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StaRProtein, A Web Server for Prediction of the Stability of Repeat Proteins
2015
PLoS ONE
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Here we developed distance-dependant statistical potentials using two classes of alpha-helical repeat proteins, tetratricopeptide and ankyrin repeat proteins respectively, and evaluated their efficiency ...
proteins with high stability. ...
VS Lee at University of Malaya for providing the crude AR protein structures and Prof. Zoltán Gáspári from Eötvös Loránd University for providing the PRIDE2 executables. ...
doi:10.1371/journal.pone.0119417
pmid:25807112
pmcid:PMC4373711
fatcat:uvgbevy2szczhbcmtv65b3yrxm
Protein Copy Number Distributions for a Self-Regulating Gene in the Presence of Decoy Binding Sites
2015
PLoS ONE
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In order to quantify this impact, we study in this paper a mathematical model for pulsatile expression of a transcription factor that autoregulates its expression and interacts with decoys. ...
Bimodal protein distributions are more feasible if the rate of degradation is the same irrespective of whether protein is bound or not. ...
Acknowledgments PB is supported by the Slovak Research and Development Agency (contract no. APVV-0134-10) and also by the VEGA grant agency (contract no. 1/0319/15). ...
doi:10.1371/journal.pone.0120555
pmid:25811868
pmcid:PMC4374843
fatcat:ld5m2hvtnjcofjjm3n5m7mxkjq
An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins
2004
Biophysical Journal
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For each protein, decoys with 2-3 Å backbone root mean-square deviation and correct experimental C b -C b distance constraints emerge as those with the lowest energy. ...
PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. ...
The decoys that were generated in this study may be used to validate force fields other than PFF01 for protein structure prediction. ...
doi:10.1529/biophysj.104.040071
pmid:15507688
pmcid:PMC1304781
fatcat:jlvwlqrsnberhk47evnr6hwvqm
Computational Docking of Antibody-Antigen Complexes, Opportunities and Pitfalls Illustrated by Influenza Hemagglutinin
2011
International Journal of Molecular Sciences
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The purpose is two-fold: on a general note, we want to illustrate the advantages and pitfalls of computational docking with a practical example, using different approaches and comparing the results to ...
Since their efficiency depends, in ultimate analysis, on their atomic interactions with an antigen, studying such interactions is important to understand how they function and, in the long run, to design ...
Acknowledgements This work has been supported by generous grants from Canton Ticino and the Swiss Vaccine Research Institute. ...
doi:10.3390/ijms12010226
pmid:21339984
pmcid:PMC3039950
fatcat:i634pmdl6vc7hdyorp43g2rscm
HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures
2009
PLoS ONE
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From Protein Structure to Function with Bioinformatics, 3 ...
This procedure, called ab initio modelling, is essential for a complete solution to the protein structure prediction problem; it can also help us understand the physicochemical principle of how proteins ...
Sloan Foundation, and Grant Number R01GM083107 of the National Institute of General Medical Sciences. ...
doi:10.1371/journal.pone.0006701
pmid:19693270
pmcid:PMC2724740
fatcat:5mswathkifdnhasddklbcvlcle
A High Affinity Hepatocyte Growth Factor-binding Site in the Immunoglobulin-like Region of Met
2008
Journal of Biological Chemistry
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These data suggest that the immunoglobulinlike region of Met cooperates with the Sema domain in binding to HGF and in controlling Met kinase activity. ...
Finally, we provide evidence that soluble Met-derived proteins containing either the low affinity or high affinity HGFbinding site antagonize HGF-induced invasive growth both in vitro and in xenografts ...
Acknowledgments-We thank Mauro Risio for histological analysis and Luigi Naldini for lentiviral technology expertise. ...
doi:10.1074/jbc.m800727200
pmid:18495663
pmcid:PMC2475716
fatcat:oikwcy3lcrgapfwuf6woffyqoq
Exploration of the free-energy surface of a three-helix peptide with stochastic optimization methods
2004
International Journal of Quantum Chemistry
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We adjusted the parameters of the solvent model to stabilize the NMR structure using a decoy approach. ...
We report our recent efforts to develop all-atom forcefields that can be used to predict the three-dimensional, tertiary structure of proteins using stochastic optimization methods. ...
Acknowledgments: This work was funded by the Deutsche Forschungsgemeinschaft (We 1863/11-1), the BMBF and the Bode foundation. ...
doi:10.1002/qua.20052
fatcat:vcu3465anzh2zbhbnafpgjvzwq
Residue-centric modeling and design of saccharide and glycoconjugate structures
2016
Journal of Computational Chemistry
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The framework integrates with Rosetta's successful modeling and design suite and addresses challenges unique to glycans. ...
This article describes the development of the framework and highlights its applications, including loop modeling and glyco-ligand docking. ...
We generated 5,000 decoys for each protein-ligand pair. ...
doi:10.1002/jcc.24679
pmid:27900782
pmcid:PMC5182120
fatcat:wcpcsf3wbjbpzobv776aexnv6m
Degradation of non-coding RNAs promotes recycling of termination factors at sites of transcription
[article]
2019
bioRxiv
pre-print
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Our results have important implications for the mechanism of termination, the general impact of ncRNAs on cellular physiology and the importance of nuclear ncRNA degradation. ...
