Article

Timsit, Youri and Varnai, Peter (2011) Cytosine, the double helix and DNA self-assembly. Journal of Molecular Recognition, 24 (2). pp. 137-138.

Tan, Li, Varnai, Peter, Lamport, Derek T A, Yuan, Chunhua, Xu, Jianfeng, Qiu, Feng and Kieliszewski, Marcia J (2010) Plant O-Hydroxyproline Arabinogalactans Are Composed of Repeating Trigalactosyl Subunits with Short Bifurcated Side Chains. Journal of Biological Chemistry, 285 (32). pp. 24575-24583. ISSN 0021-9258

Varnai, Peter and Timsit, Youri (2010) Differential stability of DNA crossovers in solution mediated by divalent cations. Nucleic Acids Research, 38 (12). pp. 4163-4172. ISSN 0305-1048

Timsit, Youri and Varnai, Peter (2010) Helical Chirality: a Link between Local Interactions and Global Topology in DNA. PLoS ONE, 5 (2). ISSN 1932-6203

Varnai, Peter, Gáspári, Zoltan, Szappanos, Balazs and Perczel, Andras (2010) Reconciling the lock-and-key and dynamic views of canonical serine protease inhibitor action. FEBS Letters, 584 (1). pp. 203-206. ISSN 0014-5793

Allison, Jane R, Varnai, Peter, Dobson, Christopher M and Vendruscolo, Michele (2009) Determination of the Free Energy Landscape of a-Synuclein Using Spin Label Nuclear Magnetic Resonance Measurements. Journal of the American Chemical Society, 131 (51). pp. 18314-18326. ISSN 0002-7863

De Marco, Giuseppe and Varnai, Peter (2009) Molecular simulation of conformational transitions in biomolecules using a combination of structure-based potential and empirical valence bond theory. Physical Chemistry Chemical Physics, 11 (45). pp. 10694-10700. ISSN 1463-9076

Hsu, Shang-Te Danny, Varnai, Peter, Bugaut, Anthony, Reszka, Anthony P, Neidle, Stephen and Balasubramanian, Shankar (2009) A G-Rich Sequence within the c-kit Oncogene Promoter Forms a Parallel G-Quadruplex Having Asymmetric G-Tetrad Dynamics. Journal of the American Chemical Society, 131 (37). pp. 13399-13409. ISSN 0002-7863

Varnai, Peter, Dobson, Christopher M and Vendruscolo, Michele (2008) Determination of the Transition State Ensemble for the Folding of Ubiquitin from a Combination of Phi and Psi Analyses. Journal of Molecular Biology, 377 (2). pp. 575-588. ISSN 0022-2836

Richter, Barbara, Gsponer, Joerg, Varnai, Peter, Salvatella, Xavier and Vendruscolo, Michele (2007) The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins. Journal of Biomolecular NMR, 37 (2). pp. 117-135. ISSN 1573-5001

Dixit, S B, Beveridge, David L, Case, D A, Cheatham, Thomas E, Giudics, Emmanuel, Lankas, Filip, Lavery, Richard, Maddocks, John H, Osman, Roman, Sklenar, Heinz, Thayer, Kelly M and Varnai, Peter (2007) Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps. Biophysical Journal, 89 (6). pp. 3721-3740.

Varnai, Peter, Canalia, Muriel and Leroy, Jean-Louis (2004) Opening mechanism of G.T/U pairs in DNA and RNA duplexes: A combined study of imino proton exchange and molecular dynamics simulation. Journal of American Chemical Society, 126 (44). pp. 14659-14667. ISSN 0002-7863

Varnai, Peter and Zakrzewska, Krystyna (2004) DNA and its counterions: A molecular dynamics study. Nucleic Acids Research, 32 (14). pp. 4269-4280. ISSN 0305-1048

Beveridge, David L, Barreiro, Gabriela, Byun, K Suzie, Case, David A, Cheatham, Thomas E, Dixit, Surjit B, Giudice, Emmanuel, Lankas, Filip, Lavery, Richard, Maddocks, John H, Osman, Roman, Seibert, Eleanore, Sklenar, Heinz, Stoll, Gautier, Thayer, Kelly M, Varnai, Peter and Young, Matthew A (2004) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(C(p)G) steps. Biophysical Journal, 87 (6). pp. 3799-3813. ISSN 0006-3495

Varnai, Peter, Giudice, Emmanuel and Lavery, Richard (2003) Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Research, 31 (5). pp. 1434-1443. ISSN 0305-1048

Varnai, Peter, Djuranovic, Dragana, Lavery, Richard and Hartmann, Brigitte (2002) Alpha/gamma Transitions in the B-DNA backbone. Nucleic Acids Research, 30 (24). pp. 5398-5406. ISSN 0305-1048

Topf, Maya, Varnai, Peter and Richards, W Graham (2002) Ab initio QM/MM dynamics simulation of the tetrahedral intermediate of serine proteases: Insights into the active site hydrogen-bonding network. Journal of the American Chemical Society, 124 (49). pp. 14780-14788. ISSN 0002-7863

Varnai, Peter and Lavery, Richard (2002) Base flipping in DNA: Pathways and energetics studied with molecular dynamic simulations. Journal of the American Chemical Society, 124 (25). pp. 7272-7273. ISSN 0002-7863

Topf, M, Varnai, Peter, Schofield, C J and Richards, W G (2002) Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases. Proteins, 47 (3). pp. 357-369. ISSN 0887-3585

Giudice, Emmanuel, Varnai, Peter and Lavery, Richard (2001) Energetic and conformational aspects of A: T base-pair opening within the DNA double helix. ChemPhysChem, 2 (11). pp. 673-677. ISSN 1439-4235

Varnai, Peter and Richards, W Graham (2001) A density functional study of the interconversion of carbonyls and alcohols in the solution: Comparison of reaction mechanisms involving NADPH, histidine, and tyrosine. International Journal of Quantum Chemistry, 84 (2). pp. 276-281. ISSN 0020-7608

Varnai, Peter and Warshel, Arieh (2000) Computer simulation studies of the catalytic mechanism of human aldose reductase. Journal of American Chemical Society, 122 (16). 3849¿3860. ISSN 00027863

Book Section

Varnai, Peter and Lavery, R (2006) Modelling DNA deformations. In: Sponer, J and Lankas, F (eds.) Computational Studies of RNA and DNA. Springer Verlag, pp. 169-210. ISBN 978-1-4020-4794-7

Conference or Workshop Item

Topf, Maya, Varnai, Peter and Richards, W Graham (2001) Quantum mechanical/molecular mechanical study of three stationary points along the deacylation step of the catalytic mechanism of elastase. In: 10th International Congress of Quantum Chemistry, NICE, FRANCE.