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2020 – today
- 2023
[j67]Aristarc Suriñach, Adam Hospital
, Yvonne Westermaier, Luis Jordà, Sergi Orozco-Ruiz, Daniel Beltrán, Francesco Colizzi, Pau Andrio, Robert Soliva, Martí Municoy, Josep Lluis Gelpí, Modesto Orozco:
High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations. J. Chem. Inf. Model. 63(1): 321-334 (2023)- [j66]Federica Battistini, Alba Sala, Adam Hospital, Modesto Orozco:
Sequence-Dependent Properties of the RNA Duplex. J. Chem. Inf. Model. 63(16): 5259-5271 (2023) - 2022
- [j65]Genis Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluis Gelpí:
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools. Bioinform. 38(12): 3302-3303 (2022) - [j64]Genis Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluis Gelpí:
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. Nucleic Acids Res. 50(W1): 99-107 (2022) - [j63]Benjamin Martin, Pablo D. Dans, Milosz Wieczór, Núria Villegas, Isabelle Brun-Heath, Federica Battistini, Montserrat Terrazas, Modesto Orozco:
Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation. PLoS Comput. Biol. 18(1) (2022) - 2021
- [j62]Federica Battistini, Pablo D. Dans, Montserrat Terrazas, Chiara L. Castellazzi, Guillem Portella, Mireia Labrador, Núria Villegas, Isabelle Brun-Heath, Carlos González, Modesto Orozco:
The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function. PLoS Comput. Biol. 17(11) (2021) - 2020
- [j61]Milosz Wieczór, Adam Hospital, Genis Bayarri, Jacek Czub, Modesto Orozco:
Molywood: streamlining the design and rendering of molecular movies. Bioinform. 36(17): 4660-4661 (2020)
2010 – 2019
- 2019
- [j60]Diego Gallego, Leonardo Darré, Pablo D. Dans, Modesto Orozco:
VeriNA3d: an R package for nucleic acids data mining. Bioinform. 35(24): 5334-5336 (2019) - 2017
- [j59]Martin Kotev, Pilar Manuel-Manresa, Elsa Hernando, Vanessa Soto-Cerrato, Modesto Orozco, Roberto Quesada, Ricardo Pérez-Tomás, Victor Guallar:
Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs. J. Chem. Inf. Model. 57(8): 2089-2098 (2017) - [j58]Víctor López-Ferrando, Andrea M. Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Lluis Gelpí:
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. Nucleic Acids Res. 45(Webserver-Issue): W222-W228 (2017) - 2016
- [j57]Ali Hosseini, Andreu Alibés, Marc Noguera-Julian, Víctor A. Gil, Roger Paredes, Robert Soliva, Modesto Orozco, Victor Guallar:
Computational Prediction of HIV-1 Resistance to Protease Inhibitors. J. Chem. Inf. Model. 56(5): 915-923 (2016) - [j56]Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codó, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Josep Ramón Goñi, Modesto Orozco, Josep Lluis Gelpí:
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. Nucleic Acids Res. 44(Database-Issue): 272-278 (2016) - [j55]Michela Candotti, Modesto Orozco:
The Differential Response of Proteins to Macromolecular Crowding. PLoS Comput. Biol. 12(7) (2016) - [j54]Ardita Shkurti, Josep Ramón Goñi, Pau Andrio, Elena Breitmoser, Iain Bethune, Modesto Orozco, Charles A. Laughton:
pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data. SoftwareX 5: 44-50 (2016) - 2015
- [j53]Carlos Fenollosa, Marcel Otón, Pau Andrio, Jorge Cortés, Modesto Orozco, Josep Ramón Goñi:
SEABED: Small molEcule activity scanner weB servicE baseD. Bioinform. 31(5): 773-775 (2015) - 2013
- [j52]Pedro Sfriso, Adam Hospital, Agustí Emperador, Modesto Orozco:
Exploration of conformational transition pathways from coarse-grained simulations. Bioinform. 29(16): 1980-1986 (2013) - [j51]Adam Hospital, Ignacio Faustino, Rosana Collepardo-Guevara, Carlos González, Josep Lluis Gelpí, Modesto Orozco:
NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res. 41(Webserver-Issue): 47-55 (2013) - [j50]Guillem Portella, Federica Battistini, Modesto Orozco:
Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations. PLoS Comput. Biol. 9(11) (2013) - [j49]Michela Candotti, Alberto Pérez, Carles Ferrer-Costa, Manuel Rueda, Tim Meyer, Josep Lluis Gelpí, Modesto Orozco:
Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale. PLoS Comput. Biol. 9(12) (2013) - 2012
- [j48]Adam Hospital, Pau Andrio, Carlos Fenollosa, Damjan Cicin-Sain, Modesto Orozco, Josep Lluis Gelpí:
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinform. 28(9): 1278-1279 (2012) - [j47]Rebeca García-Fandiño, Pau Bernadó, Sara Ayuso-Tejedor, Javier Sancho, Modesto Orozco:
Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case. PLoS Comput. Biol. 8(8) (2012) - 2011
- [j46]Oscar Flores, Modesto Orozco:
nucleR: a package for non-parametric nucleosome positioning. Bioinform. 27(15): 2149-2150 (2011) - [j45]Carles Pons, David Talavera, Xavier de la Cruz, Modesto Orozco, Juan Fernández-Recio:
Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking. J. Chem. Inf. Model. 51(2): 370-377 (2011) - [j44]Francesco Raimondi, Guillem Portella, Modesto Orozco, Francesca Fanelli:
Nucleotide Binding Switches the Information Flow in Ras GTPases. PLoS Comput. Biol. 7(3) (2011) - 2010
- [j43]Ignacio Soteras, Modesto Orozco, F. Javier Luque:
Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. J. Comput. Aided Mol. Des. 24(4): 281-291 (2010)
2000 – 2009
- 2009
- [j42]Jordi Camps, Oliver Carrillo, Agustí Emperador, Laura Orellana, Adam Hospital, Manuel Rueda, Damjan Cicin-Sain, Marco D'Abramo, Josep Lluis Gelpí, Modesto Orozco:
FlexServ: an integrated tool for the analysis of protein flexibility. Bioinform. 25(13): 1709-1710 (2009) - 2008
- [j41]Josep Ramón Goñi, Carlos Fenollosa, Alberto Pérez, David Torrents, Modesto Orozco:
DNAlive: a tool for the physical analysis of DNA at the genomic scale. Bioinform. 24(15): 1731-1732 (2008) - 2007
- [j40]David Talavera, Adam Hospital, Modesto Orozco, Xavier de la Cruz:
A procedure for identifying homologous alternative splicing events. BMC Bioinform. 8 (2007) - [j39]Flavio Forti, Xavier Barril, F. Javier Luque, Modesto Orozco:
Extension of the MST continuum solvation model to the RM1 semiempirical hamiltonian. J. Comput. Chem. 29(4): 578-587 (2007) - [j38]David Talavera, Christine Vogel, Modesto Orozco, Sarah A. Teichmann, Xavier de la Cruz:
The (In)dependence of Alternative Splicing and Gene Duplication. PLoS Comput. Biol. 3(3) (2007) - [j37]Manuel Rueda, Carles Ferrer-Costa, Tim Meyer, Alberto Pérez, Jordi Camps, Adam Hospital, Josep Lluis Gelpí, Modesto Orozco:
A consensus view of protein dynamics. Proc. Natl. Acad. Sci. USA 104(3): 796-801 (2007) - 2006
- [j36]Carles Curutchet, Modesto Orozco, F. Javier Luque, Benedetta Mennucci, Jacopo Tomasi:
Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model. J. Comput. Chem. 27(15): 1769-1780 (2006) - 2005
- [j35]Carles Ferrer-Costa, Josep Lluis Gelpí, Leire Zamakola, Ivan Parraga, Xavier de la Cruz, Modesto Orozco:
PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinform. 21(14): 3176-3178 (2005) - [j34]Jordi Muñoz-Muriedas, Samantha Perspicace, Nuria Bech, Salvatore Guccione, Modesto Orozco, F. Javier Luque:
Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient. J. Comput. Aided Mol. Des. 19(6): 401-419 (2005) - [j33]Lucía Conde, Juan M. Vaquerizas, Carles Ferrer-Costa, Xavier de la Cruz, Modesto Orozco, Joaquín Dopazo:
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res. 33(Web-Server-Issue): 501-505 (2005) - 2004
