Protein Science

Cover image for Vol. 27 Issue 1

Edited By: Brian W. Matthews

Impact Factor: 2.523

ISI Journal Citation Reports © Ranking: 2016: 160/290 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

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  • Computational design of membrane proteins using RosettaMembrane

    Computational design of membrane proteins using RosettaMembrane

    Atomic detail of designs compared to wild-type. A closer look at typical interactions at the core (A–C), surface (D–F), and homo-oligomeric interface (G–I). Representative cases were selected from PDBID (A–C), PDBID (D–F), and PDBID (G–I). Green represents respective minimized native, aquamarine is RosettaMembrane, and light orange is Talaris.

  • PixelDB: Protein–peptide complexes annotated with structural conservation of the peptide binding mode

    PixelDB: Protein–peptide complexes annotated with structural conservation of the peptide binding mode

    Examples of peptide binding modes containing one or more ECRs and exosite(s). (A) Cluster 28 binding mode 2 (ankyrin repeat), (B) Cluster 25 binding mode 1 (eukaryotic initiation factor 4E), (C) Cluster 111 binding mode 1 (apical membrane antigen 1), and (D) Cluster 9 binding mode 1 (major histocompatibility complex). Peptides are shown in cartoon representation and one receptor of each cluster is shown using a surface representation. Core residues and core-binding sites are shown in red and residues in ECRs or exosites are shown in blue. Representative PDB IDs for each binding mode are, respectively: 3UXG,5ABY,3RSI37 and 4H25.38

  • Improvements to the APBS biomolecular solvation software suite

    Improvements to the APBS biomolecular solvation software suite

    3Dmol.js interface displaying a rendering of fasciculin-2 (1FAS) protein with translucent, solvent-accessible surface using a stick model and red–green–blue color scheme.

  • Visualizing correlated motion with HDBSCAN clustering

    Visualizing correlated motion with HDBSCAN clustering

    In this example of correlation visualization with the biologically relevant, zinc-bound NEMO CYNZN, we use the (a) residue-residue correlation matrix as (b) a similarity matrix for HDSCAN clustering, and as (c) raw input for clustering. We also (d) calculate a new similarity matrix based on the dot products of all correlation vectors with one another. On the x-axis of the correlation matrix (a), we have labeled the secondary structure elements of NEMO for easy reference.

  • Single-particle cryo-EM—Improved ab initio 3D reconstruction with SIMPLE/PRIME

    Single‐particle cryo‐EM—Improved ab initio 3D reconstruction with SIMPLE/PRIME

    A gallery of ab initio maps obtained from cluster centers with the improved PRIME2D/PRIME3D approach

  • UCSF ChimeraX: Meeting modern challenges in visualization and analysis

    UCSF ChimeraX: Meeting modern challenges in visualization and analysis

    Low-resolution surfaces. Reovirus capsid proteins (PDBid: 1ej6) shown with 15-Å-resolution Gaussian surfaces.

  • Computational design of membrane proteins using RosettaMembrane
  • PixelDB: Protein–peptide complexes annotated with structural conservation of the peptide binding mode
  • Improvements to the APBS biomolecular solvation software suite
  • Visualizing correlated motion with HDBSCAN clustering
  • Single‐particle cryo‐EM—Improved ab initio 3D reconstruction with SIMPLE/PRIME
  • UCSF ChimeraX: Meeting modern challenges in visualization and analysis

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Authors Melanie Dietrich, Christina Harprecht and Thilo Stehle on their recently published Protein Science paper entitled "The bulky and the sweet: How neutralizing antibodies and glycan receptors compete for virus binding." Read the paper here

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Protein Science Awards

2017 Best Paper Award

2017 Best Paper Award Winners
We are pleased to announce the winners of the 2017 Protein Science Best Paper Award:

Charlotte Miton
Postdoctoral Research Fellow
Michael Smith Laboratories at University of British Columbia

How mutational epistasis impairs predictability in protein evolution and design
Charlotte M. Miton and Nobuhiko Tokuriki
Protein Sci. 25:1260-1272, 2016.

Zach Schaefer
Graduate Student
Department of Biochemistry and Molecular Biology at University of Chicago

A polar ring endows improved specificity to an antibody fragment
Zachary P. Schaefer, Lucas J. Bailey and Anthony A. Kossiakoff
Protein Sci. 25:1290-1298, 2016.

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2017 Young Investigator Award Winner

The Protein Science Young Investigator Award recognizes a scientist generally within the first 8 years of an independent career who has made an important contribution to the study of proteins. The 2017 winner is Dr. David Pagliarini (University of Wisconsin, Madison).

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More information on our awards can be found here.

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