Most cited publications

Over 1000 citations

Nucleic acids simulation

  • Pérez et al, (2007) Biophys.J., 92, 3817. Refinement of the AMBER force-field for nucleic acids: Improving the description of a/g conformers”.

Genomics/Bioinformatics

  • Tomato Genome Consortium including M.O. (2012). Nature, 485, 635.

Over 800 citations

Genomics/Bioinformatics

  • Puente et al., (2011) Nature, 475, 101. “Whole genome sequencing identifies recurrent mutations in Chronic Lymphocytic Leukaemia”.

 Over 500 citations

Solvent effects

  • Luque & Orozco (2000), Chem. Rev., 100, 4187. “Theoretical methods for the description of the solvent effect in biomolecular systems”.

Genomics/Bioinformatics

  • Quesada et al., (2012) Nature Genetics, 44, 47. “Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia”.

Over 300 citations

Genomics/Bioinformatics

  • Ferrer et al.,  (2005) Bioinformatics, 21, 3176. “PMUT: a web-based tool for the annotation of pathological mutations on proteins”.

Solvent effects

 

  • Luque et al., (2001),  Theor.Chem.Acc.,1, 343“Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio potentials for he prevision of solvent effects”.

Over 200 citations

Solvent effects

  • Colominas et al., (1996), J.Am.Chem.Soc., 118, 6811. “Tautomeris and protonation of guanine and cytosine. Implication in the formation of hydrogen-bonded complexes”.

Molecular interactions

  • Cubero et al. (1998). Proc. Natl. Acad. Sci. USA., 95, 5976. “Is polarization important in catión-PI interactions?.
  • Cubero et al., (1999), J.Phys.Chem.A., 103, 6394. “Hydrogen bond versus anti-hydrogen bond: A comparative analysis based on the electron topology”.

Molecular Modeling/Drug Design

  • Cozzini et al., (2008), J.Med. Chem., 51, 6237.“Target flexibility: an emerging consideration in drug discovery and design”.

 Over 100 citations

Molecular interactions

  • Sponer et al., (2006),  Chem.Eur.J.,12, 2853 “Nature of base stacking: reference chemical stacking energies in ten unique B-DNA base pair steps”.
  • Hobza et al. (2000), J.Phys.Chen. B., 104, 6286. “CH·O contacts in the adenine·uracil Watson-Crick and uracil·uracil nucleic acids base pairs: nonempirical ab initio study with inclusion of electron correlation effects”.
  • Orozco & Luque (1990). J.Comput.Chem., 11, 909. “On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges”
  • Luisi et al. (1998) J.Mol.Biol., 279, 1123. "On the potential role of the amino nitrogen atom as hydrogen bond acceptor in macromolecules"
  • Xie et al. (2009) J.Chem.Theor.Comput.,5. 459. “X-Pol potential: an electronic structure-based force-field for molecular dynamics simulation of a solvated protein in water”
  • Gao et al (1993) J.Chem.Pys., 98, 2975. “Induced dipole momento and atomic charges base don average electrostatic potentials in aqueous solution”.

Molecular Modeling/Drug Design

  • Camps et al., (2000), J.Med.Chem., 43, 4657. “New Tacrine-Huperzine A hybrids (huprines): highly potent tight-binding acetylcholinesterase inhibitors of interest for the treatment of Alzheimer’s disease”.
  • Camps,P et al. (1999). J.Med.Chem., 42, 3227. “Synthesis, in vitro pharmacology and molecular modeling of very potent tacrine-huperzine A hybrids as acetylcholinesterase inhibtiors of potential interes for the treatment of Alzheimer’s disease”.
  • Amat et al. (2000). J.Org.Chem., 65, 3074. “Synthesis of enantiopure trans-3, 4-disubstituted piperidines. An enantiodivergent synthesis of (+)-and (-)-paroxetine”.
  • Muñoz-Ruiz et al. (2005). J.Med.Chem., 48, 7223. “Design, synthesis and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Anzheimer’s disease”.
  • Alonso et al. (2005) Bioorg. Med.Chem.13, 6588. “Donepezil-tacrine hybrid related derivatives as new dual binding site inhibitors of AchE”. 

Genomics/Bioinformatics

  • Ferrer-Costa et al. (2002) J.Mol.Biol., 315, 771. “Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties”.
  • Ferrer-Costa et al. (2004). Proteins, 57, 811. “Sequence-based prediction of pathological mutations”.
  • Kullis, et al. (2012) Nature Genetics, 44, 1236. “Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leulemia”.
  • Goñi et al. (2004) Nucleic Acids Res., 32, 354. “Triplex forming oligonucleotide target sequences in the human genome”.
  • Busquets et al (2000) Genetics in Medicine,7, 315. “Glutaryl-CoA deshydrogenase deficiency in Spain: evidence of two groups of patients, genetically and biochemically distinct”. 

