Results 11 to 20 of about 914,048 (349)

Comparative Protein Structure Modeling Using MODELLER [PDF]

Current Protocols in Protein Science, 2006
AbstractFunctional characterization of a protein sequence is a common goal in biology, and is usually facilitated by having an accurate three‐dimensional (3‐D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3‐D model for a protein that is ...
Narayanan, Eswar, Ben, Webb, Marc A, Marti-Renom, M S, Madhusudhan, David, Eramian, Min-Yi, Shen, Ursula, Pieper, Andrej, Sali   +7 more
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Modeling complexes of modeled proteins [PDF]

Proteins: Structure, Function, and Bioinformatics, 2016
ABSTRACTStructural characterization of proteins is essential for understanding life processes at the molecular level. However, only a fraction of known proteins have experimentally determined structures. This fraction is even smaller for protein–protein complexes. Thus, structural modeling of protein–protein interactions (docking) primarily has to rely
Ivan, Anishchenko, Petras J, Kundrotas, Ilya A, Vakser   +2 more
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The Protein Model Portal [PDF]

Journal of Structural and Functional Genomics, 2008
Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for ...
Arnold, K., Kiefer, F., Kopp, J., Battey, J. N., Podvinec, M., Westbrook, J. D., Berman, H. M., Bordoli, L., Schwede, T.   +8 more
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De novo design of immunoglobulin-like domains

Nature Communications, 2022
The immunoglobulin domain framework of antibodies has been a long standing design challenge. Here, the authors describe design rules for tailoring these domains and show they can be accurately designed, de novo, with high stability and the ability to ...
Tamuka M. Chidyausiku, Soraia R. Mendes, Jason C. Klima, Marta Nadal, Ulrich Eckhard, Jorge Roel-Touris, Scott Houliston, Tibisay Guevara, Hugh K. Haddox, Adam Moyer, Cheryl H. Arrowsmith, F. Xavier Gomis-Rüth, David Baker, Enrique Marcos   +13 more
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Performance of Novel Antimicrobial Protein Bg_9562 and In Silico Predictions on Its Properties with Reference to Its Antimicrobial Efficiency against Rhizoctonia solani

Antibiotics, 2022
Bg_9562 is a potential broad-spectrum antifungal effector protein derived from the bacteria Burkholderia gladioli strain NGJ1 and is effective against Rhizoctonia solani, the causal agent of sheath blight in rice.
Pranathi Karnati, Rekha Gonuguntala, Kalyani M. Barbadikar, Divya Mishra, Gopaljee Jha, Vellaisamy Prakasham, Priyanka Chilumula, Hajira Shaik, Maruthi Pesari, Raman Meenakshi Sundaram, Kannan Chinnaswami   +10 more
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RosettaBackrub--a web server for flexible backbone protein structure modeling and design. [PDF]

, 2010
The RosettaBackrub server (http://kortemmelab.ucsf.edu/backrub) implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling.
Friedland, Gregory F, Humphris, Elisabeth L, Kortemme, Tanja, Lauck, Florian, Smith, Colin A   +4 more
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NanoNet: Rapid and accurate end-to-end nanobody modeling by deep learning

Frontiers in Immunology, 2022
Antibodies are a rapidly growing class of therapeutics. Recently, single domain camelid VHH antibodies, and their recognition nanobody domain (Nb) appeared as a cost-effective highly stable alternative to full-length antibodies.
Tomer Cohen, Matan Halfon, Dina Schneidman-Duhovny   +2 more
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The complex, dynamic SpliceOme of the small GTPase transcripts altered by technique, sex, genetics, tissue specificity, and RNA base editing

Frontiers in Cell and Developmental Biology, 2022
The small GTPase family is well-studied in cancer and cellular physiology. With 162 annotated human genes, the family has a broad expression throughout cells of the body. Members of the family have multiple exons that require splicing.
Akansha S. Das, Akansha S. Das, Emily C. Sherry, Emily C. Sherry, Robert M. Vaughan, Marian L. Henderson, Marian L. Henderson, Jacob Zieba, Jacob Zieba, Katie L. Uhl, Olivia Koehn, Caleb P. Bupp, Caleb P. Bupp, Surender Rajasekaran, Surender Rajasekaran, Surender Rajasekaran, Xiaopeng Li, Surya B. Chhetri, Sahar Nissim, Sahar Nissim, Sahar Nissim, Carol L. Williams, Jeremy W. Prokop, Jeremy W. Prokop, Jeremy W. Prokop   +24 more
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Elucidating glycosaminoglycan–protein–protein interactions using carbohydrate microarray and computational approaches [PDF]

, 2011
Glycosaminoglycan polysaccharides play critical roles in many cellular processes, ranging from viral invasion and angiogenesis to spinal cord injury.
Bothwell, C. J. Rogers, Chao, Clement, de Paz, Dechant, Faham, Gama, Huang, K. C. Garcia, Keiser, Khunrae, Kim, L. C. Hsieh-Wilson, Lowes, Mukai, Mulloy, Oohira, P. M. Clark, Pellegrini, Petitou, R. Abrol, Raman, Rapp, Rawat, Raza, Roux, S. E. Tully, Schlessinger, Shelton, Shipp, Spivak-Kroizman, Strom, Sugahara, Sweeney, Tully, Tully, Vaudry, W. A. Goddard, Zhang   +39 more
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Evaluating Autoencoder-Based Featurization and Supervised Learning for Protein Decoy Selection

Molecules, 2020
Rapid growth in molecular structure data is renewing interest in featurizing structure. Featurizations that retain information on biological activity are particularly sought for protein molecules, where decades of research have shown that indeed ...
Fardina Fathmiul Alam, Taseef Rahman, Amarda Shehu   +2 more
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