H-bonds in Crambin: Coherence in an alpha helix
暂无分享,去创建一个
David D. L. Minh | R. Eisenberg | Stanley Nicholson | Stanley Nicholson | David Minh | Robert Eisenberg
[1] R. Eisenberg. Structural analysis of fluid flow in complex biological systems , 2023, Modeling and Artificial Intelligence in Ophthalmology.
[2] G. Stoltz. Error estimates and variance reduction for nonequilibrium stochastic dynamics , 2022, ArXiv.
[3] A. Liwo,et al. Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery , 2022, The journal of physical chemistry. B.
[4] B. Kirchner,et al. Cluster Analysis in Liquids: A Novel Tool in TRAVIS , 2022, J. Chem. Inf. Model..
[5] B. Eisenberg. Setting Boundaries for Statistical Mechanics , 2021, Molecules.
[6] Neal Fairley,et al. The Often-Overlooked Power of Summary Statistics in Exploratory Data Analysis: Comparison of Pattern Recognition Entropy (PRE) to Other Summary Statistics and Introduction of Divided Spectrum-PRE (DS-PRE) , 2021, J. Chem. Inf. Model..
[7] Jérôme Antoni,et al. Thresholded Multiple Coherence as a tool for source separation and denoising: Theory and aeroacoustic applications , 2021, Applied Acoustics.
[8] Patrick Joseph Muldowney. Gauge Integral Structures for Stochastic Calculus and Quantum Electrodynamics , 2021 .
[9] R. Eisenberg. Thermostatics vs. Electrodynamics , 2020 .
[10] Yasuteru Shigeta,et al. Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics , 2020, J. Chem. Inf. Model..
[11] B. Kirchner,et al. TRAVIS-A free analyzer for trajectories from molecular simulation. , 2020, The Journal of chemical physics.
[12] David D L Minh,et al. Robosample: A rigid-body molecular simulation program based on robot mechanics. , 2020, Biochimica et biophysica acta. General subjects.
[13] G. Hummer,et al. Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure. , 2020, The Journal of chemical physics.
[14] G. Hummer,et al. Optimal estimates of self-diffusion coefficients from molecular dynamics simulations. , 2020, The Journal of chemical physics.
[15] R. Eisenberg. Electrodynamics Correlates Knock-on and Knock-off: Current is Spatially Uniform in Ion Channels. , 2020, 2002.09012.
[16] Ben Adcock,et al. The troublesome kernel: why deep learning for inverse problems is typically unstable , 2020, ArXiv.
[17] Laura Orellana,et al. Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier , 2019, Front. Mol. Biosci..
[18] Jacob A Bauer,et al. Normal Mode Analysis as a Routine Part of a Structural Investigation , 2019, Molecules.
[19] Francesco Renna,et al. On instabilities of deep learning in image reconstruction and the potential costs of AI , 2019, Proceedings of the National Academy of Sciences.
[20] Jean-Charles Carvaillo,et al. TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries , 2018, J. Chem. Inf. Model..
[21] Malcolm C. Smith,et al. Electrical Network Synthesis: A Survey of Recent Work , 2018 .
[22] B. Eisenberg. Asking biological questions of physical systems: The device approach to emergent properties , 2018, Journal of Molecular Liquids.
[23] David K. Ferry,et al. An Introduction to Quantum Transport in Semiconductors , 2018 .
[24] A. Onufriev,et al. Accuracy limit of rigid 3-point water models. , 2016, The Journal of chemical physics.
[25] R. Eisenberg. Electrical Structure of Biological Cells and Tissues: impedance spectroscopy, stereology, and singular perturbation theory , 2015, 1511.01339.
[26] C. Simmerling,et al. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. , 2015, Journal of chemical theory and computation.
[27] Cecil W. Thomas. Coherence Function in Noisy Linear System , 2015 .
[28] Houman Owhadi,et al. On the Brittleness of Bayesian Inference , 2013, SIAM Rev..
[29] Isaac Amidror,et al. Mastering the Discrete Fourier Transform in One, Two or Several Dimensions , 2013, Computational Imaging and Vision.
[30] Giacomo Fiorin,et al. Using collective variables to drive molecular dynamics simulations , 2013 .
[31] A. Liwo. Coarse graining: a tool for large-scale simulations or more? , 2013 .
[32] Barbara Kirchner,et al. Computing vibrational spectra from ab initio molecular dynamics. , 2013, Physical chemistry chemical physics : PCCP.
[33] P. Muldowney. A Modern Theory of Random Variation: With Applications in Stochastic Calculus, Financial Mathematics, and Feynman Integration , 2012 .
[34] T. Toh,et al. The Kurzweil-Henstock theory of stochastic integration , 2012, Czechoslovak Mathematical Journal.
[35] M. Mustyakimov,et al. Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin. , 2012, Acta crystallographica. Section F, Structural biology and crystallization communications.
