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A multifaceted study of stigma/style cysteine-rich adhesin (SCA)-like Arabidopsis lipid transfer proteins (LTPs) suggests diversified roles for these LTPs in plant growth and reproduction
Lily stigma/style cysteine-rich adhesin (SCA), a plant lipid transfer protein (LTP) which is secreted into the extracellular matrix, functions in pollen tube guidance in fertilization. AExpand
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  • Open Access
conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure
tl;dr
We developed a consensus secondary structure prediction method, conSSert, which is based on support vector machines (SVM) and provides exceptional accuracy for the prediction of beta-strands with QE accuracy of over 0.82 and a Q2-EH of 0.86. Expand
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Automated computational framework for the analysis of electrostatic similarities of proteins
Charge plays an important role in protein–protein interactions. In the case of excessively charged proteins, their electrostatic potentials contribute to the processes of recognition and binding withExpand
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Protein folding and de novo protein design for biotechnological applications.
In the postgenomic era, the medical/biological fields are advancing faster than ever. However, before the power of full-genome sequencing can be fully realized, the connection between amino acidExpand
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A Gain-of-Function Mutation of Arabidopsis Lipid Transfer Protein 5 Disturbs Pollen Tube Tip Growth and Fertilization[C][W]
During compatible pollination of the angiosperms, pollen tubes grow in the pistil transmitting tract (TT) and are guided to the ovule for fertilization. Lily (Lilium longiflorum) stigma/styleExpand
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  • Open Access
Forcefield_NCAA: Ab Initio Charge Parameters to Aid in the Discovery and Design of Therapeutic Proteins and Peptides with Unnatural Amino Acids and Their Application to Complement Inhibitors of the
We describe the development and testing of ab initio derived, AMBER ff03 compatible charge parameters for a large library of 147 noncanonical amino acids including β- and N-methylated amino acids forExpand
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De novo peptide design with C3a receptor agonist and antagonist activities: theoretical predictions and experimental validation.
Targeting the complement component 3a receptor (C3aR) with selective agonists or antagonists is believed to be a viable therapeutic option for several diseases such as stroke, heart attack,Expand
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  • Open Access
Electrostatic Clustering and Free Energy Calculations Provide a Foundation for Protein Design and Optimization
Electrostatic interactions are ubiquitous in proteins and dictate stability and function. In this review, we discuss several methods for the analysis of electrostatics in protein–proteinExpand
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The Two Sides of Complement C3d: Evolution of Electrostatics in a Link between Innate and Adaptive Immunity
tl;dr
We propose that the electrostatic “hot-spots” of C3d have evolved to optimize its dual-functionality (covalently attaching to pathogen surfaces and interaction with CR2), which are both necessary for the formation B-cell co-receptor complexes. Expand
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  • Open Access
Princeton_TIGRESS: Protein geometry refinement using simulations and support vector machines
tl;dr
We present Princeton_TIGRESS, which when benchmarked on all CASP 7,8,9, and 10 refinement targets, simultaneously increased GDT_TS 76% of the time with an average improvement of 0.83 points per structure. Expand
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