Search Results - "Valiente, Pedro A"

AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4 by Valdés-Tresanco, Mario S, Valdés-Tresanco, Mario E, Valiente, Pedro A, Moreno, Ernesto

“…AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4,…”
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HelixDiff, a Score-Based Diffusion Model for Generating All-Atom α‑Helical Structures by Xie, Xuezhi, Valiente, Pedro A, Kim, Jisun, Kim, Philip M

“…Here, we present HelixDiff, a score-based diffusion model for generating all-atom helical structures. We developed a hot spot-specific generation algorithm for…”
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Identification of Inhibitors of CD36-Amyloid Beta Binding as Potential Agents for Alzheimer’s Disease by Doens, Deborah, Valiente, Pedro A, Mfuh, Adelphe M, X. T. Vo, Anh, Tristan, Adilia, Carreño, Lizmar, Quijada, Mario, Nguyen, Vu T, Perry, George, Larionov, Oleg V, Lleonart, Ricardo, Fernández, Patricia L

“…Neuroinflammation is one of the hallmarks of Alzheimer’s disease pathology. Amyloid β has a central role in microglia activation and the subsequent secretion…”
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gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS by Valdés-Tresanco, Mario S, Valdés-Tresanco, Mario E, Valiente, Pedro A, Moreno, Ernesto

“…Molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area is one of the most popular methods to estimate binding free energies. This method has…”
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Tailored Parameterization of the LIE Method for Calculating the Binding Free Energy of Vps34–Inhibitor Complexes by Valdés-Tresanco, Mario S, Valdés-Tresanco, Mario E, Rubio-Carrasquilla, Marcela, Valiente, Pedro A, Moreno, Ernesto

“…Vps34 is the only isoform of the PI3K family in fungi, making this protein an attractive target to develop new treatments against pathogenic fungi. The high…”
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HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures by Xie, Xuezhi, Valiente, Pedro A, Kim, Philip M

“…Abstract Motivation Protein and peptide engineering has become an essential field in biomedicine with therapeutics, diagnostics and synthetic biology…”
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Computational Design of Potent and Selective d‑Peptide Agonists of the Glucagon-like Peptide‑2 Receptor by Valiente, Pedro A., Nim, Satra, Kim, Jisun, Kim, Philip M.

“…Here, we designed three d-GLP-2 agonists that activated the glucagon-like peptide-2 receptor (GLP-2R) cyclic adenosine monophosphate (cAMP) accumulation…”
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Unraveling a Conserved Conformation of the FG Loop upon the Binding of Natural Ligands to the Human and Murine PD1 by Ponce, Luis F, Leon, Kalet, Valiente, Pedro A

“…The activation of T cells is normally accompanied by inhibitory mechanisms within which the PD1 receptor stands out. PD1 drives T cells to an unresponsive…”
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Antibody-SGM, a Score-Based Generative Model for Antibody Heavy-Chain Design by Xie, Xuezhi, Valiente, Pedro A., Lee, Jin Sub, Kim, Jisun, Kim, Philip M.

“…Traditional computational methods for antibody design involved random mutagenesis followed by energy function assessment for candidate selection. Recently,…”
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Computational Design of Potent D‑Peptide Inhibitors of SARS-CoV‑2 by Valiente, Pedro A, Wen, Han, Nim, Satra, Lee, JinAh, Kim, Hyeon Ju, Kim, Jinhee, Perez-Riba, Albert, Paudel, Yagya Prasad, Hwang, Insu, Kim, Kyun-Do, Kim, Seungtaek, Kim, Philip M

“…Blocking the association between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain (RBD) and the human…”
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Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report by Perez-Riverol, Yasset, Hermjakob, Henning, Kohlbacher, Oliver, Martens, Lennart, Creasy, David, Cox, Jürgen, Leprevost, Felipe, Shan, Baozhen Paul, Pérez-Nueno, Violeta I., Blazejczyk, Michal, Punta, Marco, Vierlinger, Klemens, Valiente, Pedro A., Leon, Kalet, Chinea, Glay, Guirola, Osmany, Bringas, Ricardo, Cabrera, Gleysin, Guillen, Gerardo, Padron, Gabriel, Gonzalez, Luis Javier, Besada, Vladimir

