A5068241594- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Scientific Computing and Data Management
- Enzyme Structure and Function
- Genomics and Chromatin Dynamics
- Distributed and Parallel Computing Systems
- Spectroscopy and Quantum Chemical Studies
- Genomics and Phylogenetic Studies
- Advanced biosensing and bioanalysis techniques
- Research Data Management Practices
- Bacteriophages and microbial interactions
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Lung Cancer Treatments and Mutations
- Advanced Data Storage Technologies
- Machine Learning in Materials Science
- Cancer Genomics and Diagnostics
- Business Process Modeling and Analysis
- Mass Spectrometry Techniques and Applications
- Cancer therapeutics and mechanisms
- Hepatitis C virus research
- Crystallography and molecular interactions
- RNA modifications and cancer
Institute for Research in Biomedicine
2015-2025
Institute of Science and Technology
2015-2025
Instituto de Salud Carlos III
2024
Fraunhofer Information Center for Planning and Building
2019-2021
Barcelona Institute for Science and Technology
2020
Universitat Politècnica de Catalunya
2009-2019
Barcelona Supercomputing Center
2007-2015
Universitat de Barcelona
2009-2013
Institute for Bioengineering of Catalonia
2011
The dynamics of proteins in aqueous solution has been investigated through a massive approach based on “state the art” molecular simulations performed for all protein metafolds using four most popular force fields (OPLS, CHARMM, AMBER, and GROMOS). A detailed analysis database trajectories (>1.5 terabytes data obtained ≈50 years CPU) allowed us to obtain robust-consensus picture solution.
Abstract Summary: MDWeb and MDMoby constitute a web-based platform to help access molecular dynamics (MD) in the standard high-throughput regime. The provides tools prepare systems from PDB structures mimicking procedures followed by human experts. It inputs can send simulations for three of most popular MD packages (Amber, NAMD Gromacs). Tools analysis trajectories, either provided user or retrieved our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. has two ways access,...
Last generation of force-fields are raising expectations on the quality molecular dynamics (MD) simulations DNA, as well to belief that theoretical models can substitute experimental ones in several cases. However these claims based limited benchmarks, where MD have shown ability reproduce already existing 'experimental models', which turn, an unclear accuracy represent DNA conformation solution. In this work we explore different predict structure two new B-DNA dodecamers, determined herein...
We present a systematic study of the long-timescale dynamics Drew–Dickerson dodecamer (DDD: d(CGCGAATTGCGC)2) prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe conformational landscape DDD in variety ionic environments from minimal salt to 2 M Na+Cl− or K+Cl−. The sensitivity simulations use different solvent and ion models is analyzed detail using multi-microsecond simulations. Finally, an extended (10 μs) simulation used characterize slow infrequent...
The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability materials chemical data. Since first release OPTIMADE specification (v1.0), API has undergone significant development, leading v1.2 release, underpinned multiple scientific studies. In this work, we highlight latest features format, accompanying software tools, provide...
Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates largest amounts of data, and is using amount CPU time in supercomputing centres. MD trajectories are obtained after months calculations, analysed situ, practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists nucleic acids world. We present here a novel database system store analyses acids. The initial data set...
Abstract In the recent years, improvement of software and hardware performance has made biomolecular simulations a mature tool for study biological processes. Simulation length size complexity analyzed systems make both complementary compatible with other bioinformatics disciplines. However, characteristics packages used simulation have prevented adoption technologies accepted in fields like automated deployment systems, workflow orchestration, or use containers. We present here...
We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing large amount atomistic molecular dynamics simulations, we determine sequence-dependent DNA as expressed in equilibrium distribution its stochastic dynamics. Our analysis includes study first second moments distribution, which can be accurately captured by harmonic model, but with nonlocal sequence-dependence. characterize choreography backbone...
FlexServ is a web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols coarse-grained determination dynamics using different versions Normal Mode Analysis (NMA), Brownian (BD) and Discrete Dynamics (DMD). It can also analyze user provided trajectories. allows complete flexibility large variety metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness collectivity measures, Lindemann's indexes, residue correlation,...
