Tools for Protein Science: Protein Science: Vol 29, No 1

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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: Volume 29, Issue 1

Special Issue:Tools for Protein Science

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ISSUE INFORMATION

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INTRODUCTION

Tools 2020: A compilation of tools for protein science

TOOLS FOR PROTEIN SCIENCE

The antimicrobial peptide database provides a platform for decoding the design principles of naturally occurring antimicrobial peptides

SimpleDSFviewer: A tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions

KEGG Mapper for inferring cellular functions from protein sequences

Collection of antimicrobial peptides database and its derivatives: Applications and beyond

Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

SASBDB: Towards an automatically curated and validated repository for biological scattering data

Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations

Cryo-EM map interpretation and protein model-building using iterative map segmentation

A three-dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor-NIH protein structure determination

VarSite: Disease variants and protein structure

Molstack: A platform for interactive presentations of electron density and cryo-EM maps and their interpretations

DALI and the persistence of protein shape

An engineered ultra-high affinity Fab-Protein G pair enables a modular antibody platform with multifunctional capability

Peppy: A virtual reality environment for exploring the principles of polypeptide structure

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions—Insights from transcription factors

DISOselect: Disorder predictor selection at the protein level

NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence

Flexible docking of peptides to proteins using CABS-dock

Hybrid Electron Microscopy Normal Mode Analysis with Scipion

Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS

Prediction of impacts of mutations on protein structure and interactions: SDM, a statistical approach, and mCSM, using machine learning

ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins

Shortcuts for faster image creation in PyMOL

The Dundee Resource for Sequence Analysis and Structure Prediction

Cross-docking benchmark for automated pose and ranking prediction of ligand binding

Temperature dependence of NMR chemical shifts: Tracking and statistical analysis

New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics

Facilities that make the PDB data collection more powerful

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