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Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties

Wenxu Tong, Ying Wei, Leonel F. Murga, Mary Jo Ondrechen, Ronald J. Williams, Michael Levitt
2009 PLoS Computational Biology  
A new monotonicity-constrained maximum likelihood approach, called Partial Order Optimum Likelihood (POOL), is presented and applied to the problem of functional site prediction in protein 3D structures  ...  of sequence alignments and 3D structures.  ...  The purpose of the present paper is five-fold: (1) We present a monotonicity-constrained maximum likelihood approach, called Partial Order Optimum Likelihood (POOL), to improve performance and expand the  ... 
doi:10.1371/journal.pcbi.1000266 pmid:19148270 pmcid:PMC2612599 fatcat:jtzgq7ipdrbxlfmu5ilhbocqce

Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs)

Zhouxi Wang, Pengcheng Yin, Joslynn S Lee, Ramya Parasuram, Srinivas Somarowthu, Mary Ondrechen
2013 BMC Bioinformatics  
Acknowledgements The support of the NSF under grants number MCB-0843603 and MCB-1158176 is gratefully acknowledged. JSL is an NSF Graduate Research Fellow.  ...  Declarations This article has been published as part of BMC Bioinformatics  ...  Functional site predictions are obtained from Partial Order Optimum Likelihood (POOL) [22, 23] , a monotonicity-constrained maximum likelihood method, using computed chemical, electrostatic, and geometric  ... 
doi:10.1186/1471-2105-14-s3-s13 pmid:23514271 pmcid:PMC3584854 fatcat:d7t4pt3o3jak5mu6k7dpjpqqqi

Automatic prediction of catalytic residues by modeling residue structural neighborhood

Elisa Cilia, Andrea Passerini
2010 BMC Bioinformatics  
Results: We developed an effective representation of structural information by modeling spherical regions around candidate residues, and extracting statistics on the properties of their content such as  ...  We trained an SVM classifier combining our features with sequence-based information and previously developed 3D features, and compared its performance with the most recent state-of-the-art approaches on  ...  Authors' contributions EC proposed the use of residue structural neighborhood, implemented the feature extraction tools and conducted all the experimental evaluation.  ... 
doi:10.1186/1471-2105-11-115 pmid:20199672 pmcid:PMC2844391 fatcat:kikmtlgmgrfuxbmn5aa6onclfe

Biochemical functional predictions for protein structures of unknown or uncertain function

Caitlyn L. Mills, Penny J. Beuning, Mary Jo Ondrechen
2015 Computational and Structural Biotechnology Journal  
Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function.  ...  With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to  ...  This led to the development of Partial Order Optimum Likelihood, or POOL.  ... 
doi:10.1016/j.csbj.2015.02.003 pmid:25848497 pmcid:PMC4372640 fatcat:cuiylfqczrgctmlmuoyluxalie

Prediction of Structures and Interactions from Genome Information [article]

Sanzo Miyazawa
2017 arXiv   pre-print
Predicting three dimensional residue-residue contacts from evolutionary information in protein sequences was attempted already in the early 1990s.  ...  Here, we review statistical methods for extracting causative correlations and various approaches to describe protein structure, complex, and flexibility based on predicted contacts.  ...  of known 3D structure, predicted protein-protein contacts in 32 complexes of unknown structure, and then demonstrated how evolutionary direct couplings can be used to distinguish between interacting and  ... 
arXiv:1709.08021v1 fatcat:3sxrv2ifjzeu7a5e65ybf6siia

Positive selection in glycolysis among Australasian stick insects

Luke T Dunning, Alice B Dennis, Geoffrey Thomson, Brent J Sinclair, Richard D Newcomb, Thomas R Buckley
2013 BMC Evolutionary Biology  
Results: Using maximum likelihood methods a signature of positive selection was inferred in two core glycolysis enzymes.  ...  This permits a broad investigation to determine which steps within glycolysis and what sites within enzymes are the targets of positive selection.  ...  on the manuscript, the Department of Conservation for access to field sites, and members of the ecological genetics lab, Landcare Research.  ... 
doi:10.1186/1471-2148-13-215 pmid:24079656 pmcid:PMC3850572 fatcat:kehauzrcgvduxf7y4krm7wg56i

