLULAR DOMAIN | PHARMACOLOGY & PHARMACY | LIGAND-BINDING DOMAIN | ALPHA-CONOTOXIN RGIA | AGONIST SENSITIVITY | PHARMACOLOGICAL-PROPERTIES
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5. Full Text Unexpected challenges in treating multidrug-resistant gram-negative bacteria: Resistance to ceftazidime-avibactam in archived isolates of Pseudomonas aeruginosa
by Winkler, Marisa L and Papp-Wallace, Krisztina M and Hujer, Andrea M and Domitrovic, T. Nicholas and Hujer, Kristine M and Hurless, Kelly N and Tuohy, Marion and Hall, Geraldine and Bonomo, Robert A
Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, 02/2015, Volume 59, Issue 2, pp. 1020 - 1029
Pseudomonas aeruginosa is a notoriously difficult-to-treat pathogen that is a common cause of severe nosocomial infections. Investigating a collection of... 
STRAINS | TOBRAMYCIN | MECHANISM | SWISS-MODEL WORKSPACE | EFFLUX PUMPS | FOSFOMYCIN | MICROBIOLOGY | PHARMACOLOGY & PHARMACY | CYSTIC-FIBROSIS | BETA-LACTAMASE INHIBITOR | COMBINATION | IN-VITRO ACTIVITY | Azabicyclo Compounds - pharmacology | Microbial Sensitivity Tests | Ceftazidime - pharmacology | Fosfomycin - pharmacology | Gram-Negative Bacteria | Humans | Anti-Bacterial Agents - pharmacology | Pseudomonas aeruginosa - drug effects | Index Medicus | Mechanisms of Resistance
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6. Full Text Excess of De Novo Deleterious Mutations in Genes Associated with Glutamatergic Systems in Nonsyndromic Intellectual Disability
by Hamdan, Fadi F and Gauthier, Julie and Araki, Yoichi and Lin, Da-Ting and Yoshizawa, Yuhki and Higashi, Kyohei and Park, A-Reum and Spiegelman, Dan and Dobrzeniecka, Sylvia and Piton, Amélie and Tomitori, Hideyuki and Daoud, Hussein and Massicotte, Christine and Henrion, Edouard and Diallo, Ousmane and Shekarabi, Masoud and Marineau, Claude and Shevell, Michael and Maranda, Bruno and Mitchell, Grant and Nadeau, Amélie and D'Anjou, Guy and Vanasse, Michel and Srour, Myriam and Lafrenière, Ronald G and Drapeau, Pierre and Lacaille, Jean Claude and Kim, Eunjoon and Lee, Jae-Ran and Igarashi, Kazuei and Huganir, Richard L and Rouleau, Guy A and Michaud, Jacques L and S2D Grp and S2D Group
The American Journal of Human Genetics, ISSN 0002-9297, 2011, Volume 88, Issue 3, pp. 306 - 316
Little is known about the genetics of nonsyndromic intellectual disability (NSID). We hypothesized that de novo mutations (DNMs) in synaptic genes explain an... 
AMPA RECEPTORS | MENTAL-RETARDATION | NMDA RECEPTORS | SWISS-MODEL WORKSPACE | SCAFFOLDING PROTEIN SHANK3 | CULTURED NEURONS | GENETICS & HEREDITY | COGNITIVE IMPAIRMENT | KINESIN MOTOR KIF1A | CELL-DEATH | PLASTICITY | Protein Binding - genetics | Calcium Channels - metabolism | Cytoskeletal Proteins - genetics | Glutamic Acid - genetics | Humans | Male | Mutation, Missense - genetics | Intellectual Disability - genetics | Receptors, N-Methyl-D-Aspartate - genetics | Base Sequence | RNA Splicing - genetics | HEK293 Cells | Kinesin - genetics | Cytoskeletal Proteins - metabolism | Female | Membrane Proteins - metabolism | Neuropeptides - genetics | Calcium Channels - genetics | Receptors, AMPA - metabolism | Membrane Proteins - genetics | Rats | Neuropeptides - metabolism | Mutation - genetics | Subcellular Fractions - metabolism | Syndrome | Protein Transport | Phenotype | Animals | Amino Acid Substitution - genetics | Glutamate | Proteins | Cell culture | Learning disabilities | Mutation | Pathogenesis | Genes | Index Medicus
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7. Full Text The cholesterol-dependent cytolysins pneumolysin and streptolysin O require binding to red blood cell glycans for hemolytic activity
by Lucy K. Shewell and Richard M. Harvey and Melanie A. Higgins and Christopher J. Day and Lauren E. Hartley-Tassell and Austen Y. Chen and Christine M. Gillen and David B. A. James and Francis Alonzo III and Victor J. Torres and Mark J. Walker and Adrienne W. Paton and James C. Paton and Michael P. Jennings
Proceedings of the National Academy of Sciences, ISSN 0027-8424, 12/2014, Volume 111, Issue 49, pp. E5312 - E5320
The cholesterol-dependent cytolysin (CDC) pneumolysin (Ply) is a key virulence factor of Streptococcus pneumoniae. Membrane cholesterol is required for the... 
