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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.  ...  While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention.  ...  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

SCMCRYS: Predicting Protein Crystallization Using an Ensemble Scoring Card Method with Estimating Propensity Scores of P-Collocated Amino Acid Pairs

Phasit Charoenkwan, Watshara Shoombuatong, Hua-Chin Lee, Jeerayut Chaijaruwanich, Hui-Ling Huang, Shinn-Ying Ho, Jie Zheng
2013 PLoS ONE  
This study proposes an ensemble method, SCMCRYS, to predict protein crystallization, for which each classifier is built by using a scoring card method (SCM) with estimating propensity scores of p-collocated  ...  It is desirable to develop a simple and easily interpretable prediction method with informative sequence features to provide insights into protein crystallization.  ...  Scoring card method The scoring card method (SCM) is a general-purpose prediction method for protein functions from primary protein sequences, especially for the functions that the dipeptide composition  ... 
doi:10.1371/journal.pone.0072368 pmid:24019868 pmcid:PMC3760885 fatcat:hdb3pwarsjdktp3cd6a63lrdny

Rational identification of aggregation hotspots based on secondary structure and amino acid hydrophobicity

Daisuke Matsui, Shogo Nakano, Mohammad Dadashipour, Yasuhisa Asano
2017 Scientific Reports  
Insoluble proteins contain residues that decrease their solubility (aggregation hotspots). Mutating these hotspots to optimal amino acids is expected to improve protein solubility.  ...  After being identified, the hotspot residues are mutated to other amino acids to improve the solubility.  ...  A function to calculate the HiSol score was implemented in the graphical user interface of INTMSAlign 19 .  ... 
doi:10.1038/s41598-017-09749-2 pmid:28842596 pmcid:PMC5573320 fatcat:4bop2lyvzrepdgm5w3th2y2ivq

Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization [article]

Matthew Chan, Kui K Chan, Erik Procko, Diwakar Shukla
2021 biorxiv/medrxiv  
A potential therapeutic candidate for neutralizing SARS-CoV-2 infection is engineering high- affinity soluble ACE2 decoy proteins to compete for binding of the viral spike (S) protein.  ...  that binds RBD with similar affinity to ACE22.v.2.4.  ...  When examining the in silico mutagenesis predictions for these double mutants, TLmutation score the sACE22.v2.4 double mutants in the top 14%, with T27Y;N330Y and L79T;N330Y scoring in the upper 5%.  ... 
doi:10.1101/2021.12.22.473902 pmid:34981064 pmcid:PMC8722601 fatcat:ya4ihgzibbfkrkdupmijjufsxi

Mutagenesis-based definitions and probes of residue burial in proteins

K. Bajaj, P. Chakrabarti, R. Varadarajan
2005 Proceedings of the National Academy of Sciences of the United States of America  
in protein function (1).  ...  Mutagenesis.  ...  This work was supported by grants from The Wellcome Trust and Department of Biotechnology, Government of India (to R.V.).  ... 
doi:10.1073/pnas.0505089102 pmid:16251276 pmcid:PMC1283427 fatcat:obfq2phn3zb2zcfh6xqfem3ngu

Ligandformer: A Graph Neural Network for Predicting Compound Property with Robust Interpretation [article]

Jinjiang Guo, Qi Liu, Han Guo, Xi Lu
2022 arXiv   pre-print
Furthermore, Ligandformer can simultaneously output specific property score and visible attention map on structure, which can support researchers to investigate chemical or biological property and optimize  ...  Ligandformer can be generalized to predict different chemical or biological properties with high performance.  ...  Table 1 : 1 AUC performance comparison on aqueous solubility, Caco-2 cell permeabilty and Ames mutagenesis.  ... 
arXiv:2202.10873v3 fatcat:7tysswowknevrcft2asvutueqq

Molecular Determinants of Mutant Phenotypes, Inferred from Saturation Mutagenesis Data

Arti Tripathi, Kritika Gupta, Shruti Khare, Pankaj C. Jain, Siddharth Patel, Prasanth Kumar, Ajai J. Pulianmackal, Nilesh Aghera, Raghavan Varadarajan
2016 Molecular biology and evolution  
Mutational sensitivity data obtained with CcdB were used to derive a procedure for predicting functional effects of mutations.  ...  We used saturation mutagenesis combined with deep sequencing to determine mutational sensitivity scores for 1,664 single-site mutants of the 101 residue Escherichia coli cytotoxin, CcdB at seven different  ...  The predicted score is denoted as MS pred.  ... 
doi:10.1093/molbev/msw182 pmid:27563054 pmcid:PMC5062330 fatcat:ky4ica2nsve2dmqkwlbu2dguym

Molecular Dissection of Human Interleukin-31-mediated Signal Transduction through Site-directed Mutagenesis

Sabine Le Saux, François Rousseau, Fabien Barbier, Elisa Ravon, Linda Grimaud, Yannic Danger, Josy Froger, Sylvie Chevalier, Hugues Gascan
2009 Journal of Biological Chemistry  
cytokine-binding domain; STAT, signal transducers and activators of transcription; ELISA, enzyme-linked immunosorbent assay; mAb, monoclonal antibody; MAPK, mitogen-activated protein kinase; wt, wild type; s, soluble  ...  No key residue related to the IL-6 family binding site could be determined. To predict potential IL-31 hot spots, pMUT scoring was used.  ...  To determine an alternative consensus score, we compared the pMUT and the conservation scores for each amino acid and identified residues with the highest scores determined by the two methods.  ... 
doi:10.1074/jbc.m109.049189 pmid:19920145 pmcid:PMC2823401 fatcat:hdhluyhk2rfjlkoez55bej6yue