Broadening the Biocatalytic Toolbox—Screening and Expression of New Unspecific Peroxygenases

Sebastian Bormann, Harald Kellner, Johanna Hermes, Robert Herzog, René Ullrich, Christiane Liers, Roland Ulber, Martin Hofrichter, Dirk Holtmann
2022 Antioxidants  
Out of ten initially selected sequences, three enzymes (one from Aspergillus niger and two from Candolleomyces aberdarensis) were actively expressed.  ...  Enzymes were purified to near homogeneity and characterized regarding their specific activities and pH-optima for typical UPO substrates.  ...  The results for all three rUPOs are in agreement with predicted N-glycosylation sites, and thereby the sequence of rAniUPO having six potential N-glycosylation sites, whereas both sequences of Candolleomyces  ... 
doi:10.3390/antiox11020223 pmid:35204106 pmcid:PMC8868357 fatcat:pks53mtlfzhpfdmxif5ufo2wsi

Recognition of drug-target interaction patterns using genetic algorithm-optimized Bayesian-regularized neural networks and support vector machines

Michael Fernandez, Akinori Sarai, Shandar Ahmad
2009 2009 IEEE International Conference on Systems, Man and Cybernetics  
In addition, feature selection over large pools of molecular descriptors allowed determining the structural and atomic properties of the ligands that are ruling the biological interactions with the target  ...  The selection of optimum input variables and the adjustment of network weights and biases to optimum values to yield generalizable predictors were optimized by combining Bayesian training and GA based-variable  ...  For the huprines [24] and tacrines [25] datasets, the GA allows exploring a wide pool of 3D-descriptors.  ... 
doi:10.1109/icsmc.2009.5346852 dblp:conf/smc/FernandezSA09 fatcat:gtf6m7qonfg7ddnhwrpe73al2e

Molecular cloning, in-silico characterization and functional validation of monodehydroascorbate reductase gene in Eleusine coracana

Bhawana Negi, Prafull Salvi, Deepesh Bhatt, Manoj Majee, Sandeep Arora, Debasis Chakrabarty
2017 PLoS ONE  
The active site analysis showed presence of conserved Tyr 348 residue, facilitating the catalytic activity in electron transfer mechanism. qPCR expression profiling of Ecmdar under stress indicated that  ...  Cloning and functional characterization of this important stress inducible gene is of great significance for its imperative use in plant stress management.  ...  Active site was predicted by 1) superimposing ligand binding site of the known Cloning and functional validation of Ecmdar gene structure with query protein 3D structure and 2) mapping the conserved residues  ... 
doi:10.1371/journal.pone.0187793 pmid:29176870 pmcid:PMC5703496 fatcat:jggjijn7vrew3m3wjaq3epwglu

A Novel CalB-Type Lipase Discovered by Fungal Genomes Mining

Maria E. Vaquero, Laura I. de Eugenio, Maria J. Martínez, Jorge Barriuso, Junwen Wang
2015 PLoS ONE  
The most promising candidate (PlicB) presented interesting structural properties. PlicB was expressed in a heterologous host, purified and partially characterized.  ...  The candidates were selected taking into account homology and conserved motifs criteria, as well as, phylogeny and 3D model analyses.  ...  Selected candidates were aligned using MUSCLE, and an un-rooted tree was created using Maximum-likelihood methods with a boostrap of 2000(MEGA6 software).  ... 
doi:10.1371/journal.pone.0124882 pmid:25898146 pmcid:PMC4405274 fatcat:q444hrnyibbm3bhoj4rhf2s2ue

First Dye-Decolorizing Peroxidase from an Ascomycetous Fungus Secreted by Xylaria grammica

