Stabilizing proteins, simplified: A Rosetta-based webtool for predicting favorable mutations.

Autor: Thieker DF; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA., Maguire JB; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA., Kudlacek ST; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA., Leaver-Fay A; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA., Lyskov S; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA., Kuhlman B; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.; Lineburger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

Publikováno v: Protein science : a publication of the Protein Society [Protein Sci] 2022 Oct; Vol. 31 (10), pp. e4428.

Perturbing the energy landscape for improved packing during computational protein design.

Autor: Maguire JB; Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA., Haddox HK; Department of Biochemistry, University of Washington, Seattle, Washington, USA.; Institute for Protein Design, University of Washington, Seattle, Washington, USA., Strickland D; Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, USA., Halabiya SF; Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, USA., Coventry B; Institute for Protein Design, University of Washington, Seattle, Washington, USA.; Molecular Engineering PhD Program, University of Washington, Seattle, Washington, USA., Griffin JR; Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, USA., Pulavarti SVSRK; Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, USA., Cummins M; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA., Thieker DF; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA., Klavins E; Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, USA., Szyperski T; Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, USA., DiMaio F; Department of Biochemistry, University of Washington, Seattle, Washington, USA.; Institute for Protein Design, University of Washington, Seattle, Washington, USA., Baker D; Department of Biochemistry, University of Washington, Seattle, Washington, USA.; Institute for Protein Design, University of Washington, Seattle, Washington, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA., Kuhlman B; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

Publikováno v: Proteins [Proteins] 2021 Apr; Vol. 89 (4), pp. 436-449. Date of Electronic Publication: 2020 Dec 11.

Downstream Products are Potent Inhibitors of the Heparan Sulfate 2-O-Sulfotransferase.

Autor: Thieker DF; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA., Xu Y; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Rm 1044, Genetic Medicine Building, Chapel Hill, USA., Chapla D; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA., Nora C; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA., Qiu H; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA., Felix T; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA., Wang L; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA., Moremen KW; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA., Liu J; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Rm 1044, Genetic Medicine Building, Chapel Hill, USA., Esko JD; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA., Woods RJ; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA. rwoods@ccrc.uga.edu.; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA. rwoods@ccrc.uga.edu.

Publikováno v: Scientific reports [Sci Rep] 2018 Aug 07; Vol. 8 (1), pp. 11832. Date of Electronic Publication: 2018 Aug 07.

Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking.

Autor: Makeneni S; Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States., Thieker DF; Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States., Woods RJ; Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States.

Publikováno v: Journal of chemical information and modeling [J Chem Inf Model] 2018 Mar 26; Vol. 58 (3), pp. 605-614. Date of Electronic Publication: 2018 Mar 09.

Uncovering the Relationship between Sulphation Patterns and Conformation of Iduronic Acid in Heparan Sulphate.

Autor: Hsieh PH; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA., Thieker DF; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA., Guerrini M; Istituto di Ricerche Chimiche e Biochimiche 'G. Ronzoni', via G. Colombo 81, 20133 Milan, Italy., Woods RJ; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA., Liu J; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA.

Publikováno v: Scientific reports [Sci Rep] 2016 Jul 14; Vol. 6, pp. 29602. Date of Electronic Publication: 2016 Jul 14.