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D. Ripoll · SciRah

Researcher profile · Semantic Scholar

D. Ripoll

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D. Ripoll — researcher profile on SciRah

h-index: 39
Works: 125
Citations: 5,373

Most-cited papers

Transposase-Derived Transcription Factors Regulate Light Signaling in Arabidopsis
Rongcheng Lin, L. Ding, C. Casola, D. Ripoll +2 more
2007Science484 citations Open access
Semantic Scholar
Clp Protease Complexes from Photosynthetic and Non-photosynthetic Plastids and Mitochondria of Plants, Their Predicted Three-dimensional Structures, and Functional Implications*
Jean-Benoît Peltier, D. Ripoll, G. Friso, Andrea Rudella +5 more
2004Journal of Biological Chemistry222 citations Open access
Semantic Scholar
Protein structure prediction by global optimization of a potential energy function.
A. Liwo, Jooyoung Lee, D. Ripoll, J. Pillardy +1 more
1999Proceedings of the National Academy of Sciences of the United States of America194 citations Open access
Semantic Scholar
Calculated electrostatic gradients in recombinant human H‐chain ferritin
T. Douglas, D. Ripoll
1998Protein Science154 citations Open access
Semantic Scholar
Recent improvements in prediction of protein structure by global optimization of a potential energy function
J. Pillardy, C. Czaplewski, A. Liwo, Jooyoung Lee +9 more
2001Proceedings of the National Academy of Sciences of the United States of America146 citations Open access
Semantic Scholar
Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.
S. Ołdziej, C. Czaplewski, A. Liwo, M. Chinchio +14 more
2005Proceedings of the National Academy of Sciences of the United States of America145 citations Open access
Semantic Scholar
Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides.
J. Vila, D. Ripoll, H. Scheraga
2000Proceedings of the National Academy of Sciences of the United States of America141 citations Open access
Semantic Scholar
Comparative structural modeling and inference of conserved protein classes in Drosophila seminal fluid.
J. Mueller, D. Ripoll, C. Aquadro, M. Wolfner
2004Proceedings of the National Academy of Sciences of the United States of America139 citations Open access
Semantic Scholar
Functional Dissection of Naturally Occurring Amino Acid Substitutions in eIF4E That Confers Recessive Potyvirus Resistance in Plants[W][OA]
I. Yeam, J. Cavatorta, D. Ripoll, B. Kang +1 more
2007The Plant Cell Online126 citations Open access
Semantic Scholar
Arabidopsis thaliana deficient in two chloroplast ascorbate peroxidases shows accelerated light-induced necrosis when levels of cellular ascorbate are low
L. Giacomelli, A. Masi, D. Ripoll, Mi-Ja Lee +1 more
2007Plant Molecular Biology125 citations
Semantic Scholar
Structural modules for receptor dimerization in the S-locus receptor kinase extracellular domain
S. Naithani, T. Chookajorn, D. Ripoll, J. Nasrallah
2007Proceedings of the National Academy of Sciences of the United States of America115 citations Open access
Semantic Scholar
Tracing the Origin of the Fungal α1 Domain Places Its Ancestor in the HMG-Box Superfamily: Implication for Fungal Mating-Type Evolution
T. Martin, Shun-Wen Lu, H. van Tilbeurgh, D. Ripoll +3 more
2010PLoS ONE93 citations Open access
Semantic Scholar
Module evolution and substrate specificity of fungal nonribosomal peptide synthetases involved in siderophore biosynthesis
Kathryn E. Bushley, D. Ripoll, B. Turgeon
2008BMC Evolutionary Biology93 citations Open access
Semantic Scholar
Structure of the glucanase inhibitor protein (GIP) family from phytophthora species suggests coevolution with plant endo-beta-1,3-glucanases.
C. Damasceno, J. Bishop, D. Ripoll, Joe Win +2 more
2008Molecular Plant-Microbe Interactions91 citations
