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Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites

Benjamin A. Shoemaker, Dachuan Zhang, Ratna R. Thangudu, Manoj Tyagi, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Thomas Madej, Anna R. Panchenko
2009 Nucleic Acids Research  
IBIS is the NCBI Inferred Biomolecular Interaction Server. This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins.  ...  IBIS reports interactions observed in experimentally determined structural complexes of a given protein, and at the same time IBIS infers binding sites/interacting partners by inspecting protein complexes  ...  ACKNOWLEDGEMENTS The authors would like to thank Yanli Wang and Lewis Geer for useful discussions and Eugene Krissinel for help with the PISA software.  ... 
doi:10.1093/nar/gkp842 pmid:19843613 pmcid:PMC2808861 fatcat:ou6b7ft6rfdahfxns6vfbkroge

SPPS: A Sequence-Based Method for Predicting Probability of Protein-Protein Interaction Partners

Xinyi Liu, Bin Liu, Zhimin Huang, Ting Shi, Yingyi Chen, Jian Zhang, Jörg D. Hoheisel
2012 PLoS ONE  
In addition, users can refine potential protein partner hits by using annotations and possible interactive network in the SPPS web server.  ...  Results: We have developed a web-based tool "Sequence-based Protein Partners Search" (SPPS) to explore interacting partners of proteins, by searching over a large repertoire of proteins across many species  ...  Acknowledgments We would like to thank Prof. Hanyi Zhuang in Shanghai Jiaotong University for fruitful discussions on the building of web service.  ... 
doi:10.1371/journal.pone.0030938 pmid:22292078 pmcid:PMC3266917 fatcat:7prjtny4vrdcpof2bs7z6huc4a

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder

Michail Yu. Lobanov, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Jessica H. Fong, Anna R. Panchenko, Oxana V. Galzitskaya
2009 Nucleic Acids Research  
Besides that, through our web server, one can obtain necessary information for studying disorder-to-order and order-to-disorder transitions upon complex formation, and analyze structural differences between  ...  Most of the proteins in a cell assemble into complexes to carry out their function.  ...  We also give a link to a new NCBI server, IBIS (Inferred Biomolecular Interaction Server, http://www.ncbi.nlm.nih.gov/ Structure/ibis/ibis.cgi) that provides a tool to investigate biomolecular interactions  ... 
doi:10.1093/nar/gkp963 pmid:19906708 pmcid:PMC2808974 fatcat:asdz5crf3bgydgxzwbldcqiwre

New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'

Yana Bromberg, Guy Yachdav, Yanay Ofran, Reinhard Schneider, Burkhard Rost
2009 Current opinion in drug discovery & development  
First, predictions of protein binding sites and functional hotspots, and the evolution of these into the most successful type of prediction of protein function from sequence will be discussed.  ...  The availability of this direct connection, and the resulting access to a wealth of data, may impact drug discovery and development more than any existing method that contributes to protein annotation.  ...  Acknowledgements This paper was supported by the grant R01-LM07329-01 from the National Library of Medicine (NLM), and the grant  ... 
pmid:19396742 fatcat:oymcw4ptejggxlvsjl7a6c7ydu

Exploring the Binding Interaction of Raf Kinase Inhibitory Protein With the N-Terminal of C-Raf Through Molecular Docking and Molecular Dynamics Simulation

Shraddha Parate, Shailima Rampogu, Gihwan Lee, Jong Chan Hong, Keun Woo Lee
2021 Frontiers in Molecular Biosciences  
In the current investigation, the binding of RKIP with C-Raf was explored by knowledge-based protein-protein docking web-servers including HADDOCK and ZDOCK and a consensus binding mode of C-Raf/RKIP structural  ...  The acquired information on the predicted 3D structural complex and the detected sites aid as promising targets in designing novel inhibitors to block the C-Raf/RKIP interaction.  ...  Innumerable protein-protein docking web-servers have been developed with diverse sampling algorithms and scoring functions in order to accurately predict the binding mode between two protein structures  ... 
doi:10.3389/fmolb.2021.655035 pmid:34124147 pmcid:PMC8194344 fatcat:vddo4lz5znd6vo3r2raidhdara

