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Mariani, S. Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases. McCammon, J. Dynamics of folded proteins. Motlagh, H. Interplay between allostery and intrinsic disorder in an ensemble. Nussinov, R. Allostery in disease and in drug discovery. Cell , — Osawa, M. Functional dynamics of proteins revealed by solution NMR. Palazzesi, F. Accuracy of current all-atom force-fields in modeling protein disordered states.

Pandini, A. GSATools: analysis of allosteric communication and functional local motions using a structural alphabet. Bioinformatics 29, — Papaleo, E. Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation. Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation. Conformational changes and free energies in a proline isomerase. Pasi, M. Piana, S. Water dispersion interactions strongly influence simulated structural properties of disordered protein states.

B , — Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. A bias-exchange approach to protein folding. Popovych, N. Dynamically driven protein allostery. Pronk, S. Rapaport, D. The Art of Molecular Dynamics Simulation. Reif, M. Ribeiro, A. Determination of signaling pathways in proteins through network theory: importance of the topology. Sahakyan, A.

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Structure-based prediction of methyl chemical shifts in proteins. NMR 50, — Salvatella, X. Understanding protein dynamics using conformational ensembles. Saunders, M.

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Coarse-graining methods for computational biology. Schlick, T. Seeber, M. Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Shaw, D. Sherwood, P. Multiscale methods for macromolecular simulations. Snow, C. How well can simulation predict protein folding kinetics and thermodynamics? Spiwok, V. Enhanced sampling techniques in biomolecular simulations.

Stacklies, W. Implementation of force distribution analysis for molecular dynamics simulations.

Basics of Molecular Dynamics Simulations

BMC Bioinformatics Sutto, L. Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase. New advances in metadynamics. Wiley Interdiscip. Tang, C. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Tiberti, M. PyInteraph: a framework for the analysis of interaction networks in structural ensembles of proteins.

Tomlinson, J. Characterization of salt bridges to lysines in the protein G B1 domain. Tsai, C. Van den Bedem, H. Automated identification of functional dynamic contact networks from X-ray crystallography. Methods 10, — Vendruscolo, M. Determination of conformationally heterogeneous states of proteins. Small-world view of the amino acids that play a key role in protein folding.

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E Stat. Soft Matter Phys. Villali, J. Choreographing an enzyme's dance. Vishveshwara, S. Intra and inter-molecular communications through protein structure network. Protein Pept. Wand, A. The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation. Warshel, A.

Computer simulations of enzyme catalysis: methods, progress, and insights. Whitley, M. Frameworks for understanding long-range intra-protein communication. Xia, Y. Simulating protein evolution in sequence and structure space. Zhuravlev, P. Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. Keywords: protein dynamics, molecular dynamics, protein NMR, enhanced sampling, metadynamics, protein structure.

Citation: Papaleo E Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity. The use, distribution or reproduction in other forums is permitted, provided the original author s or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice.

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A few abstracts will be selected for oral presentations. Gartner, Z. Unraveling cell-to-cell signaling networks with chemical biology. Smith, J.

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  7. Architecture of the polyketide synthase module: surprises from electron cryo-microscopy. Curr Opin Struct Biol 31, 9—19 Laddach, A. Genetic variants and protein—protein interactions: a multidimensional network-centric view. Degiacomi, M. Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. Demir, O. Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants. Peng L. Generation of high-density biskyrmions by electric current. Npj Quantum Materials 2 , 7. Quirinale D.


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    Molecular dynamics simulations: advances and applications

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