Works matching AU Honig, Barry

Results: 91

Nectin ectodomain structures reveal a canonical adhesive interface.

Published in:

Nature Structural & Molecular Biology, 2012, v. 19, n. 9, p. 906, doi. 10.1038/nsmb.2366

By:

Harrison, Oliver J;
Vendome, Jeremie;
Brasch, Julia;
Jin, Xiangshu;
Hong, Soonjin;
Katsamba, Phinikoula S;
Ahlsen, Goran;
Troyanovsky, Regina B;
Troyanovsky, Sergey M;
Honig, Barry;
Shapiro, Lawrence

Publication type:

Article

Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins.

Published in:

Nature Structural & Molecular Biology, 2011, v. 18, n. 6, p. 693, doi. 10.1038/nsmb.2051

By:

Vendome, Jeremie;
Posy, Shoshana;
Jin, Xiangshu;
Bahna, Fabiana;
Ahlsen, Goran;
Shapiro, Lawrence;
Honig, Barry

Publication type:

Article

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs.

Published in:

Nature Structural & Molecular Biology, 2010, v. 17, n. 4, p. 423, doi. 10.1038/nsmb.1800

By:

Kitayner, Malka;
Rozenberg, Haim;
Rohs, Remo;
Suad, Oded;
Rabinovich, Dov;
Honig, Barry;
Shakked, Zippora

Publication type:

Article

T-cadherin structures reveal a novel adhesive binding mechanism.

Published in:

Nature Structural & Molecular Biology, 2010, v. 17, n. 3, p. 339, doi. 10.1038/nsmb.1781

By:

Ciatto, Carlo;
Bahna, Fabiana;
Zampieri, Niccolò;
VanSteenhouse, Harper C.;
Katsamba, Phini S.;
Ahlsen, Goran;
Harrison, Oliver J.;
Brasch, Julia;
Xiangshu Jin;
Posy, Shoshana;
Vendome, Jeremie;
Ranscht, Barbara;
Jessell, Thomas M;
Honig, Barry;
Shapiro, Lawrence

Publication type:

Article

Two-step adhesive binding by classical cadherins.

Published in:

Nature Structural & Molecular Biology, 2010, v. 17, n. 3, p. 348, doi. 10.1038/nsmb.1784

By:

Harrison, Oliver J.;
Bahna, Fabiana;
Katsamba, Phini S.;
Xiangshu Jin;
Brasch, Julia;
Vendome, Jeremie;
Ahlsen, Goran;
Carroll, Kilpatrick J.;
Price, Stephen R.;
Honig, Barry;
Shapiro, Lawrence

Publication type:

Article

Protein structure space is much more than the sum of its folds.

Published in:

2007

By:

Honig, Barry

Publication type:

Letter

Calculation of electrostatic potentials in an enzyme active site.

Published in:

Nature, 1987, v. 330, n. 6143, p. 84, doi. 10.1038/330084a0

By:

Gilson, Michael K.;
Honig, Barry H.

Publication type:

Article

VISTAL—a new 2D visualization tool of protein 3D structural alignments.

Published in:

Bioinformatics, 2006, v. 22, n. 17, p. 2166

By:

Barry Honig

Publication type:

Article

Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects.

Published in:

Journal of Computational Chemistry, 2002, v. 23, n. 1, p. 128, doi. 10.1002/jcc.1161

By:

Rocchia, Walter;
Sridharan, Sundaram;
Nicholls, Anthony;
Alexov, Emil;
Chiabrera, Alessandro;
Honig, Barry

Publication type:

Article

The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems.

Published in:

Journal of Computational Chemistry, 1995, v. 16, n. 7, p. 898, doi. 10.1002/jcc.540160707

By:

Bharadwaj, Ranganathan;
Windemuth, Andreas;
Sridharan, S.;
Honig, Barry;
Nicholls, Anthony

Publication type:

Article

A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation.

Published in:

Journal of Computational Chemistry, 1991, v. 12, n. 4, p. 435, doi. 10.1002/jcc.540120405

By:

Nicholls, Anthony;
Honig, Barry

Publication type:

Article

Calculating the electrostatic potential of molecules in solution: Method and error assessment.

Published in:

Journal of Computational Chemistry, 1988, v. 9, n. 4, p. 327, doi. 10.1002/jcc.540090407

By:

Gilson, Michael K.;
Sharp, Kim A.;
Honig, Barry H.