MutaBind2: predicting the impacts of single and multiple mutations on protein-protein interactions

Ning Zhang, Yuting Chen, Haoyu Lu, Feiyang Zhao, Roberto Vera Alvarez, Alexander Goncearenco, Anna R. Panchenko, Minghui Li
2020 iScience  
Predicting the effects of stabilizing mutations on protein-protein interactions is notoriously difficult because existing experimental sets are skewed toward mutations reducing protein-protein binding  ...  To address this issue, we developed a method MutaBind2, which estimates the impacts of single as well as multiple mutations on protein-protein interactions.  ...  We would like to thank Dr. Thomas Madej for proofreading of the manuscript. AUTHOR CONTRIBUTIONS Conceptualization DECLARATION OF INTERESTS The authors declare no competing interests.  ... 
doi:10.1016/j.isci.2020.100939 pmid:32169820 pmcid:PMC7068639 fatcat:jkqlnyucwnefnecao2vmboipwy

Knowledge-based annotation of small molecule binding sites in proteins

Ratna R Thangudu, Manoj Tyagi, Benjamin A Shoemaker, Stephen H Bryant, Anna R Panchenko, Thomas Madej
2010 BMC Bioinformatics  
The method also facilitates a succinct and informative representation of observed and inferred binding sites from homologs with known three-dimensional structures, thereby providing the means to analyze  ...  The method was validated by comparison to other binding site prediction methods and to a collection of manually curated binding site annotations.  ...  Acknowledgements The authors are grateful to Aron Märchler-Bauer, Dachuan Zhang, and Jessica Fong.  ... 
doi:10.1186/1471-2105-11-365 pmid:20594344 pmcid:PMC2909224 fatcat:em4aumldr5acvds6d2f3qpzone

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function

Dennis M. Krüger, Prakash Chandra Rathi, Christopher Pfleger, Holger Gohlke
2013 Nucleic Acids Research  
The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility.  ...  of a biomolecular structure.  ...  ACKNOWLEDGEMENTS The authors are grateful to Prof. Michael F. Thorpe Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt292 pmid:23609541 pmcid:PMC3692064 fatcat:4c47bs2saba6dcswwy7jolwu5u

Three-Dimensional Models of the Oligomeric Human Asialoglycoprotein Receptor (ASGP-R)

Ilaria Massarelli, Federica Chiellini, Emo Chiellini, Anna Maria Bianucci
2010 International Journal of Molecular Sciences  
The ultimate target of the study is to contribute to increasing the knowledge of interactions between the human ASGP-R and carbohydrate ligands, at the molecular level, pertinent to applications in the  ...  An articulated step-wise modeling protocol was used in order to build the receptor model in a minimal oligomeric form, necessary for it to bind multi-antennary carbohydrate ligands.  ...  Acknowledgements The Authors are grateful to the International Centre for studies and research in Biomedicine" (ICB) A.s.b.l.  ... 
doi:10.3390/ijms11103867 pmid:21152305 pmcid:PMC2996795 fatcat:7rnxvjvrgnbdvdqsxvvoxnm3bu

Modulating Protein–Protein Interactions with Small Molecules: The Importance of Binding Hotspots

Ratna Rajesh Thangudu, Stephen H. Bryant, Anna R. Panchenko, Thomas Madej
2012 Journal of Molecular Biology  
Here, we propose a scheme that allows performing large-scale screening of all protein complexes and finding putative small-molecule and/or peptide binding sites overlapping with protein-protein binding  ...  Honig Keywords: protein structures; molecular interactions; protein-protein interactions; drug development hotspots The modulation of protein-protein interactions (PPIs) by small drug-like molecules is  ...  Acknowledgements This work was supported by National Institutes of Health/Department of Health and Human Services (Intramural Research Program of the National Library of Medicine).  ... 
doi:10.1016/j.jmb.2011.12.026 pmid:22198293 pmcid:PMC3433052 fatcat:fofx6a7zgreprbztv3epdl6dvy

Computational Molecular Phenotypic Analysis of PTPN22 (W620R), IL6R (D358A), and TYK2 (P1104A) Gene Mutations of Rheumatoid Arthritis

