A5036654109- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Photoreceptor and optogenetics research
- Spectroscopy and Quantum Chemical Studies
- Wnt/β-catenin signaling in development and cancer
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- DNA and Nucleic Acid Chemistry
- Neuroscience and Neuropharmacology Research
- Lipid Membrane Structure and Behavior
- Mass Spectrometry Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Cellular Mechanics and Interactions
- Photosynthetic Processes and Mechanisms
- Cellular transport and secretion
- Machine Learning in Bioinformatics
- Axon Guidance and Neuronal Signaling
- Genomics and Chromatin Dynamics
- Retinal Development and Disorders
- Monoclonal and Polyclonal Antibodies Research
- Genomics and Phylogenetic Studies
- Photochromic and Fluorescence Chemistry
- RNA Research and Splicing
- Cancer-related gene regulation
Columbia University
2016-2025
Columbia University Irving Medical Center
2015-2025
University of Iowa
2024
University of California, Los Angeles
2012-2024
Brain (Germany)
2016-2022
Howard Hughes Medical Institute
2012-2021
Cancer Research Center
2015-2017
Institute of Molecular Biology and Biophysics
2007-2017
Center for Systems Biology
2014-2016
Institute of Bioinformatics
2008-2014
Abstract We demonstrate in this work that the surface tension, water‐organic solvent, transfer‐free energies and thermodynamics of melting linear alkanes provide fundamental insights into nonpolar driving forces for protein folding binding reactions. first develop a model curvature dependence hydrophobic effect find macroscopic concept interfacial free energy is applicable at molecular level. Application well‐known relationship involving tension adhesion reveals dispersion play little or no...
Abstract The application of all‐atom force fields (and explicit or implicit solvent models) to protein homology‐modeling tasks such as side‐chain and loop prediction remains challenging both because the expense individual energy calculations difficulty sampling rugged surface. Here we address this challenge for problem through development numerous new algorithms, with an emphasis on multiscale hierarchical techniques. As a first step in evaluating performance our algorithm, have applied it...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAccurate Calculation of Hydration Free Energies Using Macroscopic Solvent ModelsDoree Sitkoff, Kim A. Sharp, and Barry HonigCite this: J. Phys. Chem. 1994, 98, 7, 1978–1988Publication Date (Print):February 1, 1994Publication History Published online1 May 2002Published inissue 1 February 1994https://pubs.acs.org/doi/10.1021/j100058a043https://doi.org/10.1021/j100058a043research-articleACS PublicationsRequest reuse permissionsArticle...
Abstract An efficient algorithm is presented for the numerical solution of Poisson–Boltzmann equation by finite difference method successive over‐relaxation. Improvements include rapid estimation optimum relaxation parameter, reduction in number operations per iteration, and vector‐oriented array mapping. The has been incorporated into electrostatic program DelPhi, reducing required computing time between one two orders magnitude. As a result effects such as solvent screening, ion...
Abstract We present a numerical method for calculating the electrostatic potential of molecules in solution, using linearized Poisson‐Boltzmann equation. The emphasis this work is on applications to biological macromolecules. accuracy assessed by comparisons with analytic solutions case single charge dielectric sphere (Tanford‐Kirkwood theory), which serves as model macromolecule. find that are generally accurate within 5%. Larger errors occur close and boundary, but maximum error found at...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAccurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics Continuum Dielectric TheoryDavid J. Tannor, Bryan Marten, Robert Murphy, Richard A. Friesner, Doree Sitkoff, Anthony Nicholls, Barry Honig, Murco Ringnalda, William Goddard IIICite this: Am. Chem. Soc. 1994, 116, 26, 11875–11882Publication Date (Print):December 1, 1994Publication History Published online1 May 2002Published...
We present self-consistent reaction field (SCRF) calculations, utilizing correlated ab initio quantum mechanics, of aqueous solvation free energies for a large data base molecular solutes. identify subset chemical functional groups which there are systematic deviations in the comparison theory and experiment; furthermore, one case has been extensively investigated, methylated amines, similar appear explicit solvent energy perturbation calculations employing several commonly used mechanics...
