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Computational Prediction of RNA-Binding Proteins and Binding Sites

Jingna Si, Jing Cui, Jin Cheng, Rongling Wu
2015 International Journal of Molecular Sciences  
Previously, a number of experimental methods were developed for the determination of protein-RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive.  ...  Approximately 6%-8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a major aim of structural biology.  ...  certain energy/scoring function that fitted for protein-RNA interactions.  ... 
doi:10.3390/ijms161125952 pmid:26540053 pmcid:PMC4661811 fatcat:jzvatw5qmvbf3m6xq5tn2ymrcq

A graph kernel method for DNA-binding site prediction

Changhui Yan, Yingfeng Wang
2014 BMC Systems Biology  
Results: This paper presents a method for predicting DNA-binding sites on protein structures.  ...  It provides a competitive method for predicting DNA-binding sites without requiring structure alignment.  ...  Declarations Publication costs for this work were funded by NSF award 1262265 to C. Yan  ... 
doi:10.1186/1752-0509-8-s4-s10 pmid:25521807 pmcid:PMC4290685 fatcat:fnkoxhooyrbefjz7iw4is7qdkm

ProMateus--an open research approach to protein-binding sites analysis

H. Neuvirth, U. Heinemann, D. Birnbaum, N. Tishby, G. Schreiber
2007 Nucleic Acids Research  
Here, the protein-binding site prediction server is extended into a general protein-binding sites research tool, ProMateus.  ...  For example, identification of binding site regions between interacting proteins is done using: ProMate, WHISCY, PPI-Pred, PINUP and others.  ...  ACKNOWLEDGEMENTS This research, as well as funding to pay the Open Access publication charges for this article were provided by a grant from the Israel Ministry for Science and Technology (MOST) 0263 and  ... 
doi:10.1093/nar/gkm301 pmid:17488838 pmcid:PMC1933218 fatcat:5x6h3pfi35bzzntdzowzroyshe

Prediction of Metal Ion Binding Site in Truncated Globin of Myxococcus xanthus DK1622 in Homologous Model

Ashok Kumar
2017 MOJ Proteomics & Bioinformatics  
The 3-D model structure will enhance the understanding for functional analysis of experimentally derived crystal structure. Figure 1: Classification of globins.  ...  Further, heme group was appended to the model structure of trHbN of M. xanthus by Patchdock web server and model-heme complex was further refined by Firedock.  ...  Acknowledgment Authors are thankful to Department of Biotechnology (DBT), Government of India, New Delhi, India to provide the funds necessary for financial assistance in the form of DBT-JRF programme  ... 
doi:10.15406/mojpb.2017.05.00146 fatcat:fynvzx4porcuhhgafvhjauvxt4

Structural Studies of Predicted Ligand Binding Sites and Molecular Docking Analysis of Slc2a4 as a Therapeutic Target for the Treatment of Cancer

Raphael Aruleba, Tayo Adekiya, Babatunji Oyinloye, Abidemi Kappo
2018 International Journal of Molecular Sciences  
The structures of the protein and AMPs were modelled using I-TASSER server, and the overall quality of the Slc2a4 model was validated using PROCHECK.  ...  Subsequently, the probable motifs and active site of the protein were forecasted. Also, the molecular interaction between the AMPs and Slc2a4 was ascertained using PatchDock.  ...  Acknowledgments: Research reported in this article was supported by the University of Zululand Research Committee. We like to thank Chinaza Uleanya for proofreading the final draft.  ... 
doi:10.3390/ijms19020386 pmid:29382080 pmcid:PMC5855608 fatcat:wmigdpwpfnhjpod5jtvcqaaqkq

Predicting DNA-binding sites of proteins from amino acid sequence

Changhui Yan, Michael Terribilini, Feihong Wu, Robert L Jernigan, Drena Dobbs, Vasant Honavar
2006 BMC Bioinformatics  
We present a machine learning approach for the identification of amino acid residues involved in protein-DNA interactions.  ...  Understanding the molecular details of protein-DNA interactions is critical for deciphering the mechanisms of gene regulation.  ...  Caragea for providing comments on the manuscript. We thank Dr. S. Ahmad and Dr. A. Sarai for sharing the details of their PSSM-based neural network classifier.  ... 
doi:10.1186/1471-2105-7-262 pmid:16712732 pmcid:PMC1534068 fatcat:fft646x44rbexg53prfkzloi7i

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein–protein interaction sites for PDB structures

Hugues Ripoche, Elodie Laine, Nicoletta Ceres, Alessandra Carbone
2016 Nucleic Acids Research  
Bliven for providing access to the EPPIC database.  ...  JET2 Viewer is a web server that provides binding site predictions for the full set of structures collected in the Protein Data Bank (PDB).  ...  For all interacting sites, the three scoring schemes were systematically used and the best patch or combination of patches was retained. x represents the size (number of residues) of the protein considered  ... 
doi:10.1093/nar/gkw1053 pmid:27899675 pmcid:PMC5210541 fatcat:o3fv2bopnbdb5msfhbwfmvl4ce

siteFiNDER 3D: a web-based tool for predicting the location of functional sites in proteins