In exosome mutants, these factors are sequestered by ncRNAs and cannot be efficiently recycled to sites of transcription, which induces termination defects genome-wide. ncRNA-dependent, genome-wide termination ...
#ANR-11-LABX-0071 and the Université de Paris IdEx #ANR-18-IDEX-0001 funded by the French Government through its "Investments for the Future" program. ...
doi:10.1101/822429
fatcat:ccs4ct7ceje7dcut4bap5g3zae
Predicting Potential SARS-COV-2 Drugs-In Depth Drug Database Screening Using Deep Neural Network Framework SSnet, Classical Virtual Screening and Docking
2021
International Journal of Molecular Sciences
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During an urgent crisis, rapidly identifying potential new treatments requires global and cross-discipline cooperation, together with an enhanced open-access research model to distribute new ideas and ...
Herein, we introduce an application of a deep neural network based drug screening method, validating it using a docking algorithm on approved drugs for drug repurposing efforts, and extending the screen ...
Acknowledgments: The authors thank SMU for generous supercomputer resources. The authors would also like to thank Saeedi Mohammadi for the discussion of SSnet and providing helpful tips. ...
doi:10.3390/ijms22031392
pmid:33573266
pmcid:PMC7869013
fatcat:m52gu4s7lrfenocacmr7qciyiu
Evaluating the Predictivity of Virtual Screening for Abl Kinase Inhibitors to Hinder Drug Resistance
2013
Chemical Biology and Drug Design
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'Dual active' inhibitors against both targets were grouped together with inactive ligands chosen from different decoy sets and tested with virtual screening approaches with and without explicit use of ...
Virtual screening methods are now widely used in early stages of drug discovery, aiming to rank potential inhibitors. ...
Anna Linusson, Associate Professor at the Department of Chemistry, Ume a University, Sweden for critical reading of the manuscript and introduction to several chemoinformatics methods. ...
doi:10.1111/cbdd.12170
pmid:23746052
pmcid:PMC4265857
fatcat:ssxoqcwfdjglvd64mxc77nybpq
Applying Constraint Programming to Rigid Body Protein Docking
[chapter]
2005
Lecture Notes in Computer Science
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BiGGER prunes the search space by maintaining bounds consistency on interval c onstraints t hat model the requirement for the shapes to be in contact but not overlapping, and by using a branch and bound ...
We use BiGGER [ 1] (Bimolecular complex Generation with Global Evaluation and Ranking) to illustrate the method as applied to modelling protein interactions, an important effort in current bioinformatics ...
Acknowledgements: We thank Nuno Palma and José Moura for their role in the development of BiGGER and Chemera, and we thank the financial support of the Fundação para a Ciencia e Tecnologia (BD 19628/99 ...
doi:10.1007/11564751_29
fatcat:67ndyeiabzg45fqeg2rzxusae4
Studying the uptake of cell-penetrating peptides
2006
Nature Protocols
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Ü TP10, a delivery vector for decoy oligonucleotides targeting the Myc protein. J. Control. ...
In addition, the CPP TP10 efficiently delivered dsDNA decoy oligonucleotides for sequestering of the transcription factor Myc with a concomitant biological response, i.e. reduced proliferation. ...
Among the cationic polymers, polyethyleneimine (PEI) has been most extensively used with a number of variants, differing in size and degree of branching. ...
doi:10.1038/nprot.2006.174
pmid:17406337
fatcat:uhdxdjpblneglhwp7ylkz4fygm
Binding MOAD (Mother Of All Databases)
2005
Proteins: Structure, Function, and Bioinformatics
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Ligand-Protein DataBase The The LPDB is designed to be used along with a continuum set of pre-generated decoys to assess scoring-function performance. ...
In general, higher ligand efficiencies mean that drug-like affinities can be obtained with smaller molecules. ...
Binding MOAD uses a Java 2 Enterprise Edition (J2EE) framework and 3-tier model (client, application, and database). ...
doi:10.1002/prot.20512
pmid:15971202
fatcat:qya7yxhipzes7ng3dgnc6da4au
Caspase-2 pre-mRNA alternative splicing: Identification of an intronic element containing a decoy 3' acceptor site
2001
Proceedings of the National Academy of Sciences of the United States of America
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We provide evidence that this sequence acts as a "decoy" acceptor site that engages in U2 snRNP-dependent but nonproductive splicing complexes with the 5 splice site of exon 9, hence conferring competitive ...
We have established a model system using the caspase-2 pre-mRNA and initiated a study on the role of alternative splicing in regulation of programmed cell death. ...
We acknowledge Smitha Rajasekhar and Michael Nolan for their excellent technical assistance. We thank Drs. Marc T. McNally and Woan-Yuh Tarn for their generous gifts of 2Ј-O-methyl oligos, Dr. ...
doi:10.1073/pnas.031564098
pmid:11158574
pmcid:PMC14688
fatcat:m4mme2zxrbe3jaenuay2euhb7m
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