Noor Ahmad Shaik, Babajan Banaganapalli
2019 Frontiers in Genetics  
However, whether these variants prompt changes in the protein phenotype with regards to its stability, structure, and interaction with other molecules, remains unknown.  ...  We observed that simple nucleotide predictions of SIFT, PolyPhen, CADD and FATHMM yields mixed findings in screening the RA-missense variants which showed a ≥P-value threshold of 5 × 10-8 in genome wide  ...  ACKNOWLEDGMENTS The authors gratefully acknowledge the DSRs technical and financial support.  ... 
doi:10.3389/fgene.2019.00168 pmid:30899276 pmcid:PMC6416176 fatcat:wl4teqo4fnhghjftyczeprkede

Proteins: Sequence to Structure and Function – Current Status

Sandhya R. Shenoy, B. Jayaram
2010 Current protein and peptide science  
infer related structures and functions; in the second ab initio prediction methods are used to deduce 3D structure, and ultimately to infer function, directly from the linear sequence.  ...  In this article, we attempt to provide a critical assessment of what one may and may not expect from the biological sequences and to identify major issues yet to be resolved.  ...  Flexibility in Protein-Protein Interactions Flexibility is of overwhelming importance for protein function, and the changes in protein structure during interactions with binding partners can be dramatic  ... 
doi:10.2174/138920310794109094 pmid:20887265 fatcat:d7jfqzg7lvg5bf3lt4uefm25me

In Silico-In Vitro Screening of Protein-Protein Interactions: Towards the Next Generation of Therapeutics

Bruno Villoutreix, Karine Bastard, Olivier Sperandio, Robin Fahraeus, Jean-Luc Poyet, Fabien Calvo, Benoit Deprez, Maria Miteva
2008 Current Pharmaceutical Biotechnology  
Protein-protein interface: a brief overview Proteins are usually involved in interactions with an estimated average of 5-10 protein partners [41] , the binding site(s) with these partners may or may not  ...  Different in silico methods have been developed to analyze the physical properties of proteins and learn more about how these properties are associated with binding.  ...  Acknowledgments Supports from the Inserm institute and Inserm-Transfert are greatly appreciated.  ... 
doi:10.2174/138920108783955218 pmid:18393867 fatcat:db63x2enijagzdo34ttc4hqshy

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

Jeffrey R. Wagner, Christopher T. Lee, Jacob D. Durrant, Robert D. Malmstrom, Victoria A. Feher, Rommie E. Amaro
2016 Chemical Reviews  
To date, the discovery of allosteric binding sites and lead compounds has been mostly serendipitous, achieved through high-throughput screening.  ...  state models and topology analyses provide insight into the relationship between protein dynamics and allosteric drug binding.  ...  MISTIC (Mutual Information Server to Infer Coevolution) is an automated web server that accepts user-submitted MSAs or collects them from PFAM. 82 MISTIC uses a corrected form of MI to infer coevolving  ... 
doi:10.1021/acs.chemrev.5b00631 pmid:27074285 pmcid:PMC4901368 fatcat:x72bgr3if5acdlyz2rznhwqtge

Study of intra–inter species protein–protein interactions for potential drug targets identification and subsequent drug design for Escherichia coli O104:H4 C277-11

Shakhinur Islam Mondal, Zabed Mahmud, Montasir Elahi, Arzuba Akter, Nurnabi Azad Jewel, Md. Muzahidul Islam, Sabiha Ferdous, Taisei Kikuchi
2017 In Silico Pharmacology  
Protein-protein interaction (PPI) and hostpathogen interactions (HPI) proteomic analysis has been successfully practiced for potential drug target identification in pathogenic infections.  ...  Our systematic in silico analysis on PPI and HPI of E. coli O104:H4 was able to identify bacterial D-galactose-binding periplasmic and UDP-N-acetylglucosamine 1-carboxyvinyltransferase as attractive candidates  ...  Muhammed Zafar Iqbal, SUST for his cooperation and supportive hands throughout the research. We would like to thank Md. Mokkaram Hossain for his valuable support during blasting in cluster computer.  ... 
doi:10.1007/s40203-017-0021-5 pmid:28401513 pmcid:PMC5391048 fatcat:25cofeqsdjdrljq5mswfnsztpe
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