C. A. Innis
2007 Nucleic Acids Research  
rate at which sequence and structural information is being accumulated. siteFiNDER|3D is an online tool for the prediction of functionally important regions in proteins of known structure.  ...  Although knowledge of a protein's functional site is a key requirement for understanding its mode of action at the molecular level, our ability to locate such sites experimentally is far exceeded by the  ...  Thomas A. Steitz for support and for providing the necessary infrastructure to host the siteFiNDER|3D Server, together with Scott Bailey, Miljan Simonovic´and Satwik Kamtekar for useful discussions.  ... 
doi:10.1093/nar/gkm422 pmid:17553829 pmcid:PMC1933183 fatcat:6u5qyq37gfbhpaixahwde7tzsq

An Overview of the Prediction of Protein DNA-Binding Sites

Jingna Si, Rui Zhao, Rongling Wu
2015 International Journal of Molecular Sciences  
for comparison and selection, evaluation methods, performance comparison of different tools, and future directions in protein DNA-binding site prediction.  ...  Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair.  ...  By learning from the protein fold recognition community [85] and protein-protein interaction meta-server [86] , a meta-server for DNA-binding site prediction has been developed [29] .  ... 
doi:10.3390/ijms16035194 pmid:25756377 pmcid:PMC4394471 fatcat:syzihxgpqvfj7o5hwx4nbgcj7q

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

Adrien Saladin, Julien Rey, Pierre Thévenet, Martin Zacharias, Gautier Moroy, Pierre Tufféry
2014 Nucleic Acids Research  
the experimental patch of interaction for close to 90% complexes.  ...  When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological  ...  SUPPLEMENTARY DATA Supplementary Data are available at NAR Online.  ... 
doi:10.1093/nar/gku404 pmid:24803671 pmcid:PMC4086095 fatcat:g3s25e5s3rcd3aaxelstwzktcu

DBSI: DNA-binding site identifier

Xiaolei Zhu, Spencer S. Ericksen, Julie C. Mitchell
2013 Nucleic Acids Research  
In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding.  ...  DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30) protein  ...  ACKNOWLEDGEMENTS The authors thank Gary Wesenberg and Shravan Sukumar for helpful discussions. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt617 pmid:23873960 pmcid:PMC3763564 fatcat:avjsmsh5ifhejll5w7jkjbmfa4

A survey on prediction of specificity-determining sites in proteins

A. Chakraborty, S. Chakrabarti
2014 Briefings in Bioinformatics  
Specificity-determining sites (SDS) are the key positions of a protein family that show a specific conservation of amino acids, related to the subfamily members of that family.  ...  Thus, it is important to identify SDS to understand the evolutionary process of diversification of biological functions within a protein family.  ...  Research over the years led to a series of methods and algorithms that identify sites responsible for specific functions of a subset of proteins within a protein family.  ... 
doi:10.1093/bib/bbt092 pmid:24413183 fatcat:dslrtmhyijghthij5gt5wlzybm

Structural evolutionary analysis predicts functional sites in the artemisinin resistance malaria protein K13 [article]

Romain Coppee, Daniel Jeffares, Audrey Sabbagh, Jerome Clain
2018 bioRxiv   pre-print
An amino acid electropositive patch in the K13 propeller domain has a dense concentration of extraordinarily conserved positions located at a shallow pocket, suggesting a role as binding surface.  ...  Another patch of slowly evolving sites is identified in the K13 BTB domain which partially overlaps the surface that binds to Cullin proteins in BTB-Cullin complexes.  ...  proteins and exhibits a predicted functional 156 patch.  ... 
doi:10.1101/346668 fatcat:2tqnvrfb7rbsjn2owpkp6562sq

A Deep Learning and XGBoost-Based Method for Predicting Protein-Protein Interaction Sites

Pan Wang, Guiyang Zhang, Zu-Guo Yu, Guohua Huang
2021 Frontiers in Genetics  
We also validated the positive role of global features in predicting protein-protein interaction sites.  ...  The Extreme Gradient Boosting algorithm was used to construct a classifier for predicting protein-protein interaction sites.  ...  Protein binding site prediction using an empirical scoring function.  ... 
doi:10.3389/fgene.2021.752732 pmid:34764983 pmcid:PMC8576272 fatcat:eob52q6byjckdfubikcabslfpy

Structure of the Pseudokinase VRK3 Reveals a Degraded Catalytic Site, a Highly Conserved Kinase Fold, and a Putative Regulatory Binding Site

Eric D. Scheeff, Jeyanthy Eswaran, Gabor Bunkoczi, Stefan Knapp, Gerard Manning
2009 Structure  
VRK3 also conserves residue interactions that are surprising in the absence of enzymatic function; these appear to play important architectural roles required for the residual functions of VRK3.  ...  About 10% of all protein kinases are predicted to be enzymatically inactive pseudokinases, but the structural details of kinase inactivation have remained unclear.  ...  interaction site, allowing VRK3 to be retained even in the absence of any catalytic function.  ... 
doi:10.1016/j.str.2008.10.018 pmid:19141289 pmcid:PMC2639636 fatcat:yq3ho27vwngdpcxpsbirvuj2e4
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