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pyFoldX: enabling biomolecular analysis and engineering along structural ensembles [article]

Leandro G Radusky, Luis Serrano
2021 bioRxiv   pre-print
Recent years have seen an increase in the number of structures available, not only for new proteins but also for the same protein crystallized with different molecules and proteins. While protein design software have proven to be successful in designing and modifying proteins, they can also be overly sensitive to small conformational differences between structures of the same protein. To cope with this, we introduce here pyFoldX, a python library that allows the integrative analysis of
more » ... s of the same protein using FoldX, an established forcefield and modeling software. The library offers new functionalities for handling different structures of the same protein, an improved molecular parametrization module, and an easy integration with the data analysis ecosystem of the python programming language.
doi:10.1101/2021.08.16.456210 fatcat:dzpnu5ayjbdlpkyjjiirhrbdjy

pyFoldX: enabling biomolecular analysis and engineering along structural ensembles

Leandro G Radusky, Luis Serrano, Alfonso Valencia
2022 Bioinformatics  
Recent years have seen an increase in the number of structures available, not only for new proteins but also for the same protein crystallized with different molecules and proteins. While protein design software have proven to be successful in designing and modifying proteins, they can also be overly sensitive to small conformational differences between structures of the same protein. To cope with this, we introduce here pyFoldX, a python library that allows the integrative analysis of
more » ... s of the same protein using FoldX, an established forcefield and modeling software. The library offers new functionalities for handling different structures of the same protein, an improved molecular parametrization module, and an easy integration with the data analysis ecosystem of the python programming language. Availability pyFoldX rely on the FoldX software for energy calculations and modelling, which can be downloaded upon registration in http://foldxsuite.crg.eu/ and its licence is free of charge for academics. The pyFoldX library is open-source. Full details on installation, tutorials covering the library functionality, and the scripts used to generate the data and figures presented in this paper are available at https://github.com/leandroradusky/pyFoldX. Supplementary information Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btac072 pmid:35176149 pmcid:PMC9004634 fatcat:674nlys23ne6ngjieps3aikxpy

ProteinFishing: A protein complex generator within the ModelX toolsuite

Damiano Cianferoni, Leandro G Radusky, Sarah A Head, Luis Serrano, Javier Delgado, Arne Elofsson
2020 Bioinformatics  
Summary Accurate three-dimensional modelling of protein–protein interactions (PPI) is essential to compensate for the absence of experimentally-determined complex structures. Here, we present a new set of commands within the ModelX toolsuite capable of generating atomic-level protein complexes suitable for interface design. Among these commands, the new tool ProteinFishing proposes known and/or putative alternative 3D PPI for a given protein complex. The algorithm exploits backbone
more » ... of protein fragments to generate mutually exclusive protein interfaces that are quickly evaluated with a knowledge-based statistical force field. Using interleukin-10-R2 co-crystalized with interferon-lambda-3, and a database of X-ray structures containing interleukin-10, this algorithm was able to generate interleukin-10-R2/interleukin-10 structural models in agreement with experimental data. Implementation and dependencies ProteinFishing is a portable command-line tool included in the ModelX toolsuite, written in C ++, that makes use of an SQL (tested for MySQL and MariaDB) relational database delivered with a template SQL dump called FishXDB. FishXDB contains the empty tables of ModelX fragments and the data used by the embedded statistical force field. ProteinFishing is compiled for Linux-64bit, MacOS-64bit, and Windows-32bit operating systems. Supplementary information Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btaa533 pmid:32437555 pmcid:PMC7390992 fatcat:xv4p2dyhwnethb5ko3cwtr4oue

VarQ: a tool for the structural analysis of Human Protein Variants [article]

Leandro Radusky, Carlos P Modenutti, Javier Delgado, Juan P Bustamante, Sebastian Vishnopolska, Christina Kiel, Luis Serrano, Marcelo Marti, Adrian G Turjanski
2018 bioRxiv   pre-print
VarQ: a tool for the structural analysis of Human Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales, F o r P e e r R e v i e w Protein Variants Leandro Radusky  ...  Figure 3 shows the histogram of the ∆∆G energy, estimated using the FoldX software, for neutral and pathogenic SAS.  ... 
doi:10.1101/277491 fatcat:6s2hewwqpfamdo6suqvvfbiuka

FrustratometeR: an R-package to compute Local frustration in protein structures, point mutants and MD simulations [article]

