ParmBSC1 forcefield Nucleotide MD Simulations Database

ParmBSC1 Portfolio, a BigData approach to efficiently manage large nucleic acids simulation data.


Nucleic Acids Flexibility Server

Adam Hospital, Ignacio Faustino, Rosana Collepardo-Guevara, Carlos González, Josep Lluís Gelpí, Modesto Orozco.
NAFlex: A web server for the study of nucleic acid flexibility.
Nucleic Acids Research, 2013, 41(W1), W47-W55. NAR Featured Article June 2013.

ParmBSC0 Force Field

Pérez, Alberto, Marchán Ivan, Svozil Daniel, Sponer Jiri, Cheatham Thomas E., Laughton Charles A., and Orozco Modesto.
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.
Biophys J. (2007) 92 (11), 3817-29.

Ascona B-DNA Consortium (ABC)

Marco Pasi, John H. Maddocks, David Beveridge, Thomas C. Bishop, David A. Case, Thomas Cheatham, III, Pablo D. Dans, B. Jayaram, Filip Lankas, Charles Laughton, Jonathan Mitchell, Roman Osman, Modesto Orozco, Alberto Pérez, Daiva Petkeviciute, Nada Spackova, Jiri Sponer, Krystyna Zakrzewska and Richard Lavery.
microABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.
Nucleic Acids Research. (2014) 42 (19), 12272-12283.

Pablo D. Dans, Alberto Pérez, Ignacio Faustino, Richard Lavery and Modesto Orozco.
Exploring polymorphisms in B-DNA helical conformations.
Nucleic Acids Research. (2012) 40, 10668-10678.

R. Lavery, K. Zakrzewska, D. Beveridge, T.C. Bishop, D.A. Case, T. Cheatham III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton, J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Spackova, J. Sponer.
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.
Nucleic Acids Research. (2010) 38, 299-313.

Nucleic Acids Helical Parameters

R. Lavery, M. Moakher, J.H. Maddocks, D. Petkeviciute, K. Zakrzewska.
Conformational analysis of nucleic acids revisited: Curves+.
Nucleic Acids Research. (2009) 37, 5917-5929.

Nucleic Acids MD Studies

Ignacio Faustino, Alberto Pérez, Modesto Orozco.
Toward a consensus view of duplex RNA flexibility.
Biophysical Journal. (2010) 99(6), 1876-1885.

A. Pérez, F. Lankas, FJ. Luque and M. Orozco.
Towards a molecular dynamics consensus view of B-DNA flexibility.
Nucleic Acids Research. (2008) 36(7), 2379-2394.

Molecular Viewers

Humphrey, W., Dalke, A. and Schulten, K.
VMD - Visual Molecular Dynamics.
J. of Molec. Graphics. (1996) 14, 33-38.

Jsmol: JavaScript-Based Molecular Viewer From Jmol.

Essential Dynamics

Tim Meyer, Carles Ferrer-Costa, Alberto Pérez, Manuel Rueda, Axel Bidon-Chanal, Francisco Javier Luque, Charles A. Laughton, Modesto Orozco.
Essential Dynamics: A Tool for Efficient Trajectory Compression and Management.
J.Chem.Theor.Comput (2006) 2, 251-258.

MD Databases

Tim Meyer, Marco D'Abramo, Adam Hospital, Manuel Rueda, Carles Ferrer-Costa, Alberto Pérez, Oliver Carrillo, Jordi Camps, Carles Fenollosa, Dmitry Repchevsky, Josep Lluís Gelpí, Modesto Orozco.
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.
Structure. (2010) 18(11), 1399-1409.

Kehl C, Simms AM, Toofanny RD, and Daggett V.
Dynameomics: A multi-dimensional analysis-optimized database for dynamic protein data.
Protein Engineering Design & Selection. (2008) 21, 379-386.