Publication type:

Article

EXCITED STATE PROPERTIES OF VISUAL PIGMENTS AND BACTERIORHODOPSIN.

Published in:

Annals of the New York Academy of Sciences, 1981, v. 367, n. 1, p. 269, doi. 10.1111/j.1749-6632.1981.tb50573.x

By:

Honig, Barry

Publication type:

Article

Bioinformatics in structural genomics.

Published in:

Bioinformatics, 2002, v. 18, n. 7, p. 897, doi. 10.1093/bioinformatics/18.7.897

By:

Rost, Burkhard;
Honig, Barry;
Valencia, Alfonso

Publication type:

Article

How clustered protocadherin binding specificity is tuned for neuronal self-/ nonself-recognition.

Published in:

eLife, 2022, p. 1, doi. 10.7554/eLife.72416

By:

Goodman, Kerry Marie;
Katsamba, Phinikoula S.;
Rubinstein, Rotem;
Ahlsén, Göran;
Bahna, Fabiana;
Mannepalli, Seetha;
Dan, Hanbin;
Sampogna, Rosemary V.;
Shapiro, Lawrence;
Honig, Barry

Publication type:

Article

Using systems and structure biology tools to dissect cellular phenotypes.

Published in:

Journal of the American Medical Informatics Association, 2012, v. 19, n. 2, p. 171, doi. 10.1136/amiajnl-2011-000490

By:

Floratos, Aris;
Honig, Barry;
Pe'er, Dana;
Califano, Andrea

Publication type:

Article

Implications of Torsional Potential of Retinal Isomers for Visual Excitation.

Published in:

Nature, 1971, v. 229, n. 5286, p. 558, doi. 10.1038/229558a0

By:

HONIG, BARRY;
KARPLUS, MARTIN

Publication type:

Article

Searching for Neuronal Left/Right Asymmetry: Genomewide Analysis of Nematode Receptor-Type Guanylyl Cyclases.

Published in:

Genetics, 2006, v. 173, n. 1, p. 131, doi. 10.1534/genetics.106.055749

By:

Ortiz, Christopher O.;
Etchberger, John F.;
Posy, Shoshana L.;
Frøkjær-Jensen, Christian;
Lockery, Shawn;
Honig, Barry;
Hobert, Oliver

Publication type:

Article

A High-Throughput Strategy for Dissecting Mammalian Genetic Interactions.

Published in:

PLoS ONE, 2016, v. 11, n. 12, p. 1, doi. 10.1371/journal.pone.0167617

By:

Stockman, Victoria B.;
Ghamsari, Lila;
Lasso, Gorka;
Honig, Barry;
Shapira, Sagi D.;
Wang, Harris H.

Publication type:

Article

Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus.

Published in:

Proteins, 2009, v. 74, n. 2, p. 515, doi. 10.1002/prot.22267

By:

Rossi, Paolo;
Aramini, James M.;
Xiao, Rong;
Chen, Chen X.;
Nwosu, Chioma;
Owens, Leah A.;
Maglaqui, Melissa;
Nair, Rajesh;
Fischer, Markus;
Acton, Thomas B.;
Honig, Barry;
Rost, Burkhard;
Montelione, Gaetano T.

Publication type:

Article

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials.

Published in:

Proteins, 2008, v. 72, n. 4, p. 1171, doi. 10.1002/prot.22005

By:

Zhu, Jiang;
Fan, Hao;
Periole, Xavier;
Honig, Barry;
Mark, Alan E.

Publication type:

Article

Loop modeling: Sampling, filtering, and scoring.

Published in:

Proteins, 2008, v. 70, n. 3, p. 834, doi. 10.1002/prot.21612

By:

Soto, Cinque S.;
Fasnacht, Marc;
Zhu, Jiang;
Forrest, Lucy;
Honig, Barry

Publication type:

Article

NMR structure of protein yjbR from Escherichia coli reveals 'double-wing' DNA binding motif.

Published in:

Proteins, 2007, v. 67, n. 2, p. 501, doi. 10.1002/prot.21297

By:

Singarapu, Kiran Kumar;
Liu, Gaohua;
Xiao, Rong;
Bertonati, Claudia;
Honig, Barry;
Montelione, Gaetano T.;
Szyperski, Thomas

Publication type:

Article

Prediction of side-chain conformations on protein surfaces.

