Barry Honig

发表

Visualization of clustered protocadherin neuronal self-recognition complexes

Bonnie Berger, Bridget Carragher, Julia Brasch, 2019, Nature.

Predicting Peptide-Mediated Interactions on a Genome-Wide Scale

Barry Honig, José Ignacio Garzón, T. Scott Chen, 2015, PLoS Comput. Biol..

Mutli-Features Prediction of Protein Translational Modification Sites

Kyungsook Han, Asoke K. Nandi, Wenzheng Bao, 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Bioinformatics in structural genomics - Editorial

Barry Honig, Alfonso Valencia, Burkhard Rost, 2002, Bioinform..

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

Li Xie, Barry Honig, Jiang Zhu, 2006, Proteins.

Theory and simulation

Barry Honig, 1995 .

miRNA-Disease Association Prediction with Collaborative Matrix Factorization

Kyungsook Han, De-Shuang Huang, Zhen Shen, 2017, Complex..

Integration of Multi-Omics Data for Gene Regulatory Network Inference and Application to Breast Cancer

Kyungsook Han, De-Shuang Huang, Lin Yuan, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Outcome of a workshop on applications of protein models in biomedical research.

Roland L Dunbrack, Roland L. Dunbrack, Andrej Sali, 2009, Structure.

Using Structure to Explore the Sequence Alignment Space of Remote Homologs

Barry Honig, Donald Petrey, Andrew Kuziemko, 2011, PLoS Comput. Biol..

PredUs: a web server for predicting protein interfaces using structural neighbors

Jihong Guan, Lei Deng, Qiangfeng Cliff Zhang, 2011, Nucleic Acids Res..

Using systems and structure biology tools to dissect cellular phenotypes

Aris Floratos, Andrea Califano, Barry Honig, 2012, J. Am. Medical Informatics Assoc..

The inclusion of electrostatic hydration energies in molecular mechanics calculations

Michael K. Gilson, Barry Honig, B. Honig, 1991, J. Comput. Aided Mol. Des..

PUDGE: a flexible, interactive server for protein structure prediction

Raquel Norel, Barry Honig, Donald Petrey, 2010, Nucleic Acids Res..

OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites

Shula Shazman, Barry Honig, Hunjoong Lee, 2013, Nucleic Acids Res..

Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors

Barry Honig, Richard S. Mann, Alona Sosinsky, 2003, Nucleic Acids Res..

PrePPI: a structure-informed database of protein–protein interactions

Lei Deng, Qiangfeng Cliff Zhang, Barry Honig, 2012, Nucleic Acids Res..

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

Emil Alexov, Barry Honig, Anthony Nicholls, 2002, J. Comput. Chem..

MarkUs: a server to navigate sequence–structure–function space

Markus Fischer, Qiangfeng Cliff Zhang, Barry Honig, 2011, Nucleic Acids Res..

GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences.

Barry Honig, Donald Petrey, B. Honig, 2003, Methods in enzymology.

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

Barry Honig, Brian Y. Chen, B. Honig, 2010, PLoS Comput. Biol..

Aligning and modeling protein-dna interfaces: towards an understanding of protein-dna binding specificity

Barry Honig, Trevor William Siggers, 2006 .

Local quality assessment in homology models using statistical potentials and support vector machines

Barry Honig, Jiang Zhu, Marc Fasnacht, 2007, Protein science : a publication of the Protein Society.

Loop modeling: Sampling, filtering, and scoring

Barry Honig, Jiang Zhu, Cinque S. Soto, 2007, Proteins.

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

Rachel Kolodny, Barry Honig, B. Honig, 2006, Bioinform..

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

Lei Xie, Avner Schlessinger, Emil Alexov, 2003, Proteins.

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

S. Sriharan, Barry Honig, Ranganathan Bharadwaj, 1995, J. Comput. Chem..

Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1

Tongqing Zhou, Baoshan Zhang, Robert Abel, 2017, Journal of molecular biology.

Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions†

Barry Honig, Walter Rocchia, B. Honig, 2001 .

Electrostatic Potentials near the Surface of DNA: Comparing Theory and Experiment

Barry Honig, B. Honig, W. Hubbell, 1995 .

Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation

Barry Honig, Kim A. Sharp, K. Sharp, 1990 .

Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations

Anna Tempczyk, Barry Honig, Anthony Nicholls, 1991 .

A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.

Stephen C. J. Parker, Remo Rohs, Peng Liu, 2011, ACS chemical biology.

