A5039498203- Protein Structure and Dynamics
- Enzyme Structure and Function
- Advanced Electron Microscopy Techniques and Applications
- RNA and protein synthesis mechanisms
- Computational Drug Discovery Methods
- Electron and X-Ray Spectroscopy Techniques
- Genomics and Phylogenetic Studies
- Simulation Techniques and Applications
- Advanced Database Systems and Queries
- Protein purification and stability
- Bioinformatics and Genomic Networks
- Polysaccharides and Plant Cell Walls
- Microbial Metabolic Engineering and Bioproduction
- Enzyme Production and Characterization
- Advanced Memory and Neural Computing
- Plant nutrient uptake and metabolism
- Neuroscience and Neural Engineering
- Machine Learning in Bioinformatics
- Advanced X-ray Imaging Techniques
- RNA Interference and Gene Delivery
- Mobile Crowdsensing and Crowdsourcing
- Data Stream Mining Techniques
- Cell Image Analysis Techniques
- Machine Learning in Materials Science
- Photoreceptor and optogenetics research
Instituto Tecnológico de Costa Rica
2020-2023
Purdue University West Lafayette
2009-2019
Hospital Madre Teresa
2015
National Hansen's Disease Program
2013
Retina Institute
2005
University of Southern California
2005
Johns Hopkins University
2005
Doheny Eye Institute
2005
We present the results for CAPRI Round 30, first joint CASP-CAPRI experiment, which brought together experts from protein structure prediction and protein-protein docking communities. The comprised 25 targets amongst those submitted CASP11 experiment of 2014. included mostly homodimers, a few homotetramers, two heterodimers, chains that could readily be modeled using templates Protein Data Bank. On average 24 groups 7 CASP predictions each target, 12 per target participated in scoring...
The tertiary structures of proteins have been solved in an increasing pace recent years. To capitalize the enormous efforts paid for accumulating structure data, efficient and effective computational methods need to be developed comparing, searching, investigating interactions protein structures. We introduce 3D Zernike descriptor (3DZD), emerging technique describe molecular surfaces. 3DZD is a series expansion mathematical three-dimensional function, thus represented compactly by vector...
Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state predictive methodology. Here we describe a community-wide assessment methods to predict effects mutations on protein-protein interactions. Twenty-two groups predicted comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful...
Abstract The tertiary structures of protein complexes provide a crucial insight about the molecular mechanisms that regulate their functions and assembly. However, solving complex by experimental methods is often more difficult than single structures. Here, we have developed novel computational multiple docking algorithm, Multi‐LZerD, builds models multimeric effectively reusing pairwise predictions component proteins. A genetic algorithm applied to explore conformational space followed...
Abstract Summary: We present 3D-SURFER, a web-based tool designed to facilitate high-throughput comparison and characterization of proteins based on their surface shape. As each protein is effectively represented by vector 3D Zernike descriptors, times for query against the entire PDB take, an average, only couple seconds. The web interface has been be as interactive possible with displays showing animated rotations, CATH codes structural alignments using CE program. In addition,...
Pectin methylesterases (PMEs) catalyze the demethylesterification of homogalacturonan domains pectin in plant cell walls and are regulated by endogenous methylesterase inhibitors (PMEIs). In Arabidopsis dark-grown hypocotyls, one PME (AtPME3) PMEI (AtPMEI7) were identified as potential interacting proteins. Using RT-quantitative PCR analysis gene promoter::GUS fusions, we first showed that AtPME3 AtPMEI7 genes had overlapping patterns expression etiolated hypocotyls. The two proteins...
A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The named EMLZerD generates pool candidate protein docking conformations component proteins, which are later compared with provided electron (EM) density to select the ones that fit well EM map. comparison and performed using 3D Zernike descriptor (3DZD), mathematical series expansion three-dimensional functions. 3DZD provides unified representation...
Crystallization of protein–protein complexes can often be problematic and therefore computational structural models are relied on. Such generated using docking algorithms, where one the main challenges is selecting which several thousand potential predictions represents most near-native complex. We have developed a novel technique that involves use steered molecular dynamics (sMD) umbrella sampling to identify among predictions. Using this technique, we found strong correlation between our...
Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number protein complex structures have been determined using experimental methods, relatively fewer studies performed to determine assembly order complexes. In addition insights into molecular mechanisms function provided by structure a complex, knowing is important for understanding process formation. Assembly also practically useful constructing subcomplexes as step toward solving...
The Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large biomolecular complex subcellular structures. Together with the Protein Data Bank (PDB), EMDB becoming a fundamental resource of tertiary structures macromolecules. To take full advantage this indispensable resource, ability to search database similarity essential. However, unlike...
ABSTRACT We report the performance of protein–protein docking predictions by our group for recent rounds Critical Assessment Prediction Interactions (CAPRI), a community‐wide assessment state‐of‐the‐art methods. Our prediction procedure uses program named LZerD developed in group. represents protein surface with 3D Zernike descriptors (3DZD), which are based on mathematical series expansion function. The appropriate soft representation 3DZD makes method more tolerant to conformational change...
A prototype electronic retinal prosthesis has been tested in three subjects. The system features an implanted stimulator and external for image acquisition, processing, telemetry. subjects general performed better than chance on psychophysical tests involving object detection, counting, discrimination, direction of movement.
Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of protein is an task bioinformatics. In the development docking methods, it to establish metric for evaluating results reasonable and practical fashion. However, since there are only few works done developing methods docking, no study that investigates how accurate structural models should be allow scientists gain biological insights. We generated series predicted (decoys)...
An increasing number of protein complex structures are determined by cryo-electron microscopy (cryo-EM). When individual have been and available, an important task in structure modeling is to fit the into density map. Here, we designed a method that fits atomic proteins cryo-EM maps medium low resolutions using Markov random fields, which allows probabilistic evaluation fitted models. The accuracy our method, MarkovFit, performed better than existing methods on datasets 31 simulated...
Macromolecular protein complexes play important roles in a cell and their tertiary structure can help understand key biological processes of functions. Multiple docking is valuable computational tool for providing information multimeric complexes. In previous study we developed implemented an algorithm this purpose, named Multi-LZerD. This method represents conformation complex as graph, where nodes denote subunits each edge connecting denotes pairwise the two subunits. Multi-LZerD employs...
A completely implantable, light-sensitive retinal prosthesis must include the capability for both phototransduction and stimulus current generation, two power intensive functions. These devices will be implanted in eye, creating a significant source of heat that dissipated by ocular tissue without damaging retina. However, technological hurdles remain. The amount can safely eye surrounding head harming retina, depends significantly on position heater. Technology for, high-density electrode...
Electron Microscopy Maps are key in the study of bio-molecular structures, ranging from borderline atomic level to sub-cellular range. These maps describe envelopes that cover possibly a very large number proteins form molecular machines within cell. Within those envelopes, we interested find what regions correspond specific so can understand how they function, and design drugs enhance or suppress process involved in, along with other experimental purposes. A classic approach by which begin...