Pneumolysin | Streptolysin O | Cholesterol-dependent cytolysin | Glycan binding | Streptococcus pneumoniae | LISTERIOLYSIN-O | MECHANISM | SWISS-MODEL WORKSPACE | MEMBRANE | MULTIDISCIPLINARY SCIENCES | HUMAN-GRANULOCYTES | SELECTIN | STREPTOCOCCUS-PNEUMONIAE | NONHEMOLYTIC PNEUMOLYSIN | HUMAN ERYTHROCYTES | cholesterol-dependent cytolysin | glycan binding | pneumolysin | streptolysin O | PORE-FORMING TOXINS | Hemolysis | Surface Plasmon Resonance | Amino Acid Sequence | Streptolysins - chemistry | Humans | Bacterial Proteins - chemistry | Molecular Sequence Data | Sequence Homology, Amino Acid | Flow Cytometry | Carbohydrates - chemistry | Mutagenesis | Oligosaccharides - chemistry | Erythrocytes - metabolism | Cell Line, Tumor | Polysaccharides - chemistry | Protein Binding | Glycolipids - chemistry | Protein Conformation | Cell Membrane - metabolism | Binding Sites | Lewis X Antigen - chemistry | Flow cytometry | Membranes | Cholesterol | Binding sites | Streptococcus infections | Index Medicus | Biological Sciences | PNAS Plus
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8. Full Text A public antibody lineage that potently inhibits malaria infection through dual binding to the circumsporozoite protein
by Tan, Joshua and Sack, Brandon K and Oyen, David and Zenklusen, Isabelle and Piccoli, Luca and Barbieri, Sonia and Foglierini, Mathilde and Fregni, Chiara Silacci and Marcandalli, Jessica and Jongo, Said and Abdulla, Salim and Perez, Laurent and Corradin, Giampietro and Varani, Luca and Sallusto, Federica and Sim, Betty Kim Lee and Hoffman, Stephen L and Kappe, Stefan H I and Daubenberger, Claudia and Wilson, Ian A and Lanzavecchia, Antonio
Nature Medicine, ISSN 1078-8956, 05/2018, Volume 24, Issue 4, pp. 401 - 407
Immunization with attenuated Plasmodium falciparum sporozoites (PfSPZs) has been shown to be protective against malaria, but the features of the antibody... 
MEDICINE, RESEARCH & EXPERIMENTAL | EFFICACY | SWISS-MODEL WORKSPACE | BIOCHEMISTRY & MOLECULAR BIOLOGY | PLASMODIUM-FALCIPARUM SPOROZOITES | CHILDREN | CELL BIOLOGY | IMMUNIZATION | MEMORY B-CELLS | PFSPZ VACCINE | IRRADIATED SPOROZOITES | MONOCLONAL-ANTIBODIES | PROTECTIVE ANTIBODIES | Animals | Malaria Vaccines | Antibodies, Protozoan - immunology | Humans | Malaria - immunology | Protozoan Proteins - chemistry | Mice | Plasmodium falciparum - immunology | Molecular targeted therapy | Care and treatment | Immunoglobulins | Malaria | Innovations | Monoclonal antibodies | Development and progression | Genetic aspects | Health aspects | Immunoglobulin M | Vector-borne diseases | Immunization | Immunoglobulin G | Tryptophan | Homology | Infections | Vaccines | Epitopes | Antibody response | Arginine | Coding | Sporozoites | Circumsporozoite protein | Index Medicus
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9. Full Text A naturally occurring feline APOBEC3 variant that loses anti-lentiviral activity by lacking two amino acid residues
by Konno, Yoriyuki and Nagaoka, Shumpei and Kimura, Izumi and Ueda, Mahoko Takahashi and Kumata, Ryuichi and Ito, Jumpei and Nakagawa, So and Kobayashi, Tomoko and Koyanagi, Yoshio and Sato, Kei
Journal of General Virology, ISSN 0022-1317, 05/2018, Volume 99, Issue 5, pp. 704 - 709
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) is a mammalian protein that restricts lentiviral replication. Various polymorphisms... 