Protein dynamics

  • Tirado-Rives et al. (1997). Biochemistry, 36, 7313. “Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea”.
  • Rueda et al. (2007). Proc.Natl.Acad.Sci.USA, 104, 796. “A consensus view of protein dynamics”.
  • Estévez et al.,(2004)  J.Physiol., 557, 363. “Functional and structural conservation of CBS domains from CLC chloride channels”.
  • Rueda et al. (2007) Structure, 15, 565. “Thorough validation of protein normal mode analysis: a comparative study with essential dynamics”.
  • Dvir,H. et al. (2002). Biochemistry41, 2970. “3D structure of torpedo californica acetylcholinesterase complexes with huprine X at 2.1 A resolution: kinetic and molecular dynamics correlate”

Solvent effects

  • Luque et al. (1996), J.Comput.Chem., 17, 806 “Extension of MST/SCRF method to organic solvents: ab inition and semiempirical parametrization for neutral solutes in CCl4”.
  • Curutchet et al. (2001). J.Comput.Chem., 22, 1180 “Solvation in octanol: parametrization of the continuum MST model”.
  • Carlson et al., (1993). J.Comput.Chem., 14, 1240. “Accuracy of free energies of hydration for organic molecules from 6-31G* derived charges”.
  • Bachs et al., (1994). J.Comput.Chem., 15, 446. “Optimization of solute cavities and van der Waals parameters in ab initio MST-SCRG calculations of neutral solutes”.
  • Trygubenko et al., (2002). Phys.Chem.Chem.Phys., 4, 4192. “Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Part 1. Cytosine”.
  • Luque et al., (1996). J.Phys.Chem., 100, 4269. “Solvent effects in chloroform solution: parametrization of the MST/SCRF continuum model”.
  • FJ Luque et al., (1993). J.Phys.Chem. 97 (37), 9380-9384. "SCRF calculation of the effect of water on the topology of the molecular electrostatic potential".
  • Orozco et al., (1995). J.Comput.Chem, 16 (5), 563-575. "Development of optimized MST/SCRF methods for semiempirical calculations: the MNDO and PM3 Hamiltonians"
  • Klamtz et al. (2009). Acc. Chem. Res.,42, 489 “On the performance of continuum solvation methods. A comment on ‘Universal approaches to solvation modeling`”.

Nucleic acids simulation

  • Shields et al., (1997). J.Am.Chem.Soc., 119, 7463. “Molecular dynamics simulation of the d(T·A·T) triple helix”.
  • Orozco et al., (2003). Chem.Soc.Rev., 32, 350. “Theoretical Methods for the simulation of nucleic acids”.
  • Harris et al., (2001). J.Am.Chem.Soc., 123, 12658. “Cooperativity in drug-DNA recognition: a molecular dynamics study”.
  • Pérez et al. (2007). J.Am.Chem.Soc., 129, 14739. “Dynamics of B-DNA on the microsecond time scale”.
  • Lavery et al., (2010). Nucleic Acids Res., 38, 299 “A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA”.
  • Banás et al. (2010). J. Chem. Theor. Comput. 6, 3836. "Performance of molecular mechanics force-fields for RNA simulations: Stability of UUCG and GNRA hairpins".
  • Pérez et al. (2008). Nucleic Acids Res, 36, 2379. "Towards a molecular dynamics consensus view of B-DNA"
  • Pérez et al. (2011). Accounts of chemical research 45 (2), 196-205. "Frontiers in molecular dynamics simulations of DNA"
  • EC Sherer et al. (1999). J.Am.Chem.Soc. 121 (25), 5981-5991. "Molecular dynamics studies of DNA A-tract structure and flexibility"
  • Rueda et al. (2003). J.Am.Chem.Soc. 125 (26), 8007-8014. "The structure and dynamics of DNA in the gas phase"
  • Sherer et al. (1999). J.Am.Chem.Soc.121 (26), 5981. "Molecular dynamics studies of DNA A-track structure and flexibility"
  • Banás et al. (2010). J. Chem. Theor. Comput. 6, 3836. "Performance of molecular mechanics force-fields for RNA simulations: Stability of UUCG and GNRA hairpins".
  • Pérez et al. (2008). Nucleic Acids Res, 36, 2379. "Towards a molecular dynamics consensus view of B-DNA"
  • Pérez et al. (2011). Accounts of chemical research 45 (2), 196-205. "Frontiers in molecular dynamics simulations of DNA"
  • EC Sherer et al. (1999). J.Am.Chem.Soc. 121 (25), 5981-5991. "Molecular dynamics studies of DNA A-tract structure and flexibility"
  • Rueda et al. (2003). J.Am.Chem.Soc. 125 (26), 8007-8014. "The structure and dynamics of DNA in the gas phase"