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firestar —advances in the prediction of functionally important residues
2011
Nucleic Acids Research
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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
2010
Bioinformation
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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
2012
Nucleic Acids Research
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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]
2018
bioRxiv
pre-print
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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
2022
Nucleic Acids Research
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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
2015
PLoS Genetics
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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
2015
Nucleic Acids Research
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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
2013
Nucleic Acids Research
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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
2009
Genome Biology
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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
2019
Nature Communications
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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
2021
Nucleic Acids Research
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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
2020
Bioinformatics
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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
2021
Scientific Reports
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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
2012
Nucleic Acids Research
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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
2012
Indian Journal of Pharmaceutical Sciences
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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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