Significance EGFR cancer mutations display an astonishing tissue-specific asymmetry: in lung cancer, target the intracellular kinase (KD), while glioblastomas (GBMs), a variety of missense clusters and deletions concentrate at ectodomain (ECD). Intriguingly, GBM-activating share paradoxical preference for inhibitors that bind inactive kinase. By integrating simulations, small-angle X-ray scattering, GBM models, we demonstrate ECD mutants converge to transition state characterized by cryptic...
Abstract By combining in silico, biophysical, and vitro experiments, we decipher the topology, physical, potential biological properties of hybrid-parallel nucleic acids triplexes, an elusive structure at basis life. We found that hybrid triplex topology follows a stability order: r(Py)-d(Pu)·r(Py) > r(Py)-d(Pu)·d(Py) d(Py)-d(Pu)·d(Py) d(Py)-d(Pu)·r(Py). The is expected to be preferred cell as it avoids need open duplex reducing torsional stress required for formation topology. Upon...
We present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound other molecules. The server allows user incorporate structures from protein data banks, completing gaps and removing structural inconsistencies. It is also possible define canonical (average sequence-adapted) acid using variety predefined internal libraries, as well create specific conformations sequence. offers methods explore flexibility, such colorless wormlike-chain model, base-pair...
We used extensive molecular dynamics simulations to study the structural and dynamic properties of central d(TpA) step in highly polymorphic d(CpTpApG) tetranucleotide. Contrary assumption dinucleotide-model its nearest neighbours (tetranucleotide-model), change quite significantly dependent on next-to-nearest (hexanucleotide) sequence context a few cases are modulated by even remote (beyond from TpA). Our results highlight existence previously undescribed dynamical mechanisms for...
We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses generalized multi-harmonic model that can represent any multi-normal distribution helical parameters, thus avoiding caveats current mesoscopic models DNA and representing breakthrough in field. has been parameterized from accurate parmbsc1 atomistic molecular dynamics simulations all unique tetranucleotide sequences embedded long duplexes takes advantage correlation between states backbone...
Abstract New hardware, massively parallel and graphical processing unit‐based computers in particular, has boosted molecular simulations to levels that would be unthinkable just a decade ago. At the classical level, it is now possible perform atomistic with systems containing over 10 million atoms collect trajectories extending millisecond range. Such achievements are moving biosimulations into mainstream of structural biology research, complementary experimental studies. The drawback this...
Abstract Molecular dynamics (MD) simulations are keeping computers busy around the world, generating a huge amount of data that is typically not open to scientific community. Pioneering efforts ensure safety and reusability MD have been based on use simple databases providing limited set standard analyses single-short trajectories. Despite their value, these do offer true solution for current community users, who want flexible analysis pipeline possibility address non-Markovian ensembles...
The mitochondrial genome (mtDNA) is assembled into nucleo-protein structures termed nucleoids and maintained differently compared to nuclear DNA, the involved molecular basis remaining poorly understood. In yeast (Saccharomyces cerevisiae), mtDNA a ∼80 kbp linear molecule Abf2p, double HMG-box protein, packages maintains it. protein binds DNA in non-sequence-specific manner, but displays distinct 'phased-binding' at specific sequences containing poly-adenine tracts (A-tracts). We present...
The ABC Consortium has been generating nucleic-acids MD trajectories for more than 20 years. This brief comment highlights the importance of this data field, which triggered a number critical studies, including force-field parameterization and development new coarse-grained mesoscopic models. With world entering into data-driven era led by artificial intelligence, where is becoming essential ever, initiative leading way nucleic acid flexibility.
This letter illustrates the opinion of molecular dynamics (MD) community on need to adopt a new FAIR paradigm for use simulations. It highlights necessity collaborative effort create, establish, and sustain database that allows findability, accessibility, interoperability, reusability simulation data. Such development would democratize field significantly improve impact MD simulations life science research. will transform our working paradigm, pushing frontier. We invite you support...