APOBEC3 | FIV | Lynx | Evolutionary arms race | Lentivirus | Felids | HIV-1 | CATS | lynx | SWISS-MODEL WORKSPACE | IMMUNODEFICIENCY-VIRUS | LEUKEMIA-VIRUS | ENZYME APOBEC3G | RD-114 VIRUS | VIF | EVOLUTION | VIROLOGY | evolutionary arms race | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | RESTRICTION FACTORS | felids | lentivirus
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10. Full Text Selective Inhibitors of Human Neuraminidase 3
by Guo, Tianlin and Dätwyler, Philipp and Demina, Ekaterina and Richards, Michele R and Ge, Peng and Zou, Chunxia and Zheng, Ruixiang and Fougerat, Anne and Pshezhetsky, Alexey V and Ernst, Beat and Cairo, Christopher W
Journal of Medicinal Chemistry, ISSN 0022-2623, 03/2018, Volume 61, Issue 5, pp. 1990 - 2008
Human neuraminidases (NEU) are associated with human diseases including cancer, atherosclerosis, and diabetes. To obtain small molecule inhibitors as research... 
MOLECULAR-DYNAMICS | IN-VITRO | CHEMISTRY, MEDICINAL | SWISS-MODEL WORKSPACE | UCSF CHIMERA | CRYSTAL-STRUCTURE | INFLUENZA | CYTOSOLIC SIALIDASE NEU2 | LYSOSOMAL STORAGE | DRUG ABSORPTION | SUBSTRATE RECOGNITION | Animals | Isoenzymes | Small Molecule Libraries | Humans | Enzyme Inhibitors - pharmacology | N-Acetylneuraminic Acid - analogs & derivatives | Neuraminidase - antagonists & inhibitors | Mice | Index Medicus
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11. Full Text Double-Cone Localization and Seasonal Expression Pattern Suggest a Role in Magnetoreception for European Robin Cryptochrome 4
by Günther, Anja and Einwich, Angelika and Sjulstok, Emil and Feederle, Regina and Bolte, Petra and Koch, Karl-Wilhelm and Solov’yov, Ilia A and Mouritsen, Henrik
Current Biology, ISSN 0960-9822, 01/2018, Volume 28, Issue 2, pp. 211 - 223.e4
Birds seem to use a light-dependent, radical-pair-based magnetic compass. In vertebrates, cryptochromes are the only class of proteins that form radical pairs... 
magnetic sense | eye | photoreceptor cells | vision | orientation | navigation | photoreceptor | magnetic sensing | magneto-perception | bird migration | ARABIDOPSIS-THALIANA | MOLECULAR-DYNAMICS | ELECTRON-TRANSFER | BLUE-LIGHT PHOTORECEPTOR | AVIAN MAGNETIC COMPASS | MESSENGER-RNA EXPRESSION | SWISS-MODEL WORKSPACE | BIOCHEMISTRY & MOLECULAR BIOLOGY | MIGRATORY BIRDS | PLANT CRYPTOCHROME | RADICAL-PAIR | CELL BIOLOGY | Retinal Cone Photoreceptor Cells - radiation effects | Avian Proteins - metabolism | Songbirds - genetics | Cryptochromes - genetics | Sequence Analysis, DNA | Animals | Songbirds - physiology | Gene Expression Regulation - radiation effects | Chickens - genetics | Perception | Magnetic Fields | Seasons | Chickens - physiology | Animal Migration - radiation effects | Avian Proteins - genetics | Cryptochromes - metabolism | Proteins | Birds | RNA | Analysis | Robins | Index Medicus
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12. Full Text Depolarized Inactivation Overcomes Impaired Activation to Produce DRG Neuron Hyperexcitability in a Na(v)1.7 Mutation in a Patient with Distal Limb Pain
by Huang, JY and Yang, Y and Dib-Hajj, SD and van Es, M and Zhao, P and Salomon, J and Drenth, JPH and Waxman, SG
JOURNAL OF NEUROSCIENCE, ISSN 0270-6474, 09/2014, Volume 34, Issue 37, pp. 12328 - 12340
Sodium channel Na(v)1.7, encoded by SCN9A, is expressed in DRG neurons and regulates their excitability. Genetic and functional studies have established a... 
pain | PRIMARY ERYTHERMALGIA | SWISS-MODEL WORKSPACE | GATED SODIUM-CHANNELS | DRG neurons | NEUROSCIENCES | mutation | SPINAL SENSORY NEURONS | sodium channel | RESTLESS LEGS SYNDROME | CLOSED-STATE INACTIVATION | VOLTAGE SENSOR | ELECTROPHYSIOLOGICAL PROPERTIES | CHANNEL ALPHA-SUBUNIT | SMALL-FIBER NEUROPATHY | Na(v)1.7
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13. Full Text Identification of functionally important conserved trans-membrane residues of bacterial P-IB-type ATPases
by Zhitnitsky, D and Lewinson, O
MOLECULAR MICROBIOLOGY, ISSN 0950-382X, 02/2014, Volume 91, Issue 4, pp. 777 - 789
Powered by ATP hydrolysis, P-IB-ATPases drive the energetically uphill transport of transition metals. These high affinity pumps are essential for heavy metal... 
