FoldX 5.0: working with RNA, small molecules and a new graphical interface-Reference-Cited by-同舟云学术

FoldX 5.0: working with RNA, small molecules and a new graphical interface

Published:2019-03-15 Issue:20 Volume:35 Page:4168-4169
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Delgado Javier¹,Radusky Leandro G¹,Cianferoni Damiano¹,Serrano Luis¹²³

Affiliation:

1. Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain

2. Universitat Pompeu Fabra (UPF), Barcelona, Spain

3. Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

Abstract

Abstract Summary A new version of FoldX, whose main new features allows running classic FoldX commands on structures containing RNA molecules and includes a module that allows parametrization of ligands or small molecules (ParamX) that were not previously recognized in old versions, has been released. An extended FoldX graphical user interface has also being developed (available as a python plugin for the YASARA molecular viewer) allowing user-friendly parametrization of new custom user molecules encoded using JSON format. Availability and implementation http://foldxsuite.crg.eu/

Funder

Spanish Ministry of Economy

Industry and Competitiveness (MEIC) Plan Nacional

Centro de Excelencia Severo Ochoa

CERCA Programme/Generalitat de Catalunya

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

http://academic.oup.com/bioinformatics/article-pdf/35/20/4168/30148988/btz184.pdf

Reference7 articles.

1. Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example;Alibés;Nucleic Acids Res,2010

2. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations;Guerois;J. Mol. Biol,2002

3. DNA-Binding Specificity Prediction with FoldX;Nadra;Methods Enzymol.,2011

4. Crystal structure of the spliceosomal U2B”-U2A’ protein complex bound to a fragment of U2 small nuclear RNA;Price;Nature,1998

5. Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases;Redondo;Nature,2008

Cited by 264 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Computational design of α-amylase from Bacillus licheniformis to increase its activity and stability at high temperatures;Computational and Structural Biotechnology Journal;2024-12

2. Structural insight into the function of human peptidyl arginine deiminase 6;Computational and Structural Biotechnology Journal;2024-12

3. Pretrainable geometric graph neural network for antibody affinity maturation;Nature Communications;2024-09-06

4. Three novel missense variants in two families with JAG2-associated limb-girdle muscular dystrophy;Neuromuscular Disorders;2024-09

5. Maple syrup urine disease diagnosis in Brazilian patients by massive parallel sequencing;Molecular Genetics and Metabolism;2024-09