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firestar —advances in the prediction of functionally important residues

Gonzalo Lopez, Paolo Maietta, Jose Manuel Rodriguez, Alfonso Valencia, Michael L. Tress
2011 Nucleic Acids Research  
firestar is a server for predicting catalytic and ligand-binding residues in protein sequences. Here, we present the important developments since the first release of firestar.  ...  the performance of firestar.  ...  ACKNOWLEDGEMENTS We would like to thank the referees for helping us to improve the firestar server and Angel Carro and Jose Maria Fernandez for providing timely technical assistance.  ... 
doi:10.1093/nar/gkr437 pmid:21672959 pmcid:PMC3125799 fatcat:77izglzwfbc5raxl4ttbc7pcjy

Structure modeling of novel DNA glycosylase enzyme from oral pathogen Streptococcus sanguinis

Ashwani Sharma, Anshul Nigam
2010 Bioinformation  
The modeled structure was further verified by PROCHECK analysis and subjected to functional site prediction servers for active site residues prediction.  ...  The YA51, LA105, RA107 residues are surrounding the EDA and matching with ligand binding residues predicted by PROFUNC server. 139 designing against DNA glycosylase protein of oral pathogen Streptococcus  ...  Firestar also confirmed our finding of functional sites residues.  ... 
doi:10.6026/97320630005136 pmid:21364794 pmcid:PMC3040489 fatcat:dyrgvxc2pje2lmv3vghhok5bo4

APPRIS: annotation of principal and alternative splice isoforms

Jose Manuel Rodriguez, Paolo Maietta, Iakes Ezkurdia, Alessandro Pietrelli, Jan-Jaap Wesselink, Gonzalo Lopez, Alfonso Valencia, Michael L. Tress
2012 Nucleic Acids Research  
Analysis of the APPRIS data shows that at least 70% of the alternative (nonprincipal) variants would lose important functional or structural information relative to the principal isoform.  ...  In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, APPRIS also selects a single reference sequence for each gene, here termed the principal isoform  ...  ACKNOWLEDGEMENTS The authors would like to thank Angel Carro and Edu Leon for invaluable technical assistance. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gks1058 pmid:23161672 pmcid:PMC3531113 fatcat:5q4zhzyzlrhvxcoqj2dkme5wpe

Investigating the unknown functions in the minimal bacterial genome reveals many transporter proteins [article]

Magdalena Antczak, Martin Michaelis, Mark Wass
2018 bioRxiv   pre-print
Application of state of the art in silico methods for functional annotation demonstrated that these proteins of unknown function lack orthologs, known protein domains, and templates to model their structure  ...  transporter proteins were identified indicating the importance of nutrient uptake into and waste disposal out of the minimal bacterial cell, where many metabolic enzymes have been removed.  ...  Stefano Toppo for advice regarding transformation of Argot2.5 scores into probabilities.  ... 
doi:10.1101/381657 fatcat:r6y4nswrzzhx3mri2h5pv4hw74

GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs

Charles A Santana, Sandro C Izidoro, Raquel C de Melo-Minardi, Jonathan D Tyzack, António J M Ribeiro, Douglas E V Pires, Janet M Thornton, Sabrina de A. Silveira
2022 Nucleic Acids Research  
The identification and characterization of these regions are of fundamental importance to determine protein function, being a fundamental step in processes such as drug design and discovery.  ...  Proteins are essential macromolecules for the maintenance of living systems. Many of them perform their function by interacting with other molecules in regions called binding sites.  ...  Taking advantage of decision tree explainability, we can rank the set of features used in the prediction of binding site residues according to its relative importance.  ... 
doi:10.1093/nar/gkac323 pmid:35524575 fatcat:dtvfmrvdcnentkcruxkzu2hwea

Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality

Nicholas C. Wu, C. Anders Olson, Yushen Du, Shuai Le, Kevin Tran, Roland Remenyi, Danyang Gong, Laith Q. Al-Mawsawi, Hangfei Qi, Ting-Ting Wu, Ren Sun, Michael Worobey
2015 PLoS Genetics  
Furthermore, the tedious process of constructing and analyzing individual mutations limits the number of residues that can be examined in a single study.  ...  Here, we developed a systematic approach to identify the functional residues of a viral protein by coupling experimental fitness profiling with protein stability prediction using the influenza virus polymerase  ...  Li for performing the high-throughput sequencing experiment, L. Jiang and D. Eisenberg for technical supports in ΔΔG predictions and computational resources, H. Luan, T. Chapa and J.  ... 
doi:10.1371/journal.pgen.1005310 pmid:26132554 pmcid:PMC4489113 fatcat:mgw55jixsvf3rgmgkbafzkq26y

I-TASSER server: new development for protein structure and function predictions

Jianyi Yang, Yang Zhang
2015 Nucleic Acids Research  
The functional insights are finally derived by matching the predicted structure models with known proteins in the function databases.  ...  In this article, we summarize recent developments on the I-TASSER server, which were designed to address the requirements from the user community and to increase the accuracy of modeling predictions.  ...  David Shultis for reading the manuscript.  ... 
doi:10.1093/nar/gkv342 pmid:25883148 pmcid:PMC4489253 fatcat:gftebps57bf2tnlibo5drjcrom

webPDBinder: a server for the identification of ligand binding sites on protein structures

Valerio Bianchi, Iolanda Mangone, Fabrizio Ferrè, Manuela Helmer-Citterich, Gabriele Ausiello
2013 Nucleic Acids Research  
The number of similarities identified with the residues in the two sets is then used to derive a propensity value for each residue of the query protein associated to the likelihood that the residue is  ...  The input is either a PDB code or a user-submitted structure. The output is a list of predicted binding pocket residues with propensity and conservation values both in text and graphical format.  ...  In this web server version, the method has been improved by the addition of a novel conservation scoring function with an improvement of 3% in positive predictive value and 13% in sensitivity both in the  ... 
doi:10.1093/nar/gkt457 pmid:23737450 pmcid:PMC3692056 fatcat:nqi6e3mh4ncsffhoewmzvpa7y4