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

Barry Honig, Lucy R Forrest, B. Honig, 2005, Proteins.

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

Barry Honig, Anna Marie Pyle, Kim A. Sharp, 1999, Nature Structural Biology.

Electrostatic Interactions between Arginines and the Minor Groove in the Nucleosome

Remo Rohs, Barry Honig, R. Mann, 2010, Journal of biomolecular structure & dynamics.

A computational interactome and functional annotation for the human proteome

Lei Deng, Barry Honig, José Ignacio Garzón, 2016, eLife.

Structure-based prediction of ligand–protein interactions on a genome-wide scale

Barry Honig, Donald Petrey, Howook Hwang, 2017, Proceedings of the National Academy of Sciences.

Salt Effects on Protein-DNA Interactions: The λcI Repressor and EcoRI Endonuclease

Barry Honig, Kim A. Sharp, K. Sharp, 1994 .

A Structure-Informed Atlas of Human-Virus Interactions

Raul Rabadan, Barry Honig, Oliver Elliot, 2019, Cell.

Comparative study of generalized born models: Born radii and peptide folding.

Emil Alexov, Barry Honig, B. Honig, 2005, The journal of physical chemistry. B.

New wavelength dependent visual pigment nomograms

Barry Honig, B. Honig, T. Ebrey, 1977, Vision Research.

Calculation of Alkane to Water Solvation Free Energies Using Continuum Solvent Models

Barry Honig, B. Honig, D. Sitkoff, 1996 .

Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface?

Barry Honig, Lawrence Shapiro, B. Honig, 2008, Journal of molecular biology.

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.

Emil Alexov, Barry Honig, Anna Marie Pyle, 2007, Journal of molecular biology.

INTERACTIONS IN MACROMOLECULES: Theory and Applications

Barry Honig, Kim A. Sharp, 1990 .

Electrostatic control of the membrane targeting of C2 domains.

Barry Honig, Diana Murray, B. Honig, 2002, Molecular cell.

An external point-charge model for bacteriorhodopsin to account for its purple color

Barry Honig, Koji Nakanishi, Kazuo Tsujimoto, 1980 .

Structural bioinformatics of the interactome.

Barry Honig, Donald Petrey, B. Honig, 2014, Annual review of biophysics.

Transforming binding affinities from 3D to 2D with application to cadherin clustering

Yinghao Wu, Barry Honig, Lawrence Shapiro, 2011, Nature.

Corrigendum: Structure-based prediction of protein–protein interactions on a genome-wide scale

Lei Deng, Qiangfeng Cliff Zhang, Andrea Califano, 2013, Nature.

Monovalent and Divalent Salt Effects on Electrostatic Free Energies Defined by the Nonlinear Poisson−Boltzmann Equation: Application to DNA Binding Reactions

Barry Honig, B. Honig, Shu‐wen W. Chen, 1997 .

Structural determinants of trypsin affinity and specificity for cationic inhibitors

Fabio Polticelli, Barry Honig, Paolo Ascenzi, 1999, Protein science : a publication of the Protein Society.

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

Barry Honig, Isaac Klapper, K. Sharp, 1986, Proteins.

Cadherin-mediated cell-cell adhesion: sticking together as a family.

Fabiana Bahna, Barry Honig, Lawrence Shapiro, 2003, Current opinion in structural biology.

Structural and energetic determinants of adhesive binding specificity in type I cadherins

Julia Brasch, Fabiana Bahna, Barry Honig, 2014, Proceedings of the National Academy of Sciences.

Correction for Briët et al., Violating the Shannon capacity of metric graphs with entanglement

Katherine A. Fitzgerald, Fabiana Bahna, Barry Honig, 2013, Proceedings of the National Academy of Sciences.

Structural relationships among proteins with different global topologies and their implications for function annotation strategies

Markus Fischer, Barry Honig, Donald Petrey, 2009, Proceedings of the National Academy of Sciences.

Lozenge directly activates argos and klumpfuss to regulate programmed cell death.

Barry Honig, Alona Sosinsky, R. Mann, 2005, Genes & development.

Type II Cadherin Ectodomain Structures: Implications for Classical Cadherin Specificity

Fabiana Bahna, Barry Honig, Thomas M. Jessell, 2006, Cell.

Solution structure of Archaeglobus fulgidis peptidyl‐tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes

Robert Powers, Nebojsa Mirkovic, Barry Honig, 2005, Protein science : a publication of the Protein Society.