[36] Leslie Glasser. Solid-state energetics and electrostatics: Madelung constants and Madelung energies. , 2012, Inorganic chemistry.
[37] Barbara Kirchner,et al. TRAVIS - a free analyzer and visualizer for Monte Carlo and molecular dynamics trajectories , 2011, Journal of Cheminformatics.
[38] David C. Swanson,et al. Signal Processing for Intelligent Sensor Systems with MATLAB : Signal Processing for Intelligent Sensor Systems with MATLAB , 2011 .
[39] David J. Nesbitt,et al. Definition of the hydrogen bond (IUPAC Recommendations 2011) , 2011 .
[40] Jan H. Jensen,et al. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. , 2011, Journal of chemical theory and computation.
[41] E. Weckert,et al. Crystal structure of small protein crambin at 0.48 Å resolution. , 2011, Acta crystallographica. Section F, Structural biology and crystallization communications.
[42] Vijay S. Pande,et al. OpenMM: A Hardware-Independent Framework for Molecular Simulations , 2010, Computing in Science & Engineering.
[43] Z. Schuss. Theory and Applications of Stochastic Processes: An Analytical Approach , 2009 .
[44] A. Kossiakoff,et al. Role of a salt bridge in the model protein crambin explored by chemical protein synthesis: X-ray structure of a unique protein analogue, [V15A]crambin-alpha-carboxamide. , 2009, Molecular bioSystems.
[45] Kui Fu Chen,et al. Against the long-range spectral leakage of the cosine window family , 2009, Comput. Phys. Commun..
[46] Arvind Ramanathan,et al. An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations , 2009, RECOMB.
[47] Kankan Bhattacharya,et al. Fundamentals of Molecular Spectroscopy , 2008 .
[48] R. Eisenberg. Atomic Biology, Electrostatics, and Ionic Channels , 2008, 0807.0715.
[49] T. Cheatham,et al. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations , 2008, The journal of physical chemistry. B.
[50] Yan Feng Li,et al. Combining the Hanning windowed interpolated FFT in both directions , 2008, Comput. Phys. Commun..
[51] Yan Feng Li,et al. Eliminating the picket fence effect of the fast Fourier transform , 2008, Comput. Phys. Commun..
[52] P. Meystre. Introduction to the Theory of Coherence and Polarization of Light , 2007 .
[53] Harold Klee,et al. Simulation of Dynamic Systems with MATLAB and Simulink , 2007 .
[54] Oliver F. Lange,et al. Can principal components yield a dimension reduced description of protein dynamics on long time scales? , 2006, The journal of physical chemistry. B.
[55] D. ben-Avraham. Van der Waals Forces: A Handbook for Biologists, Chemists, Engineers, and Physicists , 2006 .
[56] O. Pongs,et al. Two-Dimensional Solid-State NMR Applied to a Chimeric Potassium Channel , 2006, Journal of receptor and signal transduction research.
[57] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[58] Toh Tin-Lam,et al. On Ito-Kurzweil-Henstock Integral and Integration-by-Part Formula , 2005 .
[59] M. Cardona. Albert Einstein as the father of solid state physics , 2005, physics/0508237.
[60] E. Barsoukov,et al. Impedance spectroscopy : theory, experiment, and applications , 2005 .
[61] Albert Tarantola,et al. Inverse problem theory - and methods for model parameter estimation , 2004 .
[62] A. Friberg,et al. Theory of partially coherent electromagnetic fields in the space-frequency domain. , 2004, Journal of the Optical Society of America. A, Optics, image science, and vision.
[63] Tim Hesterberg,et al. Introduction to Stochastic Search and Optimization: Estimation, Simulation, and Control , 2004, Technometrics.
[64] D. Ruppert. The Elements of Statistical Learning: Data Mining, Inference, and Prediction , 2004 .
[65] C. Swartz,et al. Theories of Integration: The Integrals of Riemann, Lebesgue, Henstock-Kurzweil, and McShane , 2004 .
[66] David Eisenberg,et al. The discovery of the α-helix and β-sheet, the principal structural features of proteins , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[67] E. Wolf. Unified theory of coherence and polarization of random electromagnetic beams , 2003 .
[68] A. Friberg,et al. Degree of coherence for electromagnetic fields. , 2003, Optics express.
[69] J. Oncley. Dielectric behavior and atomic structure of serum albumin. , 2002, Biophysical chemistry.
[70] Mohammad A. Karim,et al. Continuous Signals and Systems with MATLAB® , 2001 .
[71] Benedict Leimkuhler,et al. Integration Methods for Molecular Dynamics , 1996 .
[72] Tirion,et al. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.
[73] R. S. Eisenberg,et al. Computing the Field in Proteins and Channels , 2010, 1009.2857.
[74] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[75] L. Mandel,et al. Optical Coherence and Quantum Optics , 1995 .
[76] Nicholas I. Fisher,et al. On the Nonparametric Estimation of Covariance Functions , 1994 .