Semantic Scholar
A Tomato Endo-β-1,4-glucanase, SlCel9C1, Represents a Distinct Subclass with a New Family of Carbohydrate Binding Modules (CBM49)*
B. Urbanowicz, Carmen Catalá, D. Irwin, D. Wilson +2 more
2007Journal of Biological Chemistry87 citations Open access
Semantic Scholar
Recombination and positive selection contribute to evolution of Listeria monocytogenes inlA.
R. Orsi, D. Ripoll, M. Yeung, K. Nightingale +1 more
2007Microbiology82 citations Open access
Semantic Scholar
Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures
J. Vila, D. Ripoll, H. Scheraga
2003Proceedings of the National Academy of Sciences of the United States of America81 citations Open access
Semantic Scholar
A Surface Loop of the Potato Leafroll Virus Coat Protein Is Involved in Virion Assembly, Systemic Movement, and Aphid Transmission
Lawrence Lee, I. Kaplan, D. Ripoll, Delin Liang +2 more
2005Journal of Virology79 citations Open access
Semantic Scholar
Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides.
D. Ripoll, Y. Vorobjev, A. Liwo, J. Vila +1 more
1996Journal of Molecular Biology77 citations Open access
Semantic Scholar
Calculation of protein conformation by global optimization of a potential energy function
Jooyoung Lee, A. Liwo, D. Ripoll, J. Pillardy +1 more
1999Proteins: Structure, Function, and Bioinformatics76 citations
Semantic Scholar
Molecular simulation study of cooperativity in hydrophobic association
C. Czaplewski, S. Rodziewicz-Motowidło, A. Liwo, D. Ripoll +2 more
2000Protein Science72 citations Open access
Semantic Scholar
Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH.
D. Ripoll, J. Vila, H. Scheraga
2004Journal of Molecular Biology69 citations
Semantic Scholar
Polyproline II helix conformation in a proline-rich environment: a theoretical study.
J. Vila, H. Baldoni, D. Ripoll, Avijit Ghosh +1 more
2004Biophysical Journal58 citations Open access
Semantic Scholar
Selection on Glycine beta-1,3-endoglucanase genes differentially inhibited by a Phytophthora glucanase inhibitor protein.
J. Bishop, D. Ripoll, S. Bashir, C. Damasceno +2 more
2005Genetics55 citations
Semantic Scholar
Site‐directed mutants designed to test back‐door hypotheses of acetylcholinesterase function
C. Faerman, D. Ripoll, S. Bon, Y. Le Feuvre +4 more
1996FEBS Letters55 citations Open access
Semantic Scholar
Charge is the major discriminating factor for glutathione reductase versus trypanothione reductase inhibitors.
Carlos H. Faerman, S. Savvides, C. Strickland, M. Breidenbach +5 more
1996Bioorganic & Medicinal Chemistry55 citations Open access
Semantic Scholar
Point mutations in the potato leafroll virus major capsid protein alter virion stability and aphid transmission.
I. Kaplan, Lawrence Lee, D. Ripoll, P. Palukaitis +2 more
2007Journal of General Virology51 citations Open access
Semantic Scholar
Helix-coil transitions re-visited.
H. Scheraga, J. Vila, D. Ripoll
2002Biophysical Chemistry51 citations Open access
Semantic Scholar
New developments of the electrostatically driven Monte Carlo method: test on the membrane-bound portion of melittin.
D. Ripoll, A. Liwo, H. Scheraga
1998Biopolymers49 citations
Semantic Scholar
Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing
Jooyoung Lee, D. Ripoll, C. Czaplewski, J. Pillardy +2 more
200148 citations Open access
Semantic Scholar
Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals
Jooyoung Lee, J. Pillardy, C. Czaplewski, Y. Arnautova +5 more
200044 citations Open access
Semantic Scholar
A molecular switch for biochemical logic gates: conformational studies.
G. Ashkenazi, D. Ripoll, N. Lotan, H. Scheraga
1997Biosensors & bioelectronics42 citations Open access
Semantic Scholar
