A5056170480- Protein Structure and Dynamics
- Enzyme Structure and Function
- Genetics, Bioinformatics, and Biomedical Research
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Computational Drug Discovery Methods
- Genomics and Phylogenetic Studies
- Spectroscopy and Quantum Chemical Studies
- 3D Shape Modeling and Analysis
- Glycosylation and Glycoproteins Research
- Bioinformatics and Genomic Networks
- Various Chemistry Research Topics
- DNA and Nucleic Acid Chemistry
- Evolution and Genetic Dynamics
- DNA Repair Mechanisms
- Nanopore and Nanochannel Transport Studies
- Mass Spectrometry Techniques and Applications
- Advanced NMR Techniques and Applications
- NMR spectroscopy and applications
- Gene expression and cancer classification
- Computer Graphics and Visualization Techniques
- Molecular spectroscopy and chirality
- Topological and Geometric Data Analysis
- Bacterial Genetics and Biotechnology
- RNA Research and Splicing
University of California, Davis
2015-2024
John Wiley & Sons (United States)
2021
Institut Pasteur
2009-2018
National University of Singapore
2011
Centre National de la Recherche Scientifique
1994-2009
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2009
Institut de Physique Théorique
2009
CEA Paris-Saclay
2009
Reed College
2007
Laboratoire d'Informatique de Paris-Nord
2006
Abstract Multiple sequence alignment is one of the cornerstones modern molecular biology. It used to identify conserved motifs, determine protein domains, in 2D/3D structure prediction by homology and evolutionary studies. Recently, high‐throughput technologies such as genome sequencing structural proteomics have lead an explosion amount information available. In response, several new multiple methods been developed that improve both efficiency quality alignments. Consequently, benchmarks...
Normal mode analysis (NMA) is an efficient way to study collective motions in biomolecules that bypasses the computational costs and many limitations associated with full dynamics simulations. The NOMAD-Ref web server presented here provides tools for online calculation of normal modes large molecules (up 100 000 atoms) maintaining a all-atom representation their structures, as well access number programs utilize these deformation refinement biomolecular structures. Applications include...
Proteins can be very tolerant to amino acid substitution, even within their core. Understanding the factors responsible for this behavior is of critical importance protein engineering and design. Mutations in proteins have been quantified terms changes stability they induce. For example, guest residues specific secondary structures used as probes conformational preferences acids, yielding propensity scales. Predicting these propensities would a good test any new potential energy functions...
2-Acetylaminofluorene (AAF), a potent rat liver carcinogen that binds covalently to the C-8 position of guanine residues in DNA, is an effective frameshift mutagen. The mutations are distributed nonrandomly, most located at few specific DNA sequences (i.e., mutation hot spots). Among these spots, Nar I sequence (GGCGCC) especially susceptible induction -2 (GGCGCC----GGCC). Due nature sequence, G1G2CG3CC, three different molecular events, each involving deletion two contiguous base pairs G2C,...
Small Angle X-ray Scattering (SAXS) techniques are becoming more and useful for structural biologists biochemists, thanks to better access dedicated synchrotron beamlines, detectors the relative easiness of sample preparation. The ability compute theoretical SAXS profile a given model, compare this with measured scattering intensity, yields crucial informations about macromolecule under study and/or its complexes in solution. An important contribution profile, besides itself solvent-excluded...
We have developed a fully automated protein design strategy that works on the entire sequence of and uses full atom representation. At each step procedure, an all-atom model is built using template structure current designed sequence. The energy used to drive Monte Carlo optimization in space: random moves are either accepted or rejected based Metropolis criterion. rely physical forces stabilize native structures choose optimum Our function includes van der Waals interactions, electrostatics...
Nuclear magnetic resonance (NMR) spectroscopy serves as an important tool to analyze chemicals and proteins in bioengineering. Multi-dimensional NMR offers a major improvement resolution with multi-dimensional spectrum, but significantly increases data acquisition time produces hypercomplex that is difficult be handled. To reduce this time, non-uniformly sampling can applied obtain undersampled using reconstruction approach, such the state-of-the-art low rank method, remove spectral...
The non-linear problem of simulating the structural transition between two known forms a macromolecule still remains challenge in biology. is usually addressed an approximate way using 'morphing' techniques, which are linear interpolations either Cartesian or internal coordinates initial and end states, followed by energy minimization. Here we describe web tool that implements new method to calculate most probable trajectory exact for harmonic potentials; as illustration method, classical...
We describe a new approach to explore and quantify the sequence space associated with given protein structure. A set of sequences are optimized for target structure, using all-atom models physical energy function. Specificity its is ensured by random model, which keeps amino acid composition constant. The designed provide multiple alignment that describes compatible structure interest; here size this estimated an information entropy measure. In parallel, alignments naturally occurring can be...
Hydrophobic interactions are believed to play an important role in protein folding and stability. Semi-empirical attempts estimate these usually based on a model of solvation, whose contribution the stability proteins is assumed be proportional surface area buried upon folding. Here we propose extension this idea by defining environment free energy that characterizes each atom protein, including solvent, polar or nonpolar atoms same another molecule interacts with protein. In our model,...
Assembling fragments from known protein structures is a widely used approach to construct structural models for new proteins. We describe an application of this idea important inverse kinematics problem in biology: the loop closure problem. have developed algorithm generating conformations candidate loops that fit gap given length structure framework. Our method proceeds by concatenating small chosen libraries representative fragments. has advantages ab initio methods since we are able...
We describe a new way to calculate the electrostatic properties of macromolecules which eliminates assumption constant dielectric value in solvent region, resulting Generalized Poisson–Boltzmann–Langevin equation (GPBLE). have implemented web server ( http://lorentz.immstr.pasteur.fr/pdb_hydro.php ) that both numerically solves this and uses water density profiles place molecules at preferred sites hydration. Surface atoms with high or low hydration preference can be easily displayed using...