Abstract In this report we describe an accurate numerical method for calculating the total electrostatic energy of molecules arbitrary shape and charge distribution, accounting both Coulombic solvent polarization terms. addition to solvation energies individual molecules, can be used calculate associated with conformational changes in proteins as well that accompany binding charged substrates. The validity is examined by hydration acetate, methyl ammonium, methanol. then study relationship...
A new version of the DelPhi program, which provides numerical solutions to nonlinear Poisson−Boltzmann (PB) equation, is reported. The program can divide space into multiple regions containing different dielectric constants and treat systems mixed salt where valence concentration each ion different. electrostatic free energy calculated by decomposing various terms Coulombic interactions so that energies are independent lattice used solve PB equation. This, together with algorithms optimally...
Abstract In this paper we report the implementation of a finite‐difference algorithm which solves linearized Poisson‐Boltzmann equation for molecules arbitrary shape and charge distribution includes screening effects electrolytes. The microcoding on an ST‐100 array processor allows us to obtain electrostatic potential maps in around protein, including ionic strength, about 30 minutes. We have applied dimer protein Cu‐Zn superoxide dismutase (SOD) compared our results those obtained from...
Abstract This article describes a number of algorithms that are designed to improve both the efficiency and accuracy finite difference solutions Poisson–Boltzmann equation (the FDPB method) extend its range application. The incorporated in DelPhi program. first algorithm involves an efficient accurate semianalytical method map molecular surface molecule onto three‐dimensional lattice. constitutes significant improvement over existing methods terms combination speed accuracy. program has also...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReevaluation of the Born model ion hydrationAlexander A. Rashin and Barry HonigCite this: J. Phys. Chem. 1985, 89, 26, 5588–5593Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/j100272a006https://doi.org/10.1021/j100272a006research-articleACS PublicationsRequest reuse permissionsArticle Views2075Altmetric-Citations500LEARN ABOUT THESE...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCalculating total electrostatic energies with the nonlinear Poisson-Boltzmann equationKim A. Sharp and Barry. HonigCite this: J. Phys. Chem. 1990, 94, 19, 7684–7692Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/j100382a068https://doi.org/10.1021/j100382a068research-articleACS PublicationsRequest reuse permissionsArticle...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMacroscopic models of aqueous solutions: biological and chemical applicationsBarry Honig, Kim Sharp, An Suei YangCite this: J. Phys. Chem. 1993, 97, 6, 1101–1109Publication Date (Print):February 1, 1993Publication History Published online1 May 2002Published inissue 1 February 1993https://pubs.acs.org/doi/10.1021/j100108a002https://doi.org/10.1021/j100108a002research-articleACS PublicationsRequest reuse permissionsArticle...
Abstract This paper describes a general method to calculate the p K s of ionizable groups in proteins. Electrostatic calculations are carried out using finite difference Poisson–Boltzmann (FDPB) method. A formal treatment calculation within framework FDPB is presented. The major change with respect previous work specific incorporation complete charge distribution both neutral and charged forms each group into formalism. extremely important for salt bridges. hybrid statistical...
The magnitude of the hydrophobic effect, as measured from surface area dependence solubilities hydrocarbons in water, is generally thought to be about 25 calories per mole square angstrom (cal mol -1 Å -2 ). However, tension at a hydrocarbon-water interface, which "macroscopic" measure ≈72 cal . In an attempt reconcile these values, alkane solubility data have been reevaluated account for solute-solvent size differences, leading revised "microscopic" effect 47 This value, when used simple...
Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. Transcription factors often bind as multiprotein complexes, raising the possibility that complex formation might modify their specificities. To test this hypothesis, we developed an experimental and computational platform, SELEX-seq, can be used to determine relative affinities any sequence for complex. Applying method all eight Drosophila Hox proteins, show they...