@article {555, title = {Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility}, journal = {Nucleic Acids Research}, volume = {47}, year = {2019}, month = {05}, pages = {W300-W307}, abstract = {Protein aggregation is a hallmark of a growing number of human disorders and constitutes a major bottleneck in the manufacturing of therapeutic proteins. Therefore, there is a strong need of in-silico methods that can anticipate the aggregative properties of protein variants linked to disease and assist the engineering of soluble protein-based drugs. A few years ago, we developed a method for structure-based prediction of aggregation properties that takes into account the dynamic fluctuations of proteins. The method has been made available as the Aggrescan3D (A3D) web server and applied in numerous studies of protein structure-aggregation relationship. Here, we present a major update of the A3D web server to version 2.0. The new features include: extension of dynamic calculations to significantly larger and multimeric proteins, simultaneous prediction of changes in protein solubility and stability upon mutation, rapid screening for functional protein variants with improved solubility, a REST-ful service to incorporate A3D calculations in automatic pipelines, and a new, enhanced web server interface. A3D 2.0 is freely available at: http://biocomp.chem.uw.edu.pl/A3D2/}, issn = {0305-1048}, doi = {10.1093/nar/gkz321}, url = {https://doi.org/10.1093/nar/gkz321}, author = {Aleksander Kuriata and Valentin Iglesias and Jordi Pujols and Mateusz Kurcinski and Sebastian Kmiecik and Salvador Ventura} } @article {548, title = {Aggrescan3D standalone package for structure-based prediction of protein aggregation properties}, journal = {Bioinformatics}, volume = {btz143}, year = {2019}, type = {Journal Article}, abstract = {SUMMARY: Aggrescan3D (A3D) standalone is a multiplatform Python package for structure-based prediction of protein aggregation properties and rational design of protein solubility. A3D allows the redesign of protein solubility by combining structural aggregation propensity and stability predictions, as demonstrated by a recent experimental study. It also enables predicting the impact of protein conformational fluctuations on the aggregation properties. The standalone A3D version is an upgrade of the original web server implementation - it introduces a number of customizable options, automated analysis of multiple mutations and offers a flexible computational framework for merging it with other computational tools. AVAILABILITY: A3D standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python. The A3D standalone source code, wiki with documentation and examples of use, and installation instructions for Linux, macOS, and Windows are available in the A3D standalone repository at https://bitbucket.org/lcbio/aggrescan3d.}, issn = {1367-4811 (Electronic) 1367-4803 (Linking)}, doi = {10.1093/bioinformatics/btz143}, url = {http://www.ncbi.nlm.nih.gov/pubmed/30825368}, author = {Aleksander Kuriata and Valentin Iglesias and Mateusz Kurcinski and Salvador Ventura and Sebastian Kmiecik} }