Atilio O. Rausch, Maria I. Freiberger, Cesar O. Leonetti, Diego M. Luna, Leandro G. Radusky, Peter G. Wolynes, Diego U. Ferreiro, R. Gonzalo Parra
2020 bioRxiv   pre-print
Once folded natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i.e. they have highly frustrated regions. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein-protein interactions, small ligand recognition, catalytic sites and allostery. Here we present
more » ... meteR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and MD trajectories, allowing straightforward integration of local frustration analysis in to pipelines for protein structural analysis. Availability and implementation: https://github.com/proteinphysiologylab/frustratometeR .
doi:10.1101/2020.11.26.400432 fatcat:g67y2lmfsjd3zatgkbbc5dqmj4

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

R. Gonzalo Parra, Nicholas P. Schafer, Leandro G. Radusky, Min-Yeh Tsai, A. Brenda Guzovsky, Peter G. Wolynes, Diego U. Ferreiro
2016 Nucleic Acids Research  
The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins' biological behavior. It compares the energy distributions of the native state with respect to structural decoys. The network of minimally frustrated interactions encompasses the folding core of the molecule. Sites of high local frustration often correlate with functional
more » ... regions such as binding sites and regions involved in allosteric transitions. We present here an upgraded version of a webserver that measures local frustration. The new implementation that allows the inclusion of electrostatic energy terms, important to the interactions with nucleic acids, is significantly faster than the previous version enabling the analysis of large macromolecular complexes within a user-friendly interface. The webserver is freely available at URL: http://frustratometer.qb.fcen.uba.ar.
doi:10.1093/nar/gkw304 pmid:27131359 pmcid:PMC4987889 fatcat:cjfm546phfcynek55hokhb4wpy

Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens

Ezequiel J Sosa, Germán Burguener, Esteban Lanzarotti, Lucas Defelipe, Leandro Radusky, Agustín M Pardo, Marcelo Marti, Adrián G Turjanski, Darío Fernández Do Porto
2017 Nucleic Acids Research  
Available genomic data for pathogens has created new opportunities for drug discovery and development to fight them, including new resistant and multiresistant strains. In particular structural data must be integrated with both, gene information and experimental results. In this sense, there is a lack of an online resource that allows genome widebased data consolidation from diverse sources together with thorough bioinformatic analysis that allows easy filtering and scoring for fast target
more » ... tion for drug discovery. Here, we present Target-Pathogen database (http://target.sbg.qb.fcen.uba.ar/ patho), designed and developed as an online resource that allows the integration and weighting of protein information such as: function, metabolic role, off-targeting, structural properties including druggability, essentiality and omic experiments, to facilitate the identification and prioritization of candidate drug targets in pathogens. We include in the database 10 genomes of some of the most relevant microorganisms for human health (Mycobacterium tuberculosis, Mycobacterium leprae, Klebsiella pneumoniae, Plasmodium vivax, Toxoplasma gondii, Leishmania major, Wolbachia bancrofti, Trypanosoma brucei, Shigella dysenteriae and Schistosoma Smanosoni) and show its applicability. New genomes can be uploaded upon request.
doi:10.1093/nar/gkx1015 pmid:29106651 pmcid:PMC5753371 fatcat:fohat2zws5fxddaghuc5kumg2m

An integrated structural proteomics approach along the druggable genome of Corynebacterium pseudotuberculosis species for putative druggable targets

Leandro G Radusky, Syed Hassan, Esteban Lanzarotti, Sandeep Tiwari, Syed Jamal, Javed Ali, Amjad Ali, Rafaela Ferreira, Debmalya Barh, Artur Silva, Adrián G Turjanski, Vasco AC Azevedo
2015 BMC Genomics  
A Gaussian fit of the data made to define these sets was performed in Radusky et al., 2014 [11] .  ...  1239 D9Q8X6 Diaminopimelate epimerase [36] 8 Cp1002_1270 D9Q906 Riboflavin biosynthesis protein ribF [37] 9 Cp1002_0001 D9Q5G4 Chromosomal replication initiator protein DnaA [25] Radusky  ... 
doi:10.1186/1471-2164-16-s5-s9 pmid:26041381 pmcid:PMC4460585 fatcat:w5me5vhtwjawnd7vf2rkfvtwfm

A whole genome bioinformatic approach to determine potential latent phase specific targets in Mycobacterium tuberculosis

Lucas A. Defelipe, Dario Fernández Do Porto, Pablo Ivan Pereira Ramos, Marisa Fabiana Nicolás, Ezequiel Sosa, Leandro Radusky, Esteban Lanzarotti, Adrián G. Turjanski, Marcelo A. Marti
2016 Tuberculosis  
The betweenness centrality of a given node v, C B ðvÞ, in the graph G ¼ ðV; EÞ, where V is a set of vertices or nodes and E a set of edges is given by: C B ðvÞ ¼ P sstsv2V sst ðvÞ sst [57] where s st  ... 
doi:10.1016/j.tube.2015.11.009 pmid:26791267 fatcat:3cenh36vzvhnlmxd4auo6hzqr4