[77] Timothy A. Davis,et al. MATLAB Primer , 1994 .
[78] Robert F. Stengel,et al. Optimal Control and Estimation , 1994 .
[79] K. Lutchen,et al. Pseudorandom signals to estimate apparent transfer and coherence functions of nonlinear systems: applications to respiratory mechanics , 1992, IEEE Transactions on Biomedical Engineering.
[80] A. Krall. Applied Analysis , 1986 .
[81] Brian E. Maki,et al. Interpretation of the Coherence Function When Using Pseudorandom Inputs to Identify Nonlinear Systems , 1986, IEEE Transactions on Biomedical Engineering.
[82] Aleksandr Petrovich Demchenko,et al. Ultraviolet Spectroscopy of Proteins , 1986, 1987.
[83] Jonathan M. Borwein,et al. Convergence of lattice sums and Madelung’s constant , 1985 .
[84] M. Karplus,et al. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. , 1983, Proceedings of the National Academy of Sciences of the United States of America.
[85] G. Saridis. Parameter estimation: Principles and problems , 1983, Proceedings of the IEEE.
[86] Wayne A. Hendrickson,et al. Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur , 1981, Nature.
[87] R. Eisenberg. Structural complexity, circuit models, and ion accumulation. , 1980, Federation proceedings.
[88] R. Eisenberg,et al. Measurement, modeling, and analysis of the linear electrical properties of cells. , 1977, Annals of the New York Academy of Sciences.
[89] J. S. Bendat,et al. Solutions for the multiple input/output poblem , 1976 .
[90] C. J. Dodds,et al. Partial coherence in multivariate random processes , 1975 .
[91] G. Carter,et al. Estimation of the magnitude-squared coherence function via overlapped fast Fourier transform processing , 1973 .
[92] Gabor C. Temes,et al. The optimization of bandlimited systems , 1973 .
[93] Peter D. Welch,et al. The Fast Fourier Transform and Its Applications , 1969 .
[94] J. Bendat,et al. Measurement and Analysis of Random Data , 1968 .
[95] Samuel Karlin,et al. A First Course on Stochastic Processes , 1968 .
[96] L. Goddard. Linear Differential Operators , 1962, Nature.
[97] L. Pauling,et al. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. , 1951, Proceedings of the National Academy of Sciences of the United States of America.
[98] Linus Pauling,et al. THE NATURE OF THE CHEMICAL BOND. APPLICATION OF RESULTS OBTAINED FROM THE QUANTUM MECHANICS AND FROM A THEORY OF PARAMAGNETIC SUSCEPTIBILITY TO THE STRUCTURE OF MOLECULES , 1931 .
[99] Jessica Schulze,et al. The Nature Of The Chemical Bond , 2016 .
[100] F. Diederich. Electrons And Holes In Semiconductors With Applications To Transistor Electronics , 2016 .
[101] Yvonne Feierabend,et al. Synthesis Of Rc Networks , 2016 .
[102] R. Eisenberg. Impedance Measurement of the Electrical Structure of Skeletal Muscle , 2011 .
[103] Julius S. Bendat,et al. Random Data: Analysis and Measurement Procedures, Fourth Edition , 2010 .
[104] Z. Jiang,et al. Infrared Spectroscopy , 2022 .
[105] D. Beveridge,et al. Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model , 2002, Proteins.
[106] J S Bendat and A G Piersol. Random Data Analysis and Measurement Procedures , 2000 .
[107] C. Brooks. Computer simulation of liquids , 1989 .
[108] William L. Briggs,et al. The DFT : An Owner's Manual for the Discrete Fourier Transform , 1987 .
[109] James A. Cadzow,et al. Linear modeling and the coherence function , 1987, IEEE Trans. Acoust. Speech Signal Process..
[110] R. Mathias. Analysis of Membrane Properties Using Extrinsic Noise , 1984 .
[111] S. Karlin,et al. A second course in stochastic processes , 1981 .
[112] R. Eisenberg,et al. Structural analysis of electrical properties of cells and tissues. , 1980, Critical reviews in bioengineering.
[113] J. W. Humberston. Classical mechanics , 1980, Nature.
[114] A. Zemanian,et al. Infinite electrical networks , 1976, Proceedings of the IEEE.
[115] K. Rao,et al. Molecular Spectroscopy: Modern Research , 1972 .
[116] Franklin Fa-Kun Kuo,et al. Network analysis and synthesis , 1962 .
[117] G. V. Chester,et al. Solid-State Physics , 1962, Nature.
[118] J. Ferry,et al. THE MEASUREMENT OF DIELECTRIC PROPERTIES OF PROTEIN SOLUTIONS; A DISCUSSION OF METHODS AND INTERPRETATION , 1938 .
[119] Murali M. Kolluri,et al. Frequency response function estimation techniques and the corresponding coherence functions: A review and update , 2022 .