Published in:

Proteins, 2007, v. 66, n. 4, p. 814, doi. 10.1002/prot.21099

By:

Xiang, Zhexin;
Steinbach, Peter J.;
Jacobson, Matthew P.;
Friesner, Richard A.;
Honig, Barry

Publication type:

Article

NMR structure of protein PA2021 from Pseudomonas aeruginosa.

Published in:

Proteins, 2006, v. 65, n. 3, p. 767, doi. 10.1002/prot.21098

By:

Lin, Yu-Chieh;
Liu, Gaohua;
Shen, Yang;
Bertonati, Claudia;
Yee, Adelinda;
Honig, Barry;
Arrowsmith, Cheryl H.;
Szyperski, Thomas

Publication type:

Article

Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering.

Published in:

Proteins, 2006, v. 65, n. 2, p. 463, doi. 10.1002/prot.21085

By:

Zhu, Jiang;
Xie, Li;
Honig, Barry

Publication type:

Article

On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites.

Published in:

Proteins, 2006, v. 63, n. 4, p. 892, doi. 10.1002/prot.20897

By:

Nayal, Murad;
Honig, Barry

Publication type:

Article

An assessment of the accuracy of methods for predicting hydrogen positions in protein structures.

Published in:

Proteins, 2005, v. 61, n. 2, p. 296, doi. 10.1002/prot.20601

By:

Forrest, Lucy R.;
Honig, Barry

Publication type:

Article

NMR structure of the 18 kDa protein CC1736 from Caulobacter crescentus identifies a member of the 'START' domain superfamily and suggests residues mediating substrate specificity.

Published in:

Proteins, 2005, v. 58, n. 3, p. 747, doi. 10.1002/prot.20365

By:

Shen, Yang;
Goldsmith-Fischman, Sharon;
Atreya, Hanudatta S.;
Acton, Thomas;
Ma, LiChung;
Xiao, Rong;
Honig, Barry;
Montelione, Gaetano T.;
Szyperski, Thomas

Publication type:

Article

NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis Reveals a distinct 5-helix bundle.

Published in:

Proteins, 2004, v. 55, n. 3, p. 756, doi. 10.1002/prot.20009

By:

Liu, Gaohua;
Sukumaran, Dinesh K.;
Xu, Duanxiang;
Chiang, Yiwen;
Acton, Thomas;
Goldsmith-Fischman, Sharon;
Honig, Barry;
Montelione, Gaetano T.;
Szyperski, Thomas

Publication type:

Article

A hierarchical approach to all-atom protein loop prediction.

Published in:

Proteins, 2004, v. 55, n. 2, p. 351, doi. 10.1002/prot.10613

By:

Jacobson, Matthew P.;
Pincus, David L.;
Rapp, Chaya S.;
Day, Tyler J.F.;
Honig, Barry;
Shaw, David E.;
Friesner, Richard A.

Publication type:

Article

NMR structure of the hypothetical protein AQ-1857 encoded by the Y157 gene from Aquifex aeolicus reveals a novel protein fold.

Published in:

Proteins, 2004, v. 54, n. 4, p. 794, doi. 10.1002/prot.10424

By:

Duanxiang Xu;
Gaohua Liu;
Rong Xiao;
Tom Acton;
Sharon Goldsmith-Fischman;
Barry Honig;
Gaetano T. Montelione;
Thomas Szyperski

Publication type:

Article

Crystal structures of MTH1187 and its yeast ortholog YBL001c.

Published in:

Proteins, 2003, v. 52, n. 3, p. 478, doi. 10.1002/prot.10443

By:

Xiao Tao;
Reza Khayat;
Dinesh Christendat;
Alexei Savchenko;
Xiaohui Xu;
Sharon Goldsmith-Fischman;
Barry Honig;
Aled Edwards;
Cheryl H. Arrowsmith;
Liang Tong

Publication type:

Article

Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling.

Published in:

Proteins, 2003, v. 53, n. S6, p. 430, doi. 10.1002/prot.10550

By:

Petrey, Donald;
Xiang, Zhexin;
Tang, Christopher L.;
Xie, Lei;
Gimpelev, Marina;
Mitros, Therese;
Soto, Cinque S.;
Goldsmith-Fischman, Sharon;
Kernytsky, Andrew;
Schlessinger, Avner;
Koh, Ingrid Y.Y.;
Alexov, Emil;
Honig, Barry

Publication type:

Article

Sequence to structure alignment in comparative modeling using PrISM.