Sequence-based feature prediction and annotation of proteins

Agnieszka S Juncker, Lars J Jensen, Andrea Pierleoni, Andreas Bernsel, Michael L Tress, Peer Bork, Gunnar von Heijne, Alfonso Valencia, Christos A Ouzounis, Rita Casadio, Søren Brunak
2009 Genome Biology  
trend in computational methods for annotation of protein function is that many prediction tools are combined in complex workflows and pipelines to facilitate the analysis of feature combinations, for  ...  example, the entire repertoire of kinase-binding motifs in the human proteome.  ...  Firestar highlights potential functionally important residues such as ligand-binding residues and catalytic residues and allows users to assess whether the functionally important residues can be transferred  ... 
doi:10.1186/gb-2009-10-2-206 pmid:19226438 pmcid:PMC2688272 fatcat:lsj32ln7x5h4dm7ncawzyp5g64

Environmental conditions shape the nature of a minimal bacterial genome

Magdalena Antczak, Martin Michaelis, Mark N. Wass
2019 Nature Communications  
Our findings also show that the combination of multiple different state-of-the-art in silico methods for annotating proteins is able to predict functions, even for difficult to characterise proteins and  ...  Here, we combine the results from state-of-the-art in silico methods for functional annotation and assign functions to 66 of the 149 proteins.  ...  Stefano Toppo for advice regarding transformation of Argot2.5 scores into probabilities. Author contributions All authors devised the study. M.A. performed the experiments.  ... 
doi:10.1038/s41467-019-10837-2 pmid:31308405 pmcid:PMC6629657 fatcat:6jqsn3bobbciln7bcw2jzsrykm

APPRIS: selecting functionally important isoforms

Jose Manuel Rodriguez, Fernando Pozo, Daniel Cerdán-Vélez, Tomás Di Domenico, Jesús Vázquez, Michael L Tress
2021 Nucleic Acids Research  
The most significant change in APPRIS has been the implementation of TRIFID functional isoform scores.  ...  In this paper we highlight the most recent updates to the database.  ...  ACKNOWLEDGEMENTS The authors would like to thank Thomas Walsh for all his work on the APPRIS database.  ... 
doi:10.1093/nar/gkab1058 pmid:34755885 pmcid:PMC8728124 fatcat:6qruhrxkabgb5a2q6fygyfojp4

GRaSP: a graph-based residue neighborhood strategy to predict binding sites

Charles A Santana, Sabrina de A Silveira, João P A Moraes, Sandro C Izidoro, Raquel C de Melo-Minardi, António J M Ribeiro, Jonathan D Tyzack, Neera Borkakoti, Janet M Thornton
2020 Bioinformatics  
Motivation The discovery of protein–ligand-binding sites is a major step for elucidating protein function and for investigating new functional roles.  ...  Thus, a variety of in silico methods to detect and predict binding sites was proposed as they can be scalable, fast and present low cost.  ...  Firestar (Ló pez et al., 2007; Lopez et al., 2011) is a server that uses functional information in FireDB (Lopez et al., 2007) , a database of functionally important residues, to make predictions of  ... 
doi:10.1093/bioinformatics/btaa805 pmid:33381849 fatcat:co4umhlumjg43fduhxj3vmpwrm

Genetic variants of small airways and interstitial pulmonary disease in children

Mohammed T. Alsamri, Amnah Alabdouli, Alia M. Alkalbani, Durdana Iram, Mohamed I. Tawil, Priya Antony, Ranjit Vijayan, Abdul-Kader Souid
2021 Scientific Reports  
One of the siblings also had heterozygous SFTPA1:c.675C > G, p.Asn225Lys, which resulted in a more severe respiratory disease.  ...  In addition, results of genetic studies improve the clinical care and provide opportunities for participating in clinical trials, such as those involving molecularly-targeted therapies.  ...  We are also grateful to the Genetic Service for placing some of the orders for the reported studies, and to Prof. Suhail Abdullah for his help in the lung histology.  ... 
doi:10.1038/s41598-021-81280-x pmid:33526882 pmcid:PMC7851163 fatcat:urba52l2cfbftggthnqq4gaxs4

PocketAnnotate: towards site-based function annotation

Praveen Anand, Kalidas Yeturu, Nagasuma Chandra
2012 Nucleic Acids Research  
The pipeline integrates three in-house algorithms for site-based function annotation: PocketDepth, for prediction of binding sites in protein structures; PocketMatch, for rapid comparison of binding sites  ...  A computational pipeline PocketAnnotate for functional annotation of proteins at the level of binding sites has been proposed in this study.  ...  They appreciate all the members of the laboratory for their valuable suggestions, feedbacks and inputs on the development of the web server.  ... 
doi:10.1093/nar/gks421 pmid:22618878 pmcid:PMC3394344 fatcat:a4wzjxxxubhalk2bnmjbuujr4m

Homology modeling a fast tool for drug discovery: Current perspectives

VK Vyas, RD Ukawala, C Chintha, M Ghate
2012 Indian Journal of Pharmaceutical Sciences  
Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins.  ...  Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions.  ...  The most important factor in the assessment of constructed models is scoring function.  ... 
doi:10.4103/0250-474x.102537 pmid:23204616 pmcid:PMC3507339 fatcat:axgvmmgntfbenmcs7demtzuwme
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