- [c5]Josep Ramón Goñi, Modesto Orozco:
Triplex-Forming Sequences in Regulatory Regions. Spanish Bioinformatics Conference 2004: 16-19 - [c4]David Talavera, Carles Ferrer-Costa, Modesto Orozco, Xavier de la Cruz:
Comparative Study of MAPK 9 Alternative Splicing from Human and Mouse. Spanish Bioinformatics Conference 2004: 114-117 - [c3]Carles Ferrer-Costa, Modesto Orozco, Xavier de la Cruz:
Annotation of Non-Human Pathological Mutations utilising Human-Parameterised Neural Networks. Spanish Bioinformatics Conference 2004: 128-131 - [c2]Antoni Valencia, Martín Pérez, Adam Hospital, Joan Carles Fernández, Elena Manresa, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco:
Comparison of Active Centers of Proteins: The Kinesin Family as a Test Case. Spanish Bioinformatics Conference 2004: 205 - [c1]Antonio Morreale, Xavier de la Cruz, Tim Meyer, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco:
Hydration Free Energy in Macromolecules. Spanish Bioinformatics Conference 2004: 206-207 - 2003
- [j32]Carles Curutchet, Albert Salichs, Xavier Barril, Modesto Orozco, Francisco Javier Luque:
Transferability of fragmental contributions to the octanol/water partition coefficient: An NDDO-based MST study. J. Comput. Chem. 24(1): 32-45 (2003) - [j31]Carles Curutchet, Christopher J. Cramer, Donald G. Truhlar, Manuel F. Ruiz-López, Daniel Rinaldi, Modesto Orozco, F. Javier Luque:
Electrostatic component of solvation: Comparison of SCRF continuum models. J. Comput. Chem. 24(3): 284-297 (2003) - [j30]Carles Curutchet, Josep Maria Bofill, Begoña Hernández, Modesto Orozco, F. Javier Luque:
Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations. J. Comput. Chem. 24(10): 1263-1275 (2003) - [j29]Antonio Morreale, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco:
Continuum and discrete calculation of fractional contributions to solvation free energy. J. Comput. Chem. 24(13): 1610-1623 (2003) - 2002
- [j28]Xavier Fradera, Xavier de la Cruz, Carlos H. Tomich P. Silva, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco:
Ligand-induced changes in the binding sites of proteins. Bioinform. 18(7): 939-948 (2002) - [j27]Albert Salichs, M. López, V. Segarra, Modesto Orozco, F. Javier Luque:
Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study. J. Comput. Aided Mol. Des. 16(8-9): 569-583 (2002) - [j26]Jordi Muñoz, Xavier Barril, Begoña Hernández, Modesto Orozco, F. Javier Luque:
Hydrophobic similarity between molecules: A MST-based hydrophobic similarity index. J. Comput. Chem. 23(5): 554-563 (2002) - 2001
- [j25]Carles Curutchet, Modesto Orozco, F. Javier Luque:
Solvation in octanol: parametrization of the continuum MST model. J. Comput. Chem. 22(11): 1180-1193 (2001) - 2000
- [j24]Begoña Hernández, F. Javier Luque, Modesto Orozco:
Mixed QM/MM molecular electrostatic potentials. J. Comput. Aided Mol. Des. 14(4): 329-339 (2000)
1990 – 1999
- 1999
- [j23]F. Javier Luque, Xavier Barril, Modesto Orozco:
Fractional description of free energies of solvation. J. Comput. Aided Mol. Des. 13(2): 139-152 (1999) - [j22]Carles Colominas, F. Javier Luque, Modesto Orozco:
Monte Carlo-MST: New strategy for representation of solvent configurational space in solution. J. Comput. Chem. 20(7): 665-678 (1999) - [j21]Begoña Hernández, F. Javier Luque, Modesto Orozco:
Parametrization of the GMIPp for the study of stacking interactions. J. Comput. Chem. 20(9): 937-946 (1999) - 1998
- [j20]F. Javier Luque, Modesto Orozco:
Polarization effects in generalized molecular interaction potential: New Hamiltonian for reactivity studies and mixed QM/MM calculations. J. Comput. Chem. 19(8): 866-881 (1998) - 1997
- [j19]Begoña Hernández, Modesto Orozco, F. Javier Luque:
