Citing NAFlex:

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.


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.

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.

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.

Xiang-Jun Lu & Wilma K. Olson.
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.
Nat Protoc. 3(7), 1213-27.

Guohui Zheng, Xiang-Jun Lu, Wilma K. Olson.
Web 3DNA - a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.
Nucleic Acids Research 37(Web Server Issue), W240-W246.

Marc van Dijk, Alexandre M. J. J. Bonvin.
3D-DART: a DNA structure modelling server.
Nucleic Acids Research 37(Web Server Issue), W235-W239.

Raviprasad Aduri, Brian T. Psciuk, Pirro Saro, Hariprakash Taniga, H. Bernhard Schlegel, and John SantaLucia, Jr.
AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA.
J.Chem.Theory Comput. (2007) 3(4), 1464-1475.

J. Ramon Goñi, Carles Fenollosa, Alberto Pérez, David Torrents, Modesto Orozco.
DNAlive: a tool for the physical analysis of DNA at the genomic scale.
Bioinformatics. (2008) 24(15), 1731-1732.

Hongmei Jian, Alexander V. Vologodskii, Tamar Schlick.
A Combined Wormlike-Chain and Bead Model for Dynamic Simulations of Long Linear DNA.
Journal of Computational Physics. (1997) 136(1), 168-179.

Alder B.J. and Wainwright T.E.
Studies in Molecular Dynamics.
I. General Method. Journal of Chemical Physics. (1959) 31, 459-466.

Adam Hospital, Pau Andrio, Carles Fenollosa, Damjan Cicin-Sain, Modesto Orozco, Josep Lluís Gelpí
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.
Bioinformatics, 2012, 28(9):1278-1279.

Benjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodošček, Bernard R. Brooks, H. Lee Woodcock III.
CHARMMing: A new, flexible web portal for CHARMM.
J. Chem. Inf. Model. (2008) 48, 1920-1929.

Aleksey Porollo, Jaroslaw Meller.
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulation.
Nucleic Acids Research. (2010) 38, W662-W666.

Pradeep Kota.
GUIMACS - A java based front end for GROMACS.
In Silico Biology. (2006) 10, 0008.

Sanjit Roopra, Bernhard Knapp, Ulrich Omasits, Wolfgang Schreiner.
jSimMacs for GROMACS: A java application for advanced molecular dynamics simulations with remote access capability.
J. Chem. Inf. Model. (2009) 49, 2412-2417.

Christopher Bruns, Russ Altman, Vjay Pande.
OpenMM Zephyr Project.
Ongoing Project.

Sunhwan Jo, Taehoon Kim, Vidyashankara G. Iyer, Wonpil Im.
CHARMM-GUI: A web-based graphical user interface for Charmm.
J. Comput. Chem. (2008) 29, 1859-1865.

Diamantis Sellis, Dimitrios Vlachakis, Metaxia Vlassi.
Gromita: A fully integrated graphical user interface to Gromacs 4.
Bioinformatics and Biology Insights (2009) 3, 99-102.

BioMoby Consortium.
Interoperability with Moby 1.0-It's better than sharing your toothbrush.
Brieffings in Bioinformatics. (2008) 1, 1-12.

Hui Li, Andrew D. Robertson, Jan H. Jensen.
Very Fast Empirical Prediction and Interpretation of Protein pKa Values.
Proteins. (2005) 61, 704-721.

Delphine C. Bas, David M. Rogers, Jan H. Jensen.
Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes.
Proteins. (2008) 73, 765-783.

Dmitrij Frishman, Patrick Argos.
Knowledge-based protein secondary structure assignment.
Proteins. (1995) 23(4), 566-579.

Sorin EJ, Pande VS.
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations.
Biophys. J. (2005) 88(4), 2472-93.

DePaul AJ, Thompson EJ, Patel SS, Haldeman K, Sorin EJ.
Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics.
Nucleic Acids Res. (2010) 38(14), 4856-67.

D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang, R. Woods.
The Amber biomolecular simulation programs.
Computat. Chem. (2005) 26, 1668-1688.

Hess, B., Kutzner, C., van der Spoel, D., Lindahl, E.
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
J. Chem. Theory Comput. (2008) 4, 435-447.

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten.
Scalable molecular dynamics with NAMD.
Journal of Computational Chemistry. (2005) 26, 1781-1802.

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

Jmol: an open-source Java viewer for chemical structures in 3D.

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.

Manuel Rueda, Pablo Chacón, Modesto Orozco.
Thorough Validation of Protein Normal Mode Analysis- A Comparative Study with Essential Dynamics.
Structure. (2007a) 15, 565-575.

Manuel Rueda, Carles Ferrer-Costa, Tim Meyer, Alberto Pérez, Jordi Camps, Adam Hospital, Josep Lluís Gelpí, Modesto Orozco.
A consensus view of protein dynamics.
Proc. Natl. Acad. Sci. (2007b) 104, 796-801.

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.

Agusti Emperador, Oliver Carrillo, Manuel Rueda, Modesto Orozco.
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.
Biophysical Journal. (2008) 95, 2127-2138.

Jordi Camps, Oliver Carrillo, Agustí Emperador, Laura Orellana, Adam Hospital, Manuel Rueda, Damjan Cicin-Sain, Marco D'Abramo, Josep Lluís Gelpí, Modesto Orozco.
FlexServ: An integrated tool for the analysis of protein flexibility.
Bioinformatics. (2009) 25(13), 1709-1710.