Modeling, docking, and fitting of atomic structures to 3D maps from cryo-electron microscopy

Methods in Molecular Biology

Volumn 955, Issue , 2013, Pages 229-241

  Allen, Gregory S ^a   Stokes, David L ^a  

^a NONE

Author keywords

Computational biology; Electron microscopy; P type ATPases; Protein protein docking; Structure modeling

Indexed keywords

MEMBRANE PROTEIN; PROTEIN;

CRYOELECTRON MICROSCOPY; MOLECULAR DOCKING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SARCOPLASMIC RETICULUM; SEQUENCE ANALYSIS; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; INSTRUMENTATION; METHODOLOGY; PROTEIN CONFORMATION;

COMPUTATIONAL BIOLOGY; CRYOELECTRON MICROSCOPY; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 84876044940     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-176-9_13     Document Type: Chapter

References (25)

1. Wu CC, Rice WJ, Stokes DL (2008) Structure of a copper pump suggests a regulatory role for its metal-binding domain. Structure 16: 976–985
2. Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A (1996) SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J Struct Biol 116:190–199
3. Crowther RA, Henderson R, Smith JM (1996) MRC image processing programs. J Struct Biol 116:9–16
4. van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M (1996) A new generation of the IMAGIC image processing system. J Struct Biol 116:17–24
5. Cardozo T, Totrov M, Abagyan R (1995) Homology modeling by the ICM method. Proteins 23:403–414
6. Thompson JD, Gibson TJ, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics, Chapter 2, Unit 2.3
7. Sanchez R, Sali A (2000) Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol Biol 143:97–129
8. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612
9. Emsley P, Lohkamp B, Scott W, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501
10. Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47:110–119
11. Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C (2009) Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J Chem Inf Model 49:1455–1474
12. Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750–1759
13. Jain AN (2003) Surflex: fully automatic flexible molecular docking using a molecular similaritybased search engine. J Med Chem 46:499–511
14. Goodsell DS, Morris GM, Olson AJ (1996) Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 9:1–5
15. Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC (2006) Development and validation of a modular, extensible docking program: DOCK 5. J Comput Aided Mol Des 20:601–619
16. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
17. Toyoshima C, Nomura H (2002) Structural changes in the calcium pump accompanying the dissociation of calcium. Nature 418:605–611
18. Wriggers W, Milligan RA, McCammon JA (1999) Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol 125: 185–195
19. Rusu M, Birmanns S (2010) Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. J Struct Biol 170:164–171
20. Trabuco LG, Villa E, Mitra K, Frank J, Schulten K (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16:673–683
21. Hinsen K, Reuter N, Navaza J, Stokes DL, Lacapere JJ (2005) Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. Biophys J 88:818–827
22. Brunger AT (2007) Version 1.2 of the crystallography and NMR system. Nat Protoc 2:2728–2733
23. Fernandez-Recio J, Totrov M, Abagyan R (2002) Soft protein-protein docking in internal coordinates. Protein Sci 11:280–291
24. Fernandez-Recio J, Totrov M, Abagyan R (2002) Screened charge electrostatic model in protein-protein docking simulations. Pac Symp Biocomput. 552–563.
25. McRee DE (1999) Practical protein crystallography. Academic, San Diego