Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era

PLoS Computational Biology

Volumn 10, Issue 8, 2014, Pages

  Cui, Qiang ^a   Nussinov, Ruth ^b,c  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR SIMULATION; NOBEL PRIZES;

ARTICLE; AWARDS AND PRIZES; BINDING AFFINITY; CLASSIFICATION ALGORITHM; COMPUTATIONAL FLUID DYNAMICS; CONCEPTUAL FRAMEWORK; CURRICULUM; HUMAN; LIGAND BINDING; MEDICAL RESEARCH; METHODOLOGY; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PROCESS MODEL; QUANTUM MECHANICS; SOLVATION; BIOCHEMISTRY; BIOLOGY; BIOPHYSICS; COMPUTER SIMULATION; INTERNET;

BIOCHEMISTRY; BIOPHYSICS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; INTERNET;

EID: 84927979910     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003786     Document Type: Article

References (11)

1. McCammon JA, Gelin BR, Karplus M, (1977) Dynamics of folded proteins. Nature267: 585–590.
2. Levitt M, Warshel A, (1975) Computer simulation of protein folding. Nature253: 694–698.
3. Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, et al. (2010) Atomic-level characterization of the structural dynamics of proteins. Science330: 341–346.
4. Feynman RP, Leighton RB, Sands M (1963) The Feynman Lectures in Physics. Reading: Addison-Wesley.
5. Miller BT, Singh RP, Schalk V, Pevzner Y, Sun JJ, et al. (2014) Web based computational chemistry education with CHARMMing I: Lessons and Tutorial. PLoS Comput Biol10: e1003719.
6. Pickard FC, IVMiller BT, Schalk V, Lerner MG, Woodcock HL, IIIet al. (2014) Web based computational chemistry education with CHARMMing II: Coarse Grained Protein Folding. PLoS Comput Biol10: e1003738.
7. Perrin BS, JrMiller BT, Schalk V, Woodcock HL, IIIBrooks BR, Ichiye T, (2014) Web-based computational chemistry lessons in CHARMMing III: Reduction potentials of electron transfer proteins. PLoS Comput Biol10: e1003739.
8. Jo S, Kim T, Iyer VG, Im W, (2008) CHARMM-GUI: A web-based graphical user interface for CHARMM. J Comp Chem29: 1859–1865.
9. Jo S, Lim JB, Klauda JB, Im W, (2009) CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes. Biophys J97: 50–58.
10. Jo S, Jiang W, Lee HS, Roux B, Im W, (2013) CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. J Chem Info Model53: 267–277.
11. Karplus M, Kuriyan J, (2005) Molecular dynamics and protein function. Proc Natl Acad Sci U S A102: 6679–6685.