Role of copper,zinc-superoxide dismutase in catalyzing nitrotyrosine formation in murine liver.
Jian-hong Zhu, Xiao-Mei Zhang, C. Roneker, J. Mcclung +5 more
2008Free Radical Biology & Medicine41 citations Open access
Semantic Scholar
Packing helices in proteins by global optimization of a potential energy function
M. Nanias, M. Chinchio, J. Pillardy, D. Ripoll +1 more
2003Proceedings of the National Academy of Sciences of the United States of America39 citations Open access
Semantic Scholar
Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing alpha-helices.
J. Vila, D. Ripoll, M. Villegas, Y. Vorobjev +1 more
1998Biophysical Journal37 citations Open access
Semantic Scholar
Topology of Type II REases revisited; structural classes and the common conserved core
M. Niv, D. Ripoll, J. Vila, A. Liwo +4 more
2007Nucleic Acids Research35 citations Open access
Semantic Scholar
A Fusion-Inhibiting Peptide against Rift Valley Fever Virus Inhibits Multiple, Diverse Viruses
J. Koehler, Jeffrey M. Smith, D. Ripoll, K. Spik +8 more
2013PLoS Neglected Tropical Diseases32 citations Open access
Semantic Scholar
THE PROTEIN FOLDING PROBLEM: GLOBAL OPTIMIZATION OF FORCE FIELDS
H. Scheraga, A. Liwo, S. O. Ł. dziej, C. Czaplewski +9 more
200530 citations
Semantic Scholar
Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets
Jooyoung Lee, A. Liwo, D. Ripoll, J. Pillardy +3 more
200030 citations
Semantic Scholar
Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification
D. Ripoll, S. Chaudhury, A. Wallqvist
2021PLoS Comput. Biol.29 citations Open access
Semantic Scholar
Tegaserod mimics the neurostimulatory glycan polysialic acid and promotes nervous system repair
J. Bushman, B. Mishra, M. Ezra, S. Gul +7 more
2013Neuropharmacology29 citations Open access
Semantic Scholar
Dissimilarity in the reductive unfolding pathways of two ribonuclease homologues.
M. Narayan, Guo-Qiang Xu, D. Ripoll, H. Zhai +7 more
2004Journal of Molecular Biology29 citations
Semantic Scholar
Surmounting the Multiple-Minima Problem in Protein Folding
H. Scheraga, Jooyoung Lee, J. Pillardy, Yuan-Jie Ye +2 more
1999Journal of Global Optimization29 citations
Semantic Scholar
Use of 13Cα chemical shifts in protein structure determination
J. Vila, D. Ripoll, H. Scheraga
200728 citations Open access
Semantic Scholar
Nonyloxytryptamine mimics polysialic acid and modulates neuronal and glial functions in cell culture
G. Loers, Vedangana Saini, B. Mishra, Florentia Papastefanaki +7 more
2014Journal of Neurochemistry27 citations
Semantic Scholar
Tobacco etch virus infectivity in Capsicum spp. is determined by a maximum of three amino acids in the viral virulence determinant VPg.
Kari W Perez, I. Yeam, B. Kang, D. Ripoll +3 more
2012Molecular Plant-Microbe Interactions27 citations
Semantic Scholar
Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: A theoretical study
J. Vila, D. Ripoll, H. Baldoni, H. Scheraga
2002Journal of Biomolecular NMR27 citations Open access
Semantic Scholar
Can cooperativity in hydrophobic association be reproduced correctly by implicit solvation models
C. Czaplewski, D. Ripoll, A. Liwo, S. Rodziewicz-Motowidło +2 more
200227 citations
Semantic Scholar
On the orientation of the backbone dipoles in native folds.
D. Ripoll, J. Vila, H. Scheraga
2005Proceedings of the National Academy of Sciences of the United States of America26 citations Open access
Semantic Scholar
Human Inducible Hsp70: Structures, Dynamics, and Interdomain Communication from All-Atom Molecular Dynamics Simulations.
Adrien Nicolaï, P. Senet, P. Delarue, D. Ripoll
2010Journal of Chemical Theory and Computation25 citations
Semantic Scholar

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H. Scheraga×23
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