“…The workshop “Bioinformatics for Biotechnology Applications (HavanaBioinfo 2012)”, held December 8–11, 2012 in Havana, aimed at exploring new bioinformatics…”
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Differential Effects of IL2Rα and IL15Rα over the Stability of the Common Beta-Gamma Signaling Subunits of the IL2 and IL15 Receptors by Ponce, Luis F, Montalvo, Galia, Leon, Kalet, Valiente, Pedro A

“…Interleukin (IL) 2 and IL15 are two members of the common gamma chain cytokine family, involved in the regulation of the T cell differentiation process. Both…”
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A Method to Calculate the Relative Binding Free Energy Differences of α‑Helical Stapled Peptides by Valiente, Pedro A, Becerra, David, Kim, Philip M

“…Hydrocarbon-stapled peptides are a class of bioactive α-helical ligands developed to target protein–protein interactions. Peptide stapling has benefited from…”
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Targeting the Receptor-Binding Motif of SARS-CoV‑2 with D‑Peptides Mimicking the ACE2 Binding Helix: Lessons for Inhibiting Omicron and Future Variants of Concern by Valiente, Pedro A., Nim, Satra, Lee, JinAh, Kim, Seungtaek, Kim, Philip M.

“…The COVID-19 pandemic continues to spread around the world, with several new variants emerging, particularly those of concern (VOCs). Omicron (B.1.1.529), a…”
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Assessment of Different Parameters on the Accuracy of Computational Alanine Scanning of Protein–Protein Complexes with the Molecular Mechanics/Generalized Born Surface Area Method by Valdés-Tresanco, Mario E., Valdés-Tresanco, Mario S., Moreno, Ernesto, Valiente, Pedro A.

“…Computational alanine scanning with the molecular mechanics generalized Born surface area (MM/GBSA) method constitutes a widely used approach for identifying…”
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Engineering a Rigid Nucleic Acid Structure to Improve the Limit of Detection for Genetic Assays by Malekjahani, Ayden, Lekuti, Ayokunle A., Valiente, Pedro A., Osborne, Matthew, Li, Vanessa Y. C., Kim, Philip M., Chan, Warren C. W.

“…Detecting nucleic acids at ultralow concentrations is critical for research and clinical applications. Particle-based assays are commonly used to detect…”
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Predicting a Stable Dimeric Form of the PD1-PDL1 Complex: Implications for Understanding the PD1 Activation Mechanism by Ponce, Luis F., Ramírez-Echemendia, Daniel P., León, Kalet, Valiente, Pedro A.

“…The activation of T cells is typically accompanied by inhibitory mechanisms within which the programmed cell death (PD1) receptor stands out. Upon binding the…”
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membranotropic activity of N-terminal peptides from the pore-forming proteins sticholysin I and II is modulated by hydrophobic and electrostatic interactions as well as lipid composition by Ros, Uris, Pedrera, Lohans, Díaz, Daylín, de Karam, Juan C, Sudbrack, Tatiane P, Valiente, Pedro A, Martínez, Diana, Cilli, Eduardo M, Pazos, Fabiola, Itri, Rosangela, Lanio, Maria E, Schreier, Shirley, Álvarez, Carlos

“…The sea anemone Stichodactyla helianthus produces two pore-forming proteins, sticholysins I and II (St I and St II). Despite their high identity (93%), these…”
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Exploring the conformational dynamics of PD1 in complex with different ligands: What we can learn for designing novel PD1 signaling blockers? by Ponce, Luis F., García‐Martínez, Karina, León, Kalet, Valiente, Pedro A.

“…Activation of T cells triggers the expression of regulatory molecules like the programmed cell death 1 (PD1) protein. The association of PD1 with the natural…”
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Improving the LIE Method for Binding Free Energy Calculations of Protein–Ligand Complexes by Miranda, Williams E, Noskov, Sergei Yu, Valiente, Pedro A

“…In this work, we introduced an improved linear interaction energy (LIE) method parameterization for computations of protein–ligand binding free energies. The…”
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