Virginia Kimani, René Ullrich, Enrico Büttner, Robert Herzog, Harald Kellner, Nico Jehmlich, Martin Hofrichter, Christiane Liers
2021 Biomolecules  
Mn2+ oxidation was most effective at an acidic pH (between 4.0 and 5.0) and a hypothetical surface exposed an Mn2+ binding site comprising three acidic amino acids (two aspartates and one glutamate) could  ...  be localized within the hypothetical XgrDyP structure.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biom11091391 pmid:34572604 pmcid:PMC8469222 fatcat:z3jj5cfjk5fidketd4i3nazrh4

Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins [article]

Megan Leander, Zhuang Liu, Qiang Cui, Srivatsan Raman
2022 bioRxiv   pre-print
We found hotspots to be distributed protein-wide rather than being restricted to "pathways" linking allosteric and active sites as is commonly assumed.  ...  Machine learning with our large DMS datasets revealed that global structural and dynamic properties to be a strong predictor of whether a residue is a hotspot than local and physicochemical properties.  ...  Local structural entropy (LSE) measures the likelihood of the local sequence around the residue to change secondary structure.  ... 
doi:10.1101/2022.05.01.490188 fatcat:uzf3lx2vqbghzlu6om3ze3m4ne

Origins and breadth of pairwise epistasis in an α-helix of β-lactamase TEM-1 [article]

Andre Birgy, Clement Roussel, Harry Kemble, Jimmy Mullaert, Karine Panigoni, Audrey Chapron, Jeremie Chatel, Melanie Magan, Herve Jacquier, Simona Cocco, Remi Monasson, Olivier Tenaillon
2021 bioRxiv   pre-print
Our results thus shed light on the existence and the origins of the multiple determinants of the epistatic landscape, even at the level of small structural components of a protein, and suggest that the  ...  To quantify and better understand interactions between fitness-affecting mutations, we focus on a 11 amino-acid α-helix of the protein β-lactamase TEM-1, and build a comprehensive library of more than  ...  For the sake of generality, this α-helix is not involved in the active site; it is just a structural component of the enzyme.  ... 
doi:10.1101/2021.11.29.470435 fatcat:wuh25opnyvhildae4xjomyqsxm

Evolution of Cinnamate/p-Coumarate Carboxyl Methyltransferases and Their Role in the Biosynthesis of Methylcinnamate

Jeremy Kapteyn, Anthony V. Qualley, Zhengzhi Xie, Eyal Fridman, Natalia Dudareva, David R. Gang
2007 The Plant Cell  
Structural modeling and ligand docking suggested active site residues that appear to contribute to the substrate preference of CCMTs relative to other members of the SABATH family.  ...  Site-directed mutagenesis of specific residues confirmed these findings.  ...  ACKNOWLEDGMENTS We thank Joseph Noel, Florence Pojer, and Jeannine Ross for valuable discussion and advice on the protein modeling and structural analysis; Joseph Bischoff for valuable discussion regarding  ... 
doi:10.1105/tpc.107.054155 pmid:17951447 pmcid:PMC2174721 fatcat:5mtivehuyvfvrbf2jjgajgujra

Antibody Production with Synthetic Peptides [chapter]

Bao-Shiang Lee, Jin-Sheng Huang, Lasanthi P. Jayathilaka, Jenny Lee, Shalini Gupta
2016 Msphere  
Peptides (usually 10-20 amino acid residues in length) can be used as effectively as proteins in raising antibodies producing both polyclonal and monoclonal antibodies routinely with titers higher than  ...  Although the process for designing peptide antigens is not exact, several guidelines and computational B-cell epitope prediction methods can help maximize the likelihood of producing antipeptide antibodies  ...  Acknowledgments We thank the support of the Research Resources Center at the University of Illinois at Chicago.  ... 
doi:10.1007/978-1-4939-6352-2_2 pmid:27515072 fatcat:euvfzbmbgfbwpo7ebkrwjb4lnq
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