Published in:

Proteins, 1999, v. 37, n. S3, p. 66, doi. 10.1002/(SICI)1097-0134(1999)37:3+<66::AID-PROT10>3.0.CO;2-K

By:

Yang, An-Suei;
Honig, Barry

Publication type:

Article

Evaluation of the conformational free energies of loops in proteins.

Published in:

Proteins, 1994, v. 18, n. 2, p. 119, doi. 10.1002/prot.340180205

By:

Smith, Kenneth C.;
Honig, Barry

Publication type:

Article

On the calculation of p K<sub>a</sub>s in proteins.

Published in:

Proteins, 1993, v. 15, n. 3, p. 252, doi. 10.1002/prot.340150304

By:

Yang, An-Suei;
Gunner, M. R.;
Sampogna, Rosemary;
Sharp, Kim;
Honig, Barry

Publication type:

Article

Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons.

Published in:

Proteins, 1991, v. 11, n. 4, p. 281, doi. 10.1002/prot.340110407

By:

Nicholls, Anthony;
Sharp, Kim A.;
Honig, Barry

Publication type:

Article

In memoriam: Cyrus levinthal.

Published in:

Proteins, 1991, v. 11, n. 4, p. 239, doi. 10.1002/prot.340110402

By:

Honig, Barry

Publication type:

Article

Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis.

Published in:

Proteins, 1988, v. 4, n. 1, p. 7, doi. 10.1002/prot.340040104

By:

Gilson, Michael K.;
Honig, Barry

Publication type:

Article

DIP/Dpr interactions and the evolutionary design of specificity in protein families.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15981-8

By:

Sergeeva, Alina P.;
Katsamba, Phinikoula S.;
Cosmanescu, Filip;
Brewer, Joshua J.;
Ahlsen, Goran;
Mannepalli, Seetha;
Shapiro, Lawrence;
Honig, Barry

Publication type:

Article

Molecular aspects of photoreceptor function.

Published in:

Quarterly Reviews of Biophysics, 1975, v. 8, n. 2, p. 129, doi. 10.1017/S0033583500001785

By:

Ebrey, Thomas G.;
Honig, Barry

Publication type:

Article

Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function.

Published in:

Nature Structural Biology, 1999, v. 6, n. 11, p. 1055

By:

Chin, Kevin;
Sharp, Kim A.;
Honig, Barry;
Pyle, Anna Marie

Publication type:

Article

Predicting Peptide-Mediated Interactions on a Genome-Wide Scale.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004248

By:

Chen, T. Scott;
Petrey, Donald;
Garzon, Jose Ignacio;
Honig, Barry

Publication type:

Article

Using Structure to Explore the Sequence Alignment Space of Remote Homologs.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002175

By:

Kuziemko, Andrew;
Honig, Barry;
Petrey, Donald

Publication type:

Article

VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 8, p. 1, doi. 10.1371/journal.pcbi.1000881

By:

Chen, Brian Y.;
Honig, Barry

Publication type:

Article

α-Catenin--mediated cadherin clustering couples cadherin and actin dynamics.

Published in:

Journal of Cell Biology, 2015, v. 210, n. 4, p. 647, doi. 10.1083/jcb.201412064

By:

Chi-Shuo Chen;
Soonjin Hong;
Indra, Indrajyoti;
Sergeeva, Alina P.;
Troyanovsky, Regina B.;
Shapiro, Lawrence;
Honig, Barry;
Troyanovsky, Sergey M.

Publication type:

Article

Energetics of charge-charge interactions in proteins.

Published in:

Proteins, 1988, v. 3, n. 1, p. 32, doi. 10.1002/prot.340030104

By:

Gilson, Michael K.;
Honig, Barry H.

Publication type:

Article

Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification.

Published in:

Proteins, 1986, v. 1, n. 1, p. 47, doi. 10.1002/prot.340010109

By:

Klapper, Isaac;
Hagstrom, Ray;
Fine, Richard;
Sharp, Kim;
Honig, Barry

Publication type:

Article

Salt effects on polyelectrolyte-ligand binding: Comparison of Poisson-Boltzmann, and limiting law/counterion binding models.

Published in:

Biopolymers, 1995, v. 36, n. 2, p. 245, doi. 10.1002/bip.360360211

By:

Sharp, Kim A.;
Friedman, Richard A.;
Misra, Vinod;
Hecht, Jonathan;
Honig, Barry

Publication type:

Article