AMINO-TERMINAL DOMAIN | WILSON-DISEASE | MECHANISM | SWISS-MODEL WORKSPACE | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | MICROBIOLOGY | COPPER | METAL-BINDING SITES | ZNTA | P-1-TYPE ATPASES
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14. Full Text Structural basis for the regulatory interactions of proapoptotic Par-4
by Subhramanyam, Udaya K. Tiruttani and Tiruttani Subhramanyam, Udaya K and Kubicek, Jan and Kubicek, Jan and Eidhoff, Ulf B and Eidhoff, Ulf B and Labahn, Joerg and Labahn, Joerg
Cell death and differentiation, ISSN 1350-9047, 2017, Volume 24, Issue 9, pp. 1540 - 1547
Par-4 is a unique proapoptotic protein with the ability to induce apoptosis selectively in cancer cells. The X-ray crystal structure of the C-terminal domain... 
SWISS-MODEL WORKSPACE | STRUCTURE REFINEMENT | BIOCHEMISTRY & MOLECULAR BIOLOGY | NUCLEAR EXPORT SIGNALS | CANCER-CELL SURVIVAL | DLK/ZIP KINASE | COILED-COIL | WEB SERVER | GCN4 LEUCINE-ZIPPER | PROTEIN PAR-4 | SALT BRIDGE | CELL BIOLOGY | Coils | Masking | Leucine | Position (location) | Localization | Dimerization | Nuclear transport | Crystal structure | Apoptosis | Leucine zipper proteins | Cancer | Phasing | Index Medicus | Original Paper
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15. Full Text Camphor-based CCR5 blocker lead compounds-a computational and experimental approach
by Justino, Gonçalo C and Pinheiro, Pedro F and Roseiro, Alexandra P. S and Knittel, Ana S. O and Gonçalves, João and Justino, Marta C and Carvalho, M. Fernanda N. N
RSC Advances, ISSN 2046-2069, 2016, Volume 6, Issue 61, pp. 56249 - 56259
The C-C chemokine receptor type 5 (CCR5) is a transmembrane receptor that plays a pivotal role as a HIV anchor to human cell membranes, mediating viral entry.... 
SWISS-MODEL WORKSPACE | SMALL-MOLECULE | HIV-1 ENTRY INHIBITORS | PROTEIN-STRUCTURE | INFORMATION | FORCE-FIELD | INFECTION | CHEMISTRY, MULTIDISCIPLINARY | I-TASSER | PEPTIDE | UV-FILTERS
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16. Full Text Directed evolution of a far-red fluorescent rhodopsin
by R. Scott McIsaac and Martin K. M. Engqvist and Timothy Wannier and Adam Z. Rosenthal and Lukas Herwig and Nicholas C. Flytzanis and Eleonora S. Imasheva and Janos K. Lanyi and Sergei P. Balashov and Viviana Gradinaru and Frances H. Arnold
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 9/2014, Volume 111, Issue 36, pp. 13034 - 13039
Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life. A member of this protein family,... 
Directed molecular evolution | Electric potential | Schiff bases | Bacteriorhodopsins | Mutagenesis | Neurons | Imaging | Fluorescence | Libraries | Genetic mutation | Optogenetics | Opsins | Voltage sensor | Bioelectricity | Near-infrared | PROTEIN | voltage sensor | SWISS-MODEL WORKSPACE | PHOTOISOMERIZATION | MULTIDISCIPLINARY SCIENCES | optogenetics | ESCHERICHIA-COLI | SCHIFF-BASE COUNTERION | MICROBIAL RHODOPSIN | DRIVEN PROTON PUMP | MICROSCOPY | bioelectricity | RESPONSES | near-infrared | opsins | BACTERIORHODOPSIN | Archaeal Proteins - metabolism | Halorubrum - metabolism | Green Fluorescent Proteins - metabolism | Cell Survival | Humans | Mutant Proteins - metabolism | Directed Molecular Evolution | Escherichia coli - metabolism | HEK293 Cells | Structural Homology, Protein | Mutation | Binding Sites | Protein research | Microbiological research | Rhodopsin | Physiological aspects | Halobacterium | Research | Protein-protein interactions | Proteins | Membranes | E coli | Scientific imaging | Biochemistry | Cells | Index Medicus | Biological Sciences | Biokemi och molekylärbiologi | Biochemistry and Molecular Biology
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