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Four-Body Scoring Function for Mutagenesis

C. Deutsch, B. Krishnamoorthy
2007 Bioinformatics  
The four-body scoring function correctly predicted the changes to the stability of 169 out of 210 mutants (80.5%), and the changes to the reactivity of 17 out of 27 mutants (63%).  ...  Results: We develop a Delaunay tessellation-based four-body scoring function to predict the effects of single and multiple residue mutations on the stability and reactivity of proteins.  ...  ACKNOWLEDGMENTS Both authors are thankful for the support provided by the NSF UBM Grant DEB 0531870 while working on this research project.  ... 
doi:10.1093/bioinformatics/btm481 pmid:17921497 fatcat:6iokqnevzfecdox6gjtvsgxks4

Scoring function to predict solubility mutagenesis

Ye Tian, Christopher Deutsch, Bala Krishnamoorthy
2010 Algorithms for Molecular Biology  
Results: We use concepts from computational geometry to define a three body scoring function that predicts the change in protein solubility due to mutations.  ...  We optimize the scoring function using linear programming (LP) methods to derive its weights based on training.  ...  Scoring Function for Solubility Mutagenesis DT-based scoring functions have been used for predicting the effects of mutations on the stability [3, 18, 19] , and on the reactivity of proteins [5] .  ... 
doi:10.1186/1748-7188-5-33 pmid:20929563 pmcid:PMC2958853 fatcat:coeczdaaovdrvdrjrgq6bgciwy

Structure-based prediction of protein activity changes: Assessing the impact of single residue replacements

M. Masso, I. I. Vaisman
2011 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society  
a computational mutagenesis technique relying on a four-body potential Computational Mutagenesis: IL-3 ExampleRepresenting Mutants via Common Attributes• For a protein mutation at position N, nonzero  ...  , but these cannot be used to infer activity change Structure-Based Computational Mutagenesis • The four-body potential and the computational mutagenesis technique utilize Delaunay tessellation of protein  ... 
doi:10.1109/iembs.2011.6090876 pmid:22255025 dblp:conf/embc/MassoV11 fatcat:24bwrm3o7fh65j7t7fuvct65nm

Modeling functional changes toEscherichia colithymidylate synthase upon single residue replacements: a structure-based approach

Majid Masso
2015 PeerJ  
a knowledge-based, four-body statistical potential.  ...  Global scores for the TS variants are capable of uniquely characterizing groups of residue positions in the enzyme according to their physicochemical, functional, or structural properties.  ...  Concluding remarks In this report, a knowledge-based four-body statistical potential energy function was used to empirically calculate a structural residue environment score for every amino acid position  ... 
doi:10.7717/peerj.721 pmid:25648456 pmcid:PMC4304848 fatcat:x6vvjpx2g5fvfimkof5sr3ieqi

AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation

Majid Masso, Iosif I. Vaisman
2014 Advances in Bioinformatics  
The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based  ...  Two additional classifiers are available, one for predicting activity changes due to residue replacements and the other for determining the disease potential of mutations associated with nonsynonymous  ...  We previously developed the AUTO-MUTE server, an online set of tools for predicting protein functional consequences upon mutation, by implementing a computational mutagenesis technique that employs a four-body  ... 
doi:10.1155/2014/278385 pmid:25197272 pmcid:PMC4150472 fatcat:p2z5fznlr5dgjj24iaal4naxqm

A Photon-Free Approach to Transmembrane Protein Structure Determination

Cinque S. Soto, Brett T. Hannigan, William F. DeGrado
2011 Journal of Molecular Biology  
Low-resolution structures are also sometimes generated from the results of site-directed mutagenesis when other structural data are incomplete or not available.  ...  This profile is then interpreted by assuming that positions that have large effects on structure/function when mutated project toward the center of the oligomeric bundle.  ...  Gevorg Grigoryan for carefully reading the manuscript and for allowing us to use his rapid distance-matrix-based method for scanning the PDB.  ... 
doi:10.1016/j.jmb.2011.10.016 pmid:22024595 pmcid:PMC3808161 fatcat:fdqpodpqx5g45evdbxrq3xwzja

Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity

E. A. Stone
2005 Genome Research  
By using four diverse proteins for which sufficient comparative sequence data are available, we show that grades of disease, or likelihood of developing cancer, correlate strongly with physicochemical  ...  Furthermore, we show with four diverse proteins for which sufficient data are available that constraint violations quantitatively translate to grades of disease, or likelihood of developing cancer.  ...  Acknowledgments We thank Gregory Cooper and Midori Hosobuchi for comments on the manuscript, Jonathan Binkley for supplying alignments and crystal structures, Roberta Kwok for the Java implementation of  ... 
doi:10.1101/gr.3804205 pmid:15965030 pmcid:PMC1172042 fatcat:bw42ynj2zbc5jocjo7trrht5ru

Fitness of unregulated human Ras mutants modeled by implementing computational mutagenesis and machine learning techniques

Majid Masso, Arnav Bansal, Preethi Prem, Akhil Gajjala, Iosif I. Vaisman
2019 Heliyon  
The computational mutagenesis generated a feature vector of protein structural changes for each variant, and these data correlated well with fitness.  ...  Using experimental fitness data and implementing artificial intelligence and a computational mutagenesis technique, we developed models that reliably predict fitness for all single residue mutants of H-ras  ...  Gajjala thank the Aspiring Scientists Summer Internship Program (ASSIP) at George Mason University for providing the opportunity to participate in this project.  ... 
doi:10.1016/j.heliyon.2019.e01884 pmid:31211262 pmcid:PMC6562371 fatcat:nfis5jykand4jjyxglaerijw3q

