A5071963248- Protein Structure and Dynamics
- COVID-19 epidemiological studies
- Computational Drug Discovery Methods
- Diet and metabolism studies
- Advanced NMR Techniques and Applications
- Markov Chains and Monte Carlo Methods
- Genomics and Phylogenetic Studies
- Photosynthetic Processes and Mechanisms
- RNA and protein synthesis mechanisms
- Receptor Mechanisms and Signaling
- Monoclonal and Polyclonal Antibodies Research
- Enzyme-mediated dye degradation
- Electrochemical sensors and biosensors
- FinTech, Crowdfunding, Digital Finance
- Dye analysis and toxicity
- demographic modeling and climate adaptation
- Protist diversity and phylogeny
- Enzyme Structure and Function
- Theoretical and Computational Physics
Universitat Politècnica de Catalunya
2015-2021
Barcelona Supercomputing Center
2015-2021
FC Barcelona
2019
Abstract Modeling the dynamic nature of protein-ligand binding with atomistic simulations is one main challenges in computational biophysics, important implications drug design process. Although past few years hardware and software advances have significantly revamped use molecular simulations, we still lack a fast accurate ab initio description mechanism complex systems, available only for up-to-date techniques requiring several hours or days heavy computation. Such delay limiting factors...
From laccase design to application of the overexpressed biocatalyst in an industrial environment for eco-friendly synthesis polyaniline and dyes.
For millennia tuberculosis has shown a successful strategy to survive, making it one of the world's deadliest infectious diseases. This resilient behavior is based not only on remaining hidden in most infected population, but also by showing slow evolution sick people. The course disease within population highly related its heterogeneity. Thus, classic epidemiological approaches with top-down perspective have succeeded understanding dynamics. In past decade few individual-based models were...
In this study, we present a fully automatic platform based on our Monte Carlo algorithm, the Protein Energy Landscape Exploration method (PELE), for estimation of absolute protein–ligand binding free energies, one most significant challenges in computer aided drug design. Based ligand pathway approach, an initial short enhanced sampling simulation is performed to identify reasonable starting positions more extended sampling. This stepwise approach allows faster convergence energy using...
Tuberculosis remains one of the world's deadliest infectious diseases. About one-third population is infected with tuberculosis bacteria. Understanding dynamics transmission at different spatial scales critical to progress in its control. We present an agent-based model for epidemics Barcelona, which has observatory on this disease. Our considers high heterogeneity within population, including risk factors developing active disease, and it tracks individual behavior once diagnosed....
We present a multistep protocol, combining Monte Carlo and molecular dynamics simulations, for the estimation of absolute binding free energies, one most significant challenges in computer-aided drug design. The protocol is based on an initial short enhanced simulation, followed by clustering ligand positions, which serve to identify relevant states unbinding process. From these states, extensive simulations are run estimate equilibrium probability distribution obtained with Markov State...
Tuberculosis remains one of the world's deadliest infectious diseases. About one-third population is infected with tuberculosis bacteria. Understanding dynamics transmission at different spatial scales critical to progress in its control. We present an agent-based model for epidemics Barcelona, which has observatory on this disease. Our considers high heterogeneity within population, including risk factors developing active disease, and it tracks individual behavior once diagnosed....
Type IV pili are bacterial surface-exposed filaments that built up by small monomers called pilin proteins. Pilins synthesized as longer precursors (prepilins), the N-terminal signal peptide of which must be removed processing protease PilD. A mutant cyanobacterium Synechocystis sp. PCC 6803 lacking PilD is not capable photoautotrophic growth because impaired function Sec translocons. Here, we isolated phototrophic suppressor strains original ΔpilD and, sequencing their genomes, identified...