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Evaluation of secondary structure of proteins from uv circular dichroism spectra using an unsupervised learning neural network

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A resolution of the chemotactic wave paradox

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Spatial dynamics of a model for prebiotic evolution

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Preface

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Compartimentation in replicator models

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Tubulin secondary structure analysis, limited proteolysis sites, and homology to FtsZ

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A prediction of DDP IV/CD26 domain structure from a physico-chemical investigation of dipeptidyl peptidase IV (CD26) from human seminal plasma

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Changes in microtubule protofilament number induced by taxol binding to an easily accessible site: Internal microtubule dynamics

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Using Situs for the registration of protein structures with low-resolution bead models from x-ray solution scattering

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Modeling tricks and fitting techniques for multiresolution structures

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Multi-resolution contour-based fitting of macromolecular structures

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Conformational flexibility of bacterial RNA polymerase

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Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs

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Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase

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Mega-Dalton biomolecular motion captured from electron microscopy reconstructions

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Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom

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Topology representing neural networks reconcile biomolecular shape, structure, and dynamics

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Predictions of protein flexibility: First-order measures

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Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics

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Insights into Molecular Plasticity of Choline Binding Proteins (Pneumococcal Surface Proteins) by SAXS

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Grid multi-resolution docking

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Divergent Substrate-Binding Mechanisms Reveal an Evolutionary Specialization of Eukaryotic Prefoldin Compared to Its Archaeal Counterpart

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DFprot: A webtool for predicting local chain deformability

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ADP_EM: Fast exhaustive multi-resolution docking for high-throughput coverage

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Architecture of the Pontin/Reptin Complex, Essential in the Assembly of Several Macromolecular Complexes

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Protein shape and assembly studied with X-ray solution scattering: Fundaments and practice

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Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains

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FRODOCK: A new approach for fast rotational protein-protein docking

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In memoriam. Angel Ramírez Ortiz (1966-2008).

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End-to-end cache system for grid computing: Design and efficiency analysis of a high-throughput bioinformatic docking application

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Approaching elastic network models to molecular dynamics flexibility

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iMod: Multipurpose normal mode analysis in internal coordinates

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Targeting the assembly of bacterial cell division protein FtsZ with small molecules

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Spinor product computations for protein conformations

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Normal mode analysis of molecular motions in curvilinear coordinates on a non-Eckart body-frame: An application to protein torsion dynamics

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Modeling Macromolecular Flexibility with Normal Mode Analysis in Internal Coordinates

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Curvilinear dynamics of protein complexes

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Synthetic inhibitors of bacterial cell division targeting the GTP-binding site of FtsZ

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Random coordinate descent with spinor-matrices and geometric filters for efficient loop closure

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IMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates

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Formation of an intricate helical bundle dictates the assembly of the 26S proteasome Lid

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Exploring large macromolecular functional motions on clusters of multicore processors

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Exploring Macromolecular Machine Motions

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Understanding nucleotide-regulated FtsZ filament dynamics and the monomer assembly switch with large-scale atomistic simulations

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Structural basis for selective recognition of endogenous and microbial polysaccharides by macrophage receptor SIGN-R1

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Normal mode analysis in structural biology

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Imods: Fast Exploration of Macromolecular Collective Motions

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IMODS: Internal coordinates normal mode analysis server

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FRODRUG: A virtual screening GPU accelerated approach for drug discovery

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DrugScore^PPI knowledge-based potentials used as scoring and objective function in protein-protein docking

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Structural modeling from electron microscopy data

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Molecular Dynamics and Assembly Switch of FtsZ Filaments

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Integrative Modeling Approaches to Interpret High-Resolution cryo-EM Reconstructions

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Effective GTP-replacing FtsZ inhibitors and antibacterial mechanism of action

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Structure of promoter-bound TFIID and model of human pre-initiation complex assembly

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RCD plus : Fast loop modeling server

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New generation of elastic network models

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Near-atomic cryo-EM structure of PRC1 bound to the microtubule

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FRODOCK 2.0: fast protein-protein docking server.

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A fast band-Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors

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The structural assembly switch of cell division protein FtsZ probed with fluorescent allosteric inhibitors

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The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion

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KORP: Knowledge-based 6D potential for fast protein and loop modeling

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The Structure of Human Tyrosine Hydroxylase Reveals the Mechanism for Feedback Inhibition by Dopamine

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Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures

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Atomic-level evolutionary information improves protein-protein interface scoring

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Current approaches to flexible loop modeling

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KORP-PL: a coarse-grained knowledge-based scoring function for protein–ligand interactions

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InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps

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PIFOLD: TOWARD EFFECTIVE AND EFFICIENT PROTEIN INVERSE FOLDING

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Structural mechanism for tyrosine hydroxylase inhibition by dopamine and reactivation by Ser40 phosphorylation

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Learning rotations

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Local Normal Mode Analysis for Fast Loop Conformational Sampling

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Using a Graph Transformer Network to Predict 3D Coordinates of Proteins via Geometric Algebra Modelling

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Predicting protein stability changes upon mutation using a simple orientational potential

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Geometric Algebra Models of Proteins for Three-Dimensional Structure Prediction: A Detailed Analysis

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Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage ϕ29

researcher

Test Page17

research group

AgriFood Systems Integrative Biology Lab

AgriFood Systems Integrative Biology Lab Research Topics:Amplicon Sequencing, Analysis packages (R, Python, PERL, etc.), Annotation...

researcher

Maria Salud Garcia

research line

Transcriptomics

research line

Metabolomics

research line

Antiviral therapies

research line

Neuroinflammation

research line

Virology

research group

Advanced Computing

research line

Outreach for bioinformatics reserach

We develop actions and materials to bring the bioinformatics discipline to children, schools, and the...

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The 5' end generated in the in vitro self-cleavage reaction of avocado sunblotch viroid RNAs is present in naturally occurring linear viroid molecules

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Replication of avocado sunblotch viroid: Evidence for a symmetric pathway with two rolling circles and hammerhead ribozyme processing

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In vitro characterization of a cassette to accumulate multiple proteins through synthesis of a self-processing polypeptide

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Inhibition of a plant virus infection by analogs of melittin

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The complete nucleotide sequence of yam mosaic virus (Ivory Coast isolate) genomic RNA

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Studies on the diagnosis of hop stunt viroid in fruit trees: Identification of new hosts and application of a nucleic acid extraction procedure based on non-organic solvents

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Transgenic accumulation of two plant virus coat proteins on a single self processing polypeptide

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Hop stunt viroid (HSVd) sequence variants from Prunes species: Evidence for recombination between HSVd isolates

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Studies on the incidence of hop stunt viroid in apricot trees (Prunus armeniaca) by using an easy and short extraction method to analyze a large number of samples

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Simultaneous accumulation of multiple viral coat proteins from a TEV-NIa based expression vector

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Carmovirus isolation and RNA extraction.

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Molecular characterization of an almond isolate of hop stunt viroid (HSVd) and conditions for eliminating spurious hybridization in its diagnosis in almond samples

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Characterization and in vitro translation analysis of pelargonium flower break virus