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning

Justin R. Klesmith, John-Paul Bacik, Emily E. Wrenbeck, Ryszard Michalczyk, Timothy A. Whitehead
2017 Proceedings of the National Academy of Sciences of the United States of America  
We develop predictive models to identify mutations that enhance solubility without disrupting activity with an accuracy of 90%.  ...  Five percent to 10% of all single missense mutations improve solubility, matching theoretical predictions of global protein stability.  ... 
doi:10.1073/pnas.1614437114 pmid:28196882 pmcid:PMC5338495 fatcat:bvrhu3ms55c2tg24hebkv2g4su

Evaluation of Structural and Evolutionary Contributions to Deleterious Mutation Prediction

Christopher T Saunders, David Baker
2002 Journal of Molecular Biology  
To address this, we have used a variety of structural and evolutionary features to create simple deleterious mutation models that have been tested on both experimental mutagenesis and human allele data  ...  We find that the most accurate predictions are obtained using a solvent-accessibility term, the C b density, and a score derived from homologous sequences, SIFT.  ...  Acknowledgments We thank Pauline Ng and Steven Henikoff for providing mutagenesis data, access to the SIFT source code, and for helpful discussions regarding this problem.  ... 
doi:10.1016/s0022-2836(02)00813-6 pmid:12270722 fatcat:fynta6ly3rfobgqljxbojewaxi

Systematic evaluation of soluble protein expression using a fluorescent unnatural amino acid reveals no reliable predictors of tolerability

Zachary M Hostetler, John J. Ferrie, Marc R Bornstein, Itthipol Sungwienwong, E. James Petersson, Rahul M. Kohli
2018 ACS Chemical Biology  
Nonetheless, unnatural amino acids (Uaas) pose theoretical burdens on protein solubility, and determinants of position-specific tolerability to Uaas remain underexplored.  ...  Improvements in genetic code expansion have made preparing proteins with diverse functional groups almost routine.  ...  ACKNOWLEDGMENTS We thank members of the Kohli and Petersson laboratories for general advice, and we are grateful to E. Schutsky for input in preparing the manuscript.  ... 
doi:10.1021/acschembio.8b00696 pmid:30216041 pmcid:PMC6195468 fatcat:dqs5ot5bhjau5m6xaxmlwqmkya web services for improving recombinant protein production

Bikash K Bhandari, Chun Shen Lim, Paul P Gardner
2021 Nucleic Acids Research  
Experiments that are planned using accurate prediction algorithms will mitigate failures in recombinant protein production.  ...  protein expression, solubility and signal peptide analysis, respectively.  ...  A number of methods have been suggested to improve protein solubility, for example, truncation, mutagenesis, and the use of solubility-enhancing tags (2, (29) (30) (31) .  ... 
doi:10.1093/nar/gkab175 pmid:33744969 fatcat:hjujj7ajrrevfdfd6zuqxfc34e

Predicting Deleterious Amino Acid Substitutions

P. C. Ng, S. Henikoff
2001 Genome Research  
A higher proportion of substitutions predicted to be deleterious by SIFT gives an affected phenotype than substitutions predicted to be deleterious by substitution scoring matrices in three test cases.  ...  We have constructed a tool that uses sequence homology to predict whether a substitution affects protein function.  ...  This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.  ... 
doi:10.1101/gr.176601 pmid:11337480 pmcid:PMC311071 fatcat:3pk4hisuprcspf7rj2vl27qrlm

Evolutionary Trace Analysis of Azoreductase at the Ligand Binding Site and Enhancing the Active Site through Site Directed Mutagenesis

Shobana S
2012 Journal of Proteomics & Bioinformatics  
Site directed mutagenesis was performed at the residues, in very close proximity to the active site residues, hydrogen bonded to ligand.  ...  To estimate this, the structure function relationship was determined by evolutionary trace (ET) analysis at ligand binding site.  ...  By default, Schrödinger's proprietary GlideScore multi-ligand scoring function is used to score the poses.  ... 
doi:10.4172/jpb.1000240 fatcat:ojq54av5nrgopdfyw4ma2rcb3m

Rapid and accurate in silico solubility screening of a monoclonal antibody library

Pietro Sormanni, Leanne Amery, Sofia Ekizoglou, Michele Vendruscolo, Bojana Popovic
2017 Scientific Reports  
Here we show that the selection of soluble lead antibodies from an initial library screening can be greatly facilitated by a fast computational prediction of solubility that requires only the amino acid  ...  close match, and we further benchmark our predictions with published experimental data on aggregation hotspots and solubility of mutational variants of one of these antibodies.  ...  Acknowledgements We would like to thank Andrew Buchanan, Trevor Wilkinson, Chris van der Walle and Hardeep Samra for their critical review of the manuscript.  ... 
doi:10.1038/s41598-017-07800-w pmid:28811609 pmcid:PMC5558012 fatcat:723ffoh2grh7jd57p5brmjwhcq
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