ABS-Scan: In silico alanine scanning mutagenesis forbinding site residues in protein-ligand complex

F1000Research

Volumn 3, Issue , 2014, Pages

  Chandra, Nagasuma ^a   Anand, Praveen ^a   Nagarajan, Deepesh ^a   Mukherjee, Sumanta ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE;

ARTICLE; BINDING SITE; COMPUTER INTERFACE; COMPUTER MODEL; COMPUTER PROGRAM; DNA BINDING; HUMAN; LIGAND BINDING; LOSS OF FUNCTION MUTATION; MATHEMATICAL COMPUTING; PROTEIN ANALYSIS; PROTEIN BINDING; SITE DIRECTED MUTAGENESIS; WEB BROWSER;

EID: 84923364584     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/f1000research.5165.2     Document Type: Article

References (34)

1. Rose PW Bi C Bluhm WF: The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 2013;41(Database issue):D475-82. 23193259 10.1093/nar/gks1200 3531086
2. Morrison KL Weiss GA: Combinatorial alanine-scanning. Curr Opin Chem Biol. 2001;5(3):302-7. 11479122 10.1016/S1367-5931(00)00206-4
3. Weiss GA Watanabe CK Zhong A: Rapid mapping of protein functional epitopes by combinatorial alanine scanning. Proc Natl Acad Sci U S A. 2000;97(16):8950-4. 10908667 10.1073/pnas.160252097 16802
4. Williams AD Shivaprasad S Wetzel R: Alanine scanning mutagenesis of Abeta(1-40) amyloid fibril stability. J Mol Biol. 2006;357(4): 1283-94. 16476445 10.1016/j.jmb.2006.01.041
5. Ashkenazi A Presta LG Marsters SA: Mapping the CD4 binding site for human immunodeficiency virus by alanine-scanning mutagenesis. Proc Natl Acad Sci U S A. 1990;87(18):7150-4. 2402498 10.1073/pnas.87.18.7150 54701
6. Kristensen C Kjeldsen T Wiberg FC: Alanine scanning mutagenesis of insulin. J Biol Chem. 1997;272(20):12978-83. 9148904 10.1074/jbc.272.20.12978
7. Tang WJ Stanzel M Gilman AG: Truncation and alanine-scanning mutants of type I adenylyl cyclase. Biochemistry. 1995;34(44):14563-72. 7578062 10.1021/bi00044a035
8. Jain PC Varadarajan R: A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library. Anal Biochem. 2014;449:90-8. 24333246 10.1016/j.ab.2013.12.002
9. Bromberg Y Rost B: Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics. 2008;24(16):i207-12. 18689826 10.1093/bioinformatics/btn268 2597370
10. Eswar N Eramian D Webb B: Protein structure modeling with MODELLER. Methods Mol Biol. 2008;426:145-59. 18542861 10.1007/978-1-60327-058-8_8
11. Kaufmann KW Lemmon GH Deluca SL: Practically useful: what the Rosetta protein modeling suite can do for you. Biochemistry. 2010;49(14):2987-98. 20235548 10.1021/bi902153g 2850155
12. Kim DE Chivian D Baker D: Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 2004;32(Web Server issue):W526-31. 15215442 10.1093/nar/gkh468 441606
13. Liu Y Kuhlman B: RosettaDesign server for protein design. Nucleic Acids Res. 2006;34(Web Server issue):W235-8. 16845000 10.1093/nar/gkl163 1538902
14. Lyskov S Chou FC Conchúir SÓ: Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS One. 2013;8(5):e63906. 23717507 10.1371/journal.pone.0063906 3661552
15. Schymkowitz J Borg J Stricher F: The FoldX web server: an online force field. Nucleic Acids Res. 2005;33(Web Server issue):W382-8. 15980494 10.1093/nar/gki387 1160148
16. Dehouck Y Kwasigroch JM Rooman M: BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations. Nucleic Acids Res. 2013;41(Web Server issue):W333-9. 23723246 10.1093/nar/gkt450 3692068
17. Krüger DM Gohlke H: DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. Nucleic Acids Res. 2010;38(Web Server issue):W480-6. 20511591 10.1093/nar/gkq471 2896140
18. Homeyer N Gohlke H: FEW: a workflow tool for free energy calculations of ligand binding. J Comput Chem. 2013;34(11):965-73. 23288722 10.1002/jcc.23218
19. Greenidge PA Kramer C Mozziconacci JC: MM/GBSA binding energy prediction on the PDBbind data set: successes, failures, and directions for further improvement. J Chem Inf Model. 2013;53(1):201-9. 23268595 10.1021/ci300425v
20. Kumari R Kumar R Lynn A: g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model. 2014;54(7):1951-62. 24850022 10.1021/ci500020m
21. Huey R Morris GM Olson AJ: A semiempirical free energy force field with charge-based desolvation. J Comput Chem. 2007;28(6):1145-52. 17274016 10.1002/jcc.20634
22. Sali A Blundell TL: Comparative Protein Modelling by Satisfaction of Spatial Restraints. J Mol Biol. 1993;234(3):779-815. 8254673 10.1006/jmbi.1993.1626
23. Shen MY Sali A: Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006;15(11):2507-24. 17075131 10.1110/ps.062416606 2242414
24. Liu Z Li Y Han L: PDB-wide collection of binding data: current status of the PDBbind database. Bioinformatics. 2014; pii:btu626. 25301850 10.1093/bioinformatics/btu626
25. Huang SY Zou X: An iterative knowledge-based scoring function for protein-protein recognition. Proteins. 2008;72(2):557-79. 18247354 10.1002/prot.21949
26. Bennett MJ Albert RH Jez JM: Steroid recognition and regulation of hormone action: crystal structure of testosterone and NADP+ bound to 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase. Structure. 1997;5(6):799-812. 9261071 10.1016/S0969-2126(97)00234-7
27. Shimizu M Yamamoto K Mihori M: Two-dimensional alanine scanning mutational analysis of the interaction between the vitamin D receptor and its ligands: studies of A-ring modified 19-norvitamin D analogs. J Steroid Biochem Mol Biol. 2004;89-30(1-5):75-81. 15225750 10.1016/j.jsbmb.2004.03.088
28. Combs SA Deluca SL Deluca SH: Small-molecule ligand docking into comparative models with Rosetta. Nat Protoc. 2013;8(7):1277-98. 23744289 10.1038/nprot.2013.074
29. Chang J Schwer B Shuman S: Mutational analyses of trimethylguanosine synthase (Tgs1) and Mud2: proteins implicated in pre-mRNA splicing. RNA. 2010;16(5):1018-31. 20360394 10.1261/rna.2082610 2856874
30. Trott O Olson AJ: AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455-61. 19499576 10.1002/jcc.21334 3041641
31. Andreini C Bertini I Cavallaro G: Structural analysis of metal sites in proteins: non-heme iron sites as a case study. J Mol Biol. 2009;388(2):356-80. 19265704 10.1016/j.jmb.2009.02.052
32. Mobley DL Dill KA: Binding of small-molecule ligands to proteins: "what you see is not always "what you get. Structure. 2009;17(4):489-98. 19368882 10.1016/j.str.2009.02.010 19368882
33. Ferguson AD Larsen NA Howard T: Structural basis of substrate methylation and inhibition of SMYD2. Structure. 2011;19(9):1262-73. 21782458 10.1016/j.str.2011.06.011
34. Anand P Nagarajan D Mukherjee S: ABS-Scan. Zenodo. 2014. Data Source