Search Results - "Smith, Colin A."

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction by Smith, Colin A., Kortemme, Tanja

“…Incorporation of effective backbone sampling into protein simulation and design is an important step in increasing the accuracy of computational protein…”
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Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design by Smith, Colin A, Kortemme, Tanja

“…Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing…”
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A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design by Ó Conchúir, Shane, Barlow, Kyle A, Pache, Roland A, Ollikainen, Noah, Kundert, Kale, O'Meara, Matthew J, Smith, Colin A, Kortemme, Tanja

“…The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for…”
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XCMS:  Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification by Smith, Colin A, Want, Elizabeth J, O'Maille, Grace, Abagyan, Ruben, Siuzdak, Gary

“…Metabolite profiling in biomarker discovery, enzyme substrate assignment, drug activity/specificity determination, and basic metabolic research requires new…”
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Allosteric switch regulates protein–protein binding through collective motion by Smith, Colin A., Ban, David, Pratihar, Supriya, Giller, Karin, Paulat, Maria, Becker, Stefan, Griesinger, Christian, Lee, Donghan, de Groot, Bert L.

“…Many biological processes depend on allosteric communication between different parts of a protein, but the role of internal protein motion in propagating…”
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Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy by Ban, David, Smith, Colin A., de Groot, Bert L., Griesinger, Christian, Lee, Donghan

“…Protein function can be modulated or dictated by the amplitude and timescale of biomolecular motion, therefore it is imperative to study protein dynamics…”
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Population Shuffling of Protein Conformations by Smith, Colin A., Ban, David, Pratihar, Supriya, Giller, Karin, Schwiegk, Claudia, de Groot, Bert L., Becker, Stefan, Griesinger, Christian, Lee, Donghan

“…Motions play a vital role in the functions of many proteins. Discrete conformational transitions to excited states, happening on timescales of hundreds of…”
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Altered‐specificity mutants of the HIV Rev arginine‐rich motif‐RRE IIB interaction by Raad, Nicole G., Ghattas, Ingrid R., Amano, Ryo, Watanabe, Natsuki, Sakamoto, Taiichi, Smith, Colin A.

“…Arginine‐rich motifs (ARMs) bind RNA structures with high affinity and specificity, and the human immunodeficiency virus (HIV) exploits ARM‐RNA interactions to…”
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Diverse mutants of HIV RRE IIB recognize wild-type Rev ARM or Rev ARM R35G-N40V by Abdallah, Emane Y., Smith, Colin A.

“…The binding of human immunodeficiency virus Rev protein via its arginine‐rich motif (ARM) to an internal loop in the Rev‐response element region IIB (RRE IIB)…”
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Flexible backbone sampling methods to model and design protein alternative conformations by Ollikainen, Noah, Smith, Colin A, Fraser, James S, Kortemme, Tanja

“…Sampling alternative conformations is key to understanding how proteins work and engineering them for new functions. However, accurately characterizing and…”
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Design of a Phosphorylatable PDZ Domain with Peptide-Specific Affinity Changes by Smith, Colin A., Shi, Catherine A., Chroust, Matthew K., Bliska, Thomas E., Kelly, Mark J.S., Jacobson, Matthew P., Kortemme, Tanja

“…Phosphorylation is one of the most common posttranslational modifications controlling cellular protein activity. Here, we describe a combined computational and…”
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Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains by Smith, Colin A., Kortemme, Tanja

“…Protein–protein recognition, frequently mediated by members of large families of interaction domains, is one of the cornerstones of biological function. Here,…”
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Predicting binding affinity changes from long‐distance mutations using molecular dynamics simulations and Rosetta by Wells, Nicholas G. M., Smith, Colin A.

“…Computationally modeling how mutations affect protein–protein binding not only helps uncover the biophysics of protein interfaces, but also enables the…”
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Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques by Rovó, Petra, Smith, Colin A, Gauto, Diego, de Groot, Bert L, Schanda, Paul, Linser, Rasmus

“…NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state…”
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Optimizing the function and dynamics of de novo designed fluorescent β-barrel proteins by Nguyen, Justin P., Holoman, Tyla, Cardenas, Jaime, Carrigan, Colleen, Smith, Colin A.

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ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules by Leaver-Fay, Andrew, Tyka, Michael, Lewis, Steven M, Lange, Oliver F, Thompson, James, Jacak, Ron, Kaufman, Kristian, Renfrew, P Douglas, Smith, Colin A, Sheffler, Will, Davis, Ian W, Cooper, Seth, Treuille, Adrien, Mandell, Daniel J, Richter, Florian, Ban, Yih-En Andrew, Fleishman, Sarel J, Corn, Jacob E, Kim, David E, Lyskov, Sergey, Berrondo, Monica, Mentzer, Stuart, Popović, Zoran, Havranek, James J, Karanicolas, John, Das, Rhiju, Meiler, Jens, Kortemme, Tanja, Gray, Jeffrey J, Kuhlman, Brian, Baker, David, Bradley, Philip

“…We have recently completed a full re-architecturing of the ROSETTA molecular modeling program, generalizing and expanding its existing functionality. The new…”
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Bacteriophage P22 Antitermination boxB Sequence Requirements Are Complex and Overlap with Those of λ by COCOZAKI, Alexis I, GHATTAS, Ingrid R, SMITH, Colin A

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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The RNA-Binding Domain of Bacteriophage P22 N Protein Is Highly Mutable, and a Single Mutation Relaxes Specificity toward λ by COCOZAKI, Alexis I, GHATTAS, Ingrid R, SMITH, Colin A

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Insights into the Human CD59 Complement Binding Interface Toward Engineering New Therapeutics by Huang, Yuxiang, Smith, Colin A., Song, Hongbin, Morgan, B. Paul, Abagyan, Ruben, Tomlinson, Stephen

“…CD59 is a 77-amino acid membrane glycoprotein that plays an important role in regulating the terminal pathway of complement by inhibiting formation of the…”
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Free energy calculations of ALS‐causing SOD1 mutants reveal common perturbations to stability and dynamics along the maturation pathway by Wells, Nicholas G. M., Tillinghast, Grant A., O'Neil, Alison L., Smith, Colin A.

“…With over 150 heritable mutations identified as disease‐causative, superoxide dismutase 1 (SOD1) has been a main target of amyotrophic lateral sclerosis (ALS)…”
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