Protein-assisted RNA fragment docking (RnaX) for modeling RNA–protein interactions using ModelX

Javier Delgado Blanco, Leandro G. Radusky, Damiano Cianferoni, Luis Serrano
2019 Proceedings of the National Academy of Sciences of the United States of America  
(D) FoldX ΔΔG RNA Position-Specific Scoring Matrices.  ... 
doi:10.1073/pnas.1910999116 pmid:31732673 pmcid:PMC6900601 fatcat:icduh3trj5ellp6q3zfclknn5i

The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets

Syed S. Hassan, Syed B. Jamal, Leandro G. Radusky, Sandeep Tiwari, Asad Ullah, Javed Ali, Behramand, Paulo V. S. D. de Carvalho, Rida Shams, Sabir Khan, Henrique C. P. Figueiredo, Debmalya Barh (+6 others)
2018 Frontiers in Genetics  
Adrian Gustavo Turjanski and Leandro G. Radusky for their collaboration, timely assistance in theoretical/biological discussion about the project and manuscript preparation.  ...  ., 2014; Radusky et al., 2015) , Mycobacterium. tuberculosis (Asif et al., 2009) , Burkholderia pseudomallei (Chong et al., 2006) , Neisseria gonorrhoea (Barh and Kumar, 2009) , Helicobacter pylori  ...  Copyright © 2018 Hassan, Jamal, Radusky, Tiwari, Ullah, Ali, Behramand, de Carvalho, Shams, Khan, Figueiredo, Barh, Ghosh, Silva, Baumbach, Röttger, Turjanski and Azevedo.  ... 
doi:10.3389/fgene.2018.00044 pmid:29487617 pmcid:PMC5816920 fatcat:k62er2ne7fa4nfvwnbbnvzzkoi

VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants

Leandro Radusky, Carlos Modenutti, Javier Delgado, Juan P. Bustamante, Sebastian Vishnopolska, Christina Kiel, Luis Serrano, Marcelo Marti, Adrián Turjanski
2018 Frontiers in Genetics  
ACKNOWLEDGMENTS A preprint version of this article has been deposited in bioRxiv (Radusky et al., 2018) .  ...  Those mutations that have more than 2 kcal/Mol G are labeled as "High G variation." Residue Exposure For each residue in each structure, the Solvent Accessible Surface Area (SASA) was computed.  ...  Copyright © 2018 Radusky, Modenutti, Delgado, Bustamante, Vishnopolska, Kiel, Serrano, Marti and Turjanski.  ... 
doi:10.3389/fgene.2018.00620 pmid:30574164 pmcid:PMC6291447 fatcat:mqwz4qfeafasjnblunyg474y4i

robustica: customizable robust independent component analysis [article]

Miquel Anglada-Girotto, Samuel Miravet-Verde, Luis Serrano, Sarah A. Head
2021 bioRxiv   pre-print
ACKNOWLEDGEMENTS We thank Xavier Hernandez-Alias, Marc Weber, and Leandro G. Radusky for the insightful discussions throughout the development of this project.  ... 
doi:10.1101/2021.12.10.471891 fatcat:6tht27s2bvfrhhrfko224nvove

MTS-Etomidate Selectively Reacts Within the GABAA Receptor Etomidate Binding Site

Deirdre S. Stewart, Shaukat S. Husain, Keith W. Miller, Stuart A. Forman
2009 Biophysical Journal  
at a 1 b 2 g 2 channels.  ...  The mean burst length and intra-burst open probability (P o ) for the a 3 b 3 g 2 channels was 136.7 5 16.8 ms and 0.84 5 0.05 (n ¼ 4), respectively and for the a 1 b 2 g 2 channels was 87.4 5 12.0 ms  ...  Radusky, Luciano Moffatt.  ... 
doi:10.1016/j.bpj.2008.12.2516 fatcat:aropll347neqve7mxnt24ddda4

BeEP Server: using evolutionary information for quality assessment of protein structure models

Nicolas Palopoli, Esteban Lanzarotti, Gustavo Parisi
2013 Nucleic Acids Research  
Special thanks to Leandro Radusky from EMBnet Argentina for his constant support during the development of the BeEP Server and to Dr. Richard J.  ...  Further validation of native-like models can be achieved by comparison with the BeEP scores of known structures (g). derived the alignments from the pre-computed structuresequence alignments of the HSSP  ... 
doi:10.1093/nar/gkt453 pmid:23729471 pmcid:PMC3692104 fatcat:i6ve5qeyjfdkdf774ukgzmp5lm
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