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Prediction of protein functional residues from sequence by probability density estimation

J. D. Fischer, C. E. Mayer, J. Söding
2008 Computer applications in the biosciences : CABIOS  
BENCHMARK SETS The difficulty in defining a benchmark set for the prediction of ligand-binding residues is to distinguish the physiologic ligands in crystal structures from the numerous molecules that  ...  For generating the MSAs, we run PSI-BLAST on each of the sequences with the non-redundant sequence database from NCBI filtered at 90% sequence identity by CD-HIT (Li and Godzik, 2006).  ...  (B) Predicting the probability for a functional residue by density estimation. Table 1 . 1 Overview of the benchmark sets used in this study.  ... 
doi:10.1093/bioinformatics/btm626 pmid:18174181 fatcat:fvgmzdlztrcevlkazlw3vc3nem

Prediction of phenotypes of missense mutations in human proteins from biological assemblies

Qiong Wei, Qifang Xu, Roland L. Dunbrack
2012 Proteins: Structure, Function, and Bioinformatics  
improvement in prediction over the accessible surface area of monomers from protein crystal structures (p=6e-5).  ...  from human/primate sequence differences in orthologous proteins.  ...  Acknowledgments This work was funded by NIH Grants R01 GM73784 and GM84453 and, in part, under a grant with the Pennsylvania Department of Health.  ... 
doi:10.1002/prot.24176 pmid:22965855 pmcid:PMC3552143 fatcat:iod4jfw2lvgopinf7l7n7mpctu

Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein–protein interaction sites

Yoichi Murakami, Kenji Mizuguchi
2010 Computer applications in the biosciences : CABIOS  
Only sequence features (position-specific scoring matrix and predicted accessibility) are used for training a Naïve Bayes classifier (NBC), and conditional probabilities of each sequence feature are estimated  ...  using a kernel density estimation method (KDE).  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btq302 pmid:20529890 fatcat:hjnevz6oj5dhvi6q3zbofriqii

Information-theoretic analysis and prediction of protein atomic burials: on the search for an informational intermediate between sequence and structure

Juliana R. Rocha, Marx G. van der Linden, Diogo C. Ferreira, Paulo H. Azevêdo, Antônio F. Pereira de Araújo
2012 Computer applications in the biosciences : CABIOS  
Lower estimates for the mutual information involving single burials are consistently approached by predictions from the NBC and actually surpassed by predictions from the HMM.  ...  Near-optimal prediction for the HMM is indicated by the agreement between its density of prediction information and the corresponding density of mutual information between input and output representations  ...  This procedure was used by Crooks and Brenner (2004) to estimate the mutual information density between sequences of amino acid residues and corresponding sequences of secondary structure assignments  ... 
doi:10.1093/bioinformatics/bts512 pmid:22923297 fatcat:axcb3swkzjg2tnklfum6y7pryq

Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

Andrew J Bordner
2010 BMC Bioinformatics  
The performance of the 1D (residue separation only), 3D, and 6D scoring functions were compared by their ability to identify correct threading solutions for a non-redundant benchmark set of protein backbone  ...  The second is a protein design method for determining the optimal sequence for a backbone structure by applying Belief Propagation optimization using the 6D scoring functions.  ...  Acknowledgements This work was funded by the Mayo Clinic. Author Details Mayo Clinic, 13400 East Shea Boulevard, Scottsdale, AZ 85259, USA  ... 
doi:10.1186/1471-2105-11-192 pmid:20398384 pmcid:PMC2874805 fatcat:ppovwn44ibcfjchwivlrkxg2ti

Protein single-model quality assessment by feature-based probability density functions [article]

Renzhi Cao, Jianlin Cheng
2016 arXiv   pre-print
GDT-TS scores) of protein structural models, and uses them to estimate its probability density distribution for quality assessment.  ...  These results demonstrate that this new probability density distribution based method is effective for protein single-model quality assessment and is useful for protein structure prediction.  ...  The work is supported by US National Institutes of Health (NIH) grant (R01GM093123) to JC.  ... 
arXiv:1607.04152v1 fatcat:dlx3smiksvh4rm6242trruosdm

An improved statistics-based backbone torsion potential energy for protein loop structure modeling

Ionel Rata, Kyle Wessells, Yaohang Li
2013 2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)  
Accurately modeling protein loops is critical to predicting three-dimensional structures and understanding functions of many proteins.  ...  This is based on our study showing that the second nearest neighbors along a protein sequence still have non-negligible influences on the torsion angles conformation of a loop residue while such correlations  ...  Torsion Probability Density Functions with Second Nearest Neighbors From the observed backbone correlations between the and torsion angles and the residue types, we capture a direct sequence structure  ... 
doi:10.1109/iccabs.2013.6629195 dblp:conf/iccabs/RataWL13 fatcat:z2imzfyb2vawlntlf2l5745kc4

Analysis of the code relating sequence to conformation in globular proteins. Theory and application of expected information