Prediction of Enzyme Mutant Activity Using Computational Mutagenesis and Incremental Transduction

Nada Basit, Harry Wechsler
2011 Advances in Bioinformatics  
4-body statistical potentials for representation.  ...  This paper expands on standard one-shot learning by proposing an incremental transductive method (T2bRF) for the prediction of enzyme mutant activity during mutagenesis using Delaunay tessellation and  ...  Majid Masso and Iosif Vaisman for proposing the problem and representation, and for providing the datasets.  ... 
doi:10.1155/2011/958129 pmid:22007208 pmcid:PMC3189455 fatcat:dredqf3dq5dghmzfcjrtu2wzea

Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and Computations

Andrea Saponaro, Vincenzo Maione, Alexandre Bonvin, Francesca Cantini
2020 Bio-protocol  
Based on the modelling results, a rational mutagenesis approach is used to validate the generated models.  ...  There is no size limit for the macromolecular complexes that can be characterized by HADDOCK as long as the 3D structures of the individual components are available.  ...  Figure 3 , 3 "Parameter for clustering" tab). The clusters are then ranked based on the average HADDOCK score of their top four members.  ... 
doi:10.21769/bioprotoc.3793 pmid:33659447 pmcid:PMC7842552 fatcat:kkscxuzopjd7phl5g2v6zyz4mi

Characterization of a A3G-Vif-CRL5-CBFβ structure using a cross-linking mass spectrometry pipeline for integrative modeling of host-pathogen complexes

Robyn M. Kaake, Ignacia Echeverria, Seung Joong Kim, John Von Dollen, Nicholas M. Chesarino, Yuqing Fen, Clinton Yu, Hai Ta, Linda Chelico, Lan Huang, John Gross, Andrej Sali (+1 others)
2021 Zenodo  
Finally, the model was used to rationalize previous structural, mutagenesis, and functional data not used for modeling, including information related to the A3G bound and unbound structures as well as  ...  Here, we describe a pipeline for the structural characterization of these complexes using integrative structure modeling based on chemical cross-links and residue-protein contacts inferred from mutagenesis  ...  minimum scores for the best representative peptides for each unique linkage.  ... 
doi:10.5281/zenodo.5176959 fatcat:itiug3m2ejb4nfdhqlabpedp5q

Computational mutagenesis studies of protein structure-function correlations

Majid Masso, Zhibin Lu, Iosif I. Vaisman
2006 Proteins: Structure, Function, and Bioinformatics  
Topological scores, measures of sequence-structure compatibility, are calculated for all 1,881 single point mutants of the human immunodeficiency virus (HIV)-1 protease using a four-body statistical potential  ...  For a more comprehensive treatment of the relationship between protease structure and function, mutant topological scores are compared with the activity levels for a set of 536 experimentally synthesized  ...  The authors also thank Lakshmi Kumar Matukumalli for preliminary data collection on T4 lysozyme mutants, Todd Taylor for help with the four-body potentials, and Andrew Carr for help with creating the graphical  ... 
doi:10.1002/prot.20968 pmid:16617425 fatcat:tipnikltw5avlm4xpnrxltgcpu

Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis

M. Masso, I. I. Vaisman
2008 Bioinformatics  
Results: We detail a computational mutagenesis technique based on a four-body, knowledge-based, statistical contact potential.  ...  Motivation: Accurate predictive models for the impact of single amino acid substitutions on protein stability provide insight into protein structure and function.  ...  ACKNOWLEDGEMENTS The authors thank Andrew Carr for preparing the tessellation graphic, Rita Casadio for encouraging us to test our approach on the Capriotti et al. datasets and Michael Gromiha for providing  ... 
doi:10.1093/bioinformatics/btn353 pmid:18632749 fatcat:4smnzxobwnbu7l55t7gvk4ie7q

Modeling the functional consequences of single residue replacements in bacteriophage f1 gene V protein

M. Masso, E. Mathe, N. Parvez, K. Hijazi, I. I. Vaisman
2009 Protein Engineering Design & Selection  
A computational mutagenesis methodology utilizing a four-body, knowledge-based, statistical contact potential is applied toward globally quantifying relative environmental perturbations (residual scores  ...  For each mutant, the in silico mutagenesis additionally yields local measures of environmental change (EC scores) occurring at every residue position (residual profile) relative to the native protein.  ...  , defining the four-body statistical potential (Singh et al., 1996; Vaisman et al., 1998) .  ... 
doi:10.1093/protein/gzp050 pmid:19690089 fatcat:wzxj2hej3zcg5dl3g26ufmutgy

Genetic characterization of aggregation-defective developmental mutants of Myxococcus xanthus

S Torti, D R Zusman
1981 Journal of Bacteriology  
We also thank Dale Kaiser for his hospitality and encouragement during the initial phases of the project and Daryl Faulds for many helpful discussions.  ...  ACKNOWLEDGMENTS We acknowledge and thank Jerry Kuner for making available to us his phage stocks grown on a bank of strains containing independent insertions of Tn5 and for discussing his thesis results  ...  Plates were incubated at 34°C for about 10 days before scoring.  ... 
doi:10.1128/jb.147.3.768-775.1981 fatcat:tuzy2wnxcnbbvcy7lcg2wcf6mm
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