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StaRProtein, A Web Server for Prediction of the Stability of Repeat Proteins

Yongtao Xu, Xu Zhou, Meilan Huang, Eugene A. Permyakov
2015 PLoS ONE  
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

Pavol Bokes, Abhyudai Singh, Lars Kaderali
2015 PLoS ONE  
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

T. Herges, W. Wenzel
2004 Biophysical Journal  
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

Mattia Pedotti, Luca Simonelli, Elsa Livoti, Luca Varani
2011 International Journal of Molecular Sciences  
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

Yunqi Li, Ambrish Roy, Yang Zhang, Andreas Hofmann
2009 PLoS ONE  
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

Cristina Basilico, Addolorata Arnesano, Maria Galluzzo, Paolo M. Comoglio, Paolo Michieli
2008 Journal of Biological Chemistry  
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

T. Herges, A. Schug, W. Wenzel
2004 International Journal of Quantum Chemistry  
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

Jason W. Labonte, Jared Adolf-Bryfogle, William R. Schief, Jeffrey J. Gray
2016 Journal of Computational Chemistry  
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]

Tommaso Villa, Mara Barucco, Maria-Jose Martin-Niclos, Domenico Libri
2019 bioRxiv   pre-print
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

Nischal Karki, Niraj Verma, Francesco Trozzi, Peng Tao, Elfi Kraka, Brian Zoltowski
2021 International Journal of Molecular Sciences  
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

Osman A. B. S. M. Gani, Dilip Narayanan, Richard A. Engh
2013 Chemical Biology and Drug Design  
'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]

Ludwig Krippahl, Pedro Barahona
2005 Lecture Notes in Computer Science  
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

Tina Holm, Henrik Johansson, Pontus Lundberg, Margus Pooga, Maria Lindgren, Ülo Langel
2006 Nature Protocols  
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)

Liegi Hu, Mark L. Benson, Richard D. Smith, Michael G. Lerner, Heather A. Carlson
2005 Proteins: Structure, Function, and Bioinformatics  
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

J. Cote
2001 Proceedings of the National Academy of Sciences of the United States of America  
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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