Barry Robson
1974 Biochemical Journal  
It is shown how the information transferred was estimated by inspection of proteins of known primary sequence and conformation. 4.  ...  Finally, it is shown how this process of information theory analysis can be reversed to predict the conformation of a protein by using its primary sequence and the above information estimates obtained  ...  However, the prediction of a whole protein can be carried out by predicting all the Sj values from the first residue j = 1 to the last residue j = L.  ... 
doi:10.1042/bj1410853 pmid:4463965 pmcid:PMC1168191 fatcat:plc3d5drffb3nniwnmws3kayvm

Protein secondary structure: entropy, correlations and prediction

G. E. Crooks, S. E. Brenner
2004 Bioinformatics  
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions?  ...  To answer this question we have measured the entropy densities of primary structure and secondary structure sequences, and the local inter-sequence mutual information density.  ...  entropy of a discrete probability can be estimated by available protein structures.  ... 
doi:10.1093/bioinformatics/bth132 pmid:14988117 fatcat:zpf7xkpz6bdmpk6h7raxflzeuu

Guiding belief propagation using domain knowledge for protein-structure determination

Ameet Soni, Craig Bingman, Jude Shavlik
2010 Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology - BCB '10  
Our results show that guiding BP using protein-disorder prediction improves the accuracy of marginal probability distributions and also produces more accurate, complete proteinstructure models.  ...  Specifically, we show that using predictions of protein-disorder regions effectively guides BP in our task.  ...  In b), we plot the completeness of the predictions -the percent of residues from the true solution with a corresponding prediction within 2Å.  ... 
doi:10.1145/1854776.1854816 dblp:conf/bcb/SoniBS10 fatcat:e5kwhopzrzgb7g4ohnsy62wgvm

Protein sequence-structure compatibility criteria in terms of statistical hypothesis testing

S. Sunyaev, E. Kuznetsov, I. Rodchenkov, V. Tumanyan
1997 Protein Engineering Design & Selection  
many cases by assigning one of the known folding types to a protein with unknown tertiary structure according to its amino and Vladimir Tumanyan 2 acid sequence, i.e. by recognizing an appropriate fold  ...  A variety of different approaches 117984 and 1 Institute for Control Sciences RAS, 65 Profsoyuznaya str., to this sequence-structure recognition problem have recently Moscow 117806, Russia been developed  ...  The log likelihood ratio criterion is then expressed by Equation 4.  ... 
doi:10.1093/protein/10.6.635 pmid:9278276 fatcat:dkvjpjgbvnehtfw5dk4wiaiyya

Protein single-model quality assessment by feature-based probability density functions

Renzhi Cao, Jianlin Cheng
2016 Scientific Reports  
GDT-TS scores) of protein structural models, and uses them to estimate its probability density distribution for quality assessment.  ...  These results demonstrate that this new probability density distribution based method is effective for protein single-model quality assessment and is useful for protein structure prediction.  ...  The work is supported by US National Institutes of Health (NIH) grant (R01GM093123) to JC.  ... 
doi:10.1038/srep23990 pmid:27041353 pmcid:PMC4819172 fatcat:p4y4ypxua5crnjd7h6vxwtvady

Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins

Kim T. Simons, Ingo Ruczinski, Charles Kooperberg, Brian A. Fox, Chris Bystroff, David Baker
1999 Proteins: Structure, Function, and Bioinformatics  
structure from knowledge of sequence and secondary structure.  ...  The first term captures sequence-dependent features of protein structures, such as the burial of hydrophobic residues in the core, the second term, universal sequence-independent features, such as the  ...  This work was supported by an STC NSF grant and by Young Investigator awards (to D.B.) from the NSF and the Packard Foundation. K.T.S. was supported by PHS NRSA T32 GM07270 from NIGMS.  ... 
doi:10.1002/(sici)1097-0134(19990101)34:1<82::aid-prot7>3.3.co;2-1 pmid:10336385 fatcat:ogofbwdzanbdzfeficekvgunti

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

Kim T. Simons, Ingo Ruczinski, Charles Kooperberg, Brian A. Fox, Chris Bystroff, David Baker
1999 Proteins: Structure, Function, and Bioinformatics  
structure from knowledge of sequence and secondary structure.  ...  The first term captures sequence-dependent features of protein structures, such as the burial of hydrophobic residues in the core, the second term, universal sequence-independent features, such as the  ...  This work was supported by an STC NSF grant and by Young Investigator awards (to D.B.) from the NSF and the Packard Foundation. K.T.S. was supported by PHS NRSA T32 GM07270 from NIGMS.  ... 
doi:10.1002/(sici)1097-0134(19990101)34:1<82::aid-prot7>3.0.co;2-a pmid:10336385 fatcat:2njfjfp6vbhtnmzb3kuhttkwmy

Causes of evolutionary rate variation among protein sites

Julian Echave, Stephanie J. Spielman, Claus O. Wilke
2016 Nature reviews genetics  
This work was also supported in part by US National Institutes of Health (NIH) grant F31 GM113622-01 to S.J.S. and by NIH grant R01 GM088344, NSF Cooperative agreement DBI-0939454 (BEACON Center), and  ...  Acknowledgements J.E. is Principal Investigator of CONICET.  ...  residues involved in the function of a protein.  ... 
doi:10.1038/nrg.2015.18 pmid:26781812 pmcid:PMC4724262 fatcat:ck45bfousraepbglygycms7cee
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