Role of the tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase. J. Comput. Aided Mol. Des. 11(2): 153-162 (1997) - [j18]Robert Soliva, Modesto Orozco, F. Javier Luque:
Suitability of density functional methods for calculation of electrostatic properties. J. Comput. Chem. 18(8): 980-991 (1997) - 1996
- [j17]Begoña Hernández, Modesto Orozco, F. Javier Luque:
Tautomerism of xanthine and alloxanthine: A model for substrate recognition by xanthine oxidase. J. Comput. Aided Mol. Des. 10(6): 535-544 (1996) - [j16]F. Javier Luque, Margarida Bachs, Carlos Alemán, Modesto Orozco:
Extension of MST/SCRF method to organic solvents: Ab initio and semiempirical parametrization for neutral solutes in CCl4. J. Comput. Chem. 17(7): 806-820 (1996) - 1995
- [j15]Modesto Orozco, Margarida Bachs, F. Javier Luque:
Development of Optimized MST/SCRF Methods for Semiempirical Calculations: The MNDO and PM3 Hamilitonians. J. Comput. Chem. 16(5): 563-575 (1995) - 1994
- [j14]Cristóbal Alhambra, Francisco Javier Luque, Modesto Orozco:
Comparison of NDDO and Quasi-Ab Initio Approaches to Compute Semiempirical Molecular Electrostatic Potentials. J. Comput. Chem. 15(1): 12-22 (1994) - [j13]Margarida Bachs, F. Javier Luque, Modesto Orozco:
Optimization of Solute Cavities and van der Waals Parameters in Ab Initio MST-SCRF Calculations of Neutral Molecules. J. Comput. Chem. 15(4): 446-454 (1994) - [j12]F. Javier Luque, Margarida Bachs, Modesto Orozco:
An Optimized AM1/MST Method for the MST-SCRF Representation of Solvated Systems. J. Comput. Chem. 15(8): 847-857 (1994) - 1993
- [j11]Carlos Alemán, F. Javier Luque, Modesto Orozco:
A new scaling procedure to correct semiempirical MEP and MEP-derived properties. J. Comput. Aided Mol. Des. 7(6): 721-742 (1993) - [j10]Modesto Orozco, F. Javier Luque:
Molecular interaction potential: A new tool for the theoretical study of molecular reactivity. J. Comput. Chem. 14(5): 587-602 (1993) - [j9]Carlos Alemán, F. Javier Luque, Modesto Orozco:
Suitability of the PM3-derived molecular electrostatic potentials. J. Comput. Chem. 14(7): 799-808 (1993) - [j8]Modesto Orozco, F. Javier Luque:
Ab initio study of bond stretching: Implications in force-field parametrization for molecular mechanics and dynamics. J. Comput. Chem. 14(8): 881-894 (1993) - [j7]Heather A. Carlson, Toan B. Nguyen, Modesto Orozco, William L. Jorgensen:
Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges. J. Comput. Chem. 14(10): 1240-1249 (1993) - [j6]Modesto Orozco, William L. Jorgensen, F. Javier Luque:
Comparison of 6-31G*-based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules. J. Comput. Chem. 14(12): 1498-1503 (1993) - 1992
- [j5]Carlos Alemán, Modesto Orozco:
On the suitability of semiempirical calculations as sources of force field parameters. J. Comput. Aided Mol. Des. 6(4): 331-348 (1992) - 1990
- [j4]Modesto Orozco, F. Javier Luque:
A practical procedure for the determination of electrostatic charges of large molecules. J. Comput. Aided Mol. Des. 4(4): 411-426 (1990)
1980 – 1989
- 1989
- [j3]Modesto Orozco, Rafael Franco:
TEFOOL/2: a program for theoretical drug design on microcomputers. Comput. Appl. Biosci. 5(3): 219-226 (1989) - [j2]Modesto Orozco, F. Javier Luque:
POEAMS: program for outliers elimination in 'anomalous' multidimensional space. Comput. Appl. Biosci. 5(3): 241-242 (1989) - 1988
- [j1]Modesto Orozco, F. Javier Luque:
POEMS: program for outliers elimination in multidimensional space. Comput. Appl. Biosci. 4(3): 381-385 (1988)
Coauthor Index
F. Javier Luque
aka: Francisco Javier Luque
aka: Francisco Javier Luque
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