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Predicting protein interaction sites from residue spatial sequence profile and evolution rate

Bing Wang, Peng Chen, De-Shuang Huang, Jing-jing Li, Tat-Ming Lok, Michael R. Lyu
2005 FEBS Letters  
This paper proposes a novel method that can predict protein interaction sites in heterocomplexes using residue spatial sequence profile and evolution rate approaches.  ...  The former represents the information of multiple sequence alignments while the latter corresponds to a residueÕs evolutionary conservation score based on a phylogenetic tree.  ...  The results reported here demonstrate that residue sequence profile and evolutionary rate approaches can not only predict interface residues, but can also improve prediction performance by combining these  ... 
doi:10.1016/j.febslet.2005.11.081 pmid:16376878 fatcat:ysihizesqjgrbejt5fqzujqdp4

Practical aspects of protein co-evolution

David Ochoa, Florencio Pazos
2014 Frontiers in Cell and Developmental Biology  
At the molecular level, co-evolutionary linkages between protein families have been used as indicators of protein interactions and functional relationships from long ago.  ...  Co-evolution is a fundamental aspect of Evolutionary Theory.  ...  This work was partially supported by project BIO2010-22109 from the Spanish Ministry of Science and Innovation.  ... 
doi:10.3389/fcell.2014.00014 pmid:25364721 pmcid:PMC4207036 fatcat:dgsepmbscrga5ansj2gkp3v7dy

Enhanced functional information from predicted protein networks

Jason McDermott, Ram Samudrala
2004 Trends in Biotechnology  
Prediction of protein networks A number methods based on evolutionary and/or contextual sequence information have been developed to predict protein -protein interaction and functional relationship networks  ...  Figure generated using data from [4, supplementary information] (b) Protein interactions were predicted using Bioverse [7] based on finding pairs of proteins similar in sequence to proteins from a database  ...  Acknowledgements We acknowledge support from the following sources: a Searle Scholar Award (to R.S.), NSF Grant DBI-0217241 and the University of Washington's Advanced Technology Initiative in Infectious  ... 
doi:10.1016/j.tibtech.2003.11.010 pmid:14757037 fatcat:erckyvyis5euhny3jaadb5crce

ISIS: interaction sites identified from sequence

Y. Ofran, B. Rost
2007 Bioinformatics  
Results: Here we present a machine learning-based method that identifies interacting residues from sequence alone.  ...  Our results suggest that despite the significant diversity in the nature of protein-protein interactions, they all share common basic principles and that these principles are identifiable from sequence  ...  The work of Y.O. and B.R. was supported by the grants RO1-GM63029-01 and R01-GM64633-01 from the National Institutes of Health (NIH).  ... 
doi:10.1093/bioinformatics/btl303 pmid:17237081 fatcat:xabbj2qdunfnpng3i2d54kkggi

Prediction of Protein-Protein Interactions Using Pairwise Alignment and Inter-Domain Linker Region

Nazar Zaki
2008 Engineering Letters  
In this article, we make use of both homology and inter-domain linker region knowledge to predict interaction between protein pairs solely by amino acid sequence information.  ...  High quality core set of 150 yeast proteins obtained from the Database of Interacting Proteins (DIP) was considered to test the accuracy of the proposed method.  ...  We are encouraged by the fact that compositions of contacting residues in protein sequence are unique, and that incorporating evolutionary and predicted structural information improves the prediction of  ... 
dblp:journals/engl/Zaki08 fatcat:6tonc5fu25anjf6suhbszbwqpm

Prediction of RNA-interacting residues in a protein using CNN and evolutionary profile [article]

Sumeet Patiyal, Anjali Dhall, Khushboo Bajaj, Harshita Sahu, Gajendra P.S. Raghava
2022 bioRxiv   pre-print
This paper describes a method Pprint2, which is an improved version of Pprint developed for predicting RNA-interacting residues in a protein.  ...  The performance of this model improved significantly from AUC 0.68 to 0.76 when evolutionary profile is used instead of binary profile.  ...  Our results indicate that performance of models improved significantly using evolutionary information.  ... 
doi:10.1101/2022.06.03.494705 fatcat:a4jyizpchjcuha3sq775ud3jqm

Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information

Jagat S Chauhan, Nitish K Mishra, Gajendra PS Raghava
2010 BMC Bioinformatics  
Thus prediction of GTP interacting residues in a protein is one of the major challenges in the field of the computational biology.  ...  We have developed SVM based model for predicting GTP interacting dipeptides using PSSM profile and achieved MCC 0.64 with precision 0.87, recall 0.74 and accuracy 81.37%.  ...  The performance of models improved when PSSM profile has been used instead of single amino acid sequence of protein.  ... 
doi:10.1186/1471-2105-11-301 pmid:20525281 pmcid:PMC3098072 fatcat:qpqdknkcyvbvvfmddsmy7dqmle

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins

Menachem Fromer, Julia M. Shifman, Leonid A. Mirny
2009 PLoS Computational Biology  
Natural proteins often partake in several highly specific protein-protein interactions. They are thus subject to multiple opposing forces during evolutionary selection.  ...  Starting from high-resolution structures of sixteen CaM-target complexes, we employ state-of-the-art computational methods to predict a hundred CaM sequences best suited for interaction with each individual  ...  Native sequence and evolutionary profiles The native interface sequence was extracted from the CaM structures.  ... 
doi:10.1371/journal.pcbi.1000627 pmid:20041208 pmcid:PMC2790338 fatcat:f6vhbj5dh5d75aywy4uvxnlvae

Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins

Igor B. Kuznetsov, Zhenkun Gou, Run Li, Seungwoo Hwang
2006 Proteins: Structure, Function, and Bioinformatics  
We apply Support Vector Machine (SVM), a supervised pattern recognition method, to predict DNA-binding sites in DNA-binding proteins using the following features: amino acid sequence, profile of evolutionary  ...  correlated with certain structural and sequence properties of proteins.  ...  the profile of evolutionary conservation significantly improves accuracy (Fig. 2) .  ... 
doi:10.1002/prot.20977 pmid:16568445 fatcat:dhcxoldce5agtgmtvnx53qhzda

Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading

Sutanu Bhattacharya, Rahmatullah Roche, Md Hossain Shuvo, Debswapna Bhattacharya
2021 Frontiers in Molecular Biosciences  
Despite the success, homology detection remains very challenging for weakly homologous proteins with divergent evolutionary profile.  ...  Sequence-based protein homology detection has emerged as one of the most sensitive and accurate approaches to protein structure prediction.  ...  As such, the availability of evolutionary information of distanthomology proteins is getting enriched, likely leading to improved prediction accuracy of inter-residue interaction maps and hence more accurate  ... 
doi:10.3389/fmolb.2021.643752 pmid:34046429 pmcid:PMC8148041 fatcat:s5yr72nusjbpblft3bb5ev5zia

Prediction of Protein-Protein Interactions from Phylogenetic Trees Using Partial Correlation Coefficient

Tetsuya Sato, Yoshihiro Yamanishi, Katsuhisa Horimoto, Hiroyuki Toh, Minoru Kanehisa
2003 Genome Informatics Series  
Acknowledgments This work was supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan, the Japan Society for the Promotion of Science, and the Japan Science  ...  Introduction Computational prediction of protein-protein interactions from the sequence information is an important issue in bioinformatics.  ...  This paper presents a new method to predict protein-protein interactions from the evolutionary information by using partial correlation coefficient in order to extract direct interactions rather than indirect  ... 
doi:10.11234/gi1990.14.496 fatcat:ieq5hif24fdg7py6jknrrm3s2m

Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information

Peng Chen, Jinyan Li
2010 BMC Bioinformatics  
Therefore, it is important to improve the performance for predicting protein interaction sites based on primary sequence alone.  ...  Conclusions: The integrative profile by combining hydrophobic and evolutionary information contributes most to the protein-protein interaction prediction.  ...  Therefore, we integrate a hydrophobic scale and sequence profile in the identification of protein-protein interaction residues.  ... 
doi:10.1186/1471-2105-11-402 pmid:20667087 pmcid:PMC2921408 fatcat:yk5domczi5fr3ibs2ydwefazby

Identification of ATP binding residues of a protein from its primary sequence

Jagat S Chauhan, Nitish K Mishra, Gajendra PS Raghava
2009 BMC Bioinformatics  
The performance of this model was improved significantly (MCC 0.5) from the previous one, where only the primary sequence of the proteins were used.  ...  Conclusion: This study demonstrates that it is possible to predict 'ATP interacting residues' in a protein with moderate accuracy using its sequence.  ...  In this study the evolutionary information in the form of PSSM profile has been used for predicting ATP interacting protein residues.  ... 
doi:10.1186/1471-2105-10-434 pmid:20021687 pmcid:PMC2803200 fatcat:vvqmyuju3jculecpgp3zfrmdza

Sequence and Structure Analysis of Biological Molecules Based on Computational Methods

Jia-Feng Yu, Yue-Dong Yang, Xiao Sun, Ji-Hua Wang
2015 BioMed Research International  
In "Predicting Homogeneous Pilus Structure from Monomeric Data and Sparse Constraints, " K.  ...  The protein data bank (PDB, http://www.rcsb.org/) [2] has published 107958 biological macromolecular structures, including 35542 protein sequences, 28142 structures of human sequences, and 7611 nucleic  ...  Acknowledgments We are grateful to the anonymous reviewers whose critical review helped improve the quality of the papers in this special issue.  ... 
doi:10.1155/2015/565328 pmid:26236729 pmcid:PMC4506833 fatcat:f4yu6c4vrjbaxigs4d326452ey

Prediction of dinucleotide-specific RNA-binding sites in proteins

Michael Fernandez, Yutaro Kumagai, Daron M Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad
2011 BMC Bioinformatics  
Interaction preferences of protein subsequences and dinucleotides can be inferred from protein-RNA complex structures, enabling a training-based prediction approach.  ...  Using a standard approach to represent protein subsequences by their evolutionary profile, we trained neural networks to predict multiclass target vectors corresponding to 16 possible contacting dinucleotide  ...  Acknowledgements The work was partially supported by a fusion grant for interdisciplinary research by IFREC to YK, DS, SA and MF and by a grants-in-aid (kaken-hi) award from the JSPS, Japan to SA.  ... 
doi:10.1186/1471-2105-12-s13-s5 pmid:22373260 pmcid:PMC3278845 fatcat:ftciglbyvrffdkqqps4ulnnhta
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