γ-Protocadherin structural diversity and functional implications

Seetha Mannepalli, Fabiana Bahna, Tom Maniatis, 2016, eLife.

Comparative study of generalized Born models: protein dynamics.

Barry Honig, Alan E Mark, Hao Fan, 2005, Proceedings of the National Academy of Sciences of the United States of America.

An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision in C. elegans

Barry Honig, Oliver Hobert, Marc Fasnacht, 2006, Development.

Free energy calculations of ion hydration: an analysis of the Born model in terms of microscopic simulations

Bhyravabhotla Jayaram, Barry Honig, Kim A. Sharp, 1989 .

Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains.

Bissan Al-Lazikani, Barry Honig, B. Al-Lazikani, 2003, Journal of molecular biology.

Helical packing patterns in membrane and soluble proteins.

Barry Honig, Lucy R Forrest, Diana Murray, 2004, Biophysical journal.

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

James M Aramini, Gaetano T Montelione, Markus Fischer, 2009, Proteins.

Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle.

Barry Honig, Chris L. Tang, Diana Murray, 2005, Structure.

THE ‘OPSIN SHIFT’ IN BACTERIORHODOPSIN: STUDIES WITH ARTIFICIAL BACTERIORHODOPSINS

Michael G. Motto, Barry Honig, Koji Nakanishi, 1981 .

Electrostatic Control of the Membrane Targeting of C 2 Domains bers

Barry Honig, Diana Murray, B. Honig, 2002 .

A local dielectric constant model for solvation free energies which accounts for solute polarizability

Barry Honig, Kim A. Sharp, K. Sharp, 1992 .

ELECTROSTATIC INTERACTIONS IN ALIPHATIC DICARBOXYLIC ACIDS : A COMPUTATIONAL ROUTE TO THE DETERMINATION OF PKA SHIFTS

Bhyravabhotla Jayaram, Barry Honig, E. Rajasekaran, 1994 .

Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA.

An-Suei Yang, Barry Honig, B. Honig, 1998, Biophysical journal.

Monte Carlo Simulation Studies on the Structure of the Counterion Atmosphere of B-DNA. Variations on the Primitive Dielectric Model

Bhyravabhotla Jayaram, Barry Honig, David L. Beveridge, 1990 .

Reevaluation of the Born model of ion hydration

Barry Honig, Alexander A. Rashin, B. Honig, 1985 .

Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies.

Emil Alexov, Barry Honig, B. Honig, 2007, Biophysical journal.

THROUGH-SPACE ELECTROSTATIC EFFECTS IN ELECTRONIC SPECTRA. EXPERIMENTAL EVIDENCE FOR THE EXTERNAL POINT-CHARGE MODEL OF VISUAL PIGMENTS

Barry Honig, Koji Nakanishi, B. Honig, 1979 .

On the role of electrostatic interactions in the design of protein-protein interfaces.

Barry Honig, B. Honig, F. Sheinerman, 2002, Journal of molecular biology.

Is protein classification necessary? Toward alternative approaches to function annotation.

Barry Honig, Donald Petrey, B. Honig, 2009, Current opinion in structural biology.

The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins

Marco Punta, Ming Zhou, Thomas Szyperski, 2010, Journal of Structural and Functional Genomics.

Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.

Antonina Silkov, Barry Honig, B. Honig, 2005, Journal of molecular biology.

An external point-charge model for wavelength regulation in visual pigments

Michael G. Motto, Barry Honig, Uri Dinur, 1979 .

An Automatic Method for Predicting Transmembrane Protein Structures Using Cryo-em and Evolutionary Data

Richard A Friesner, Sarel J Fleishman, Nir Ben-Tal, 2004 .

ON THE MECHANISM OF WAVELENGTH REGULATION IN VISUAL PIGMENTS

Barry Honig, B. Honig, Toshiaki Kakitani, 1985, Photochemistry and photobiology.

Identification of a chloride ion binding site in Na+/Cl−-dependent transporters

Barry Honig, Lucy R Forrest, B. Honig, 2007, Proceedings of the National Academy of Sciences.

Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics.

Barry Honig, B. Honig, Z. Zhou, 2010, Journal of molecular biology.

Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions.

Antonina Silkov, Nitin Bhardwaj, Hui Lu, 2012, Molecular cell.

Electrostatic effects on protein stability: Current Opinion in Structural Biology 1992, 2:40…-45

An-Suei Yang, Barry Honig, B. Honig, 1992 .

Extending the accuracy limits of prediction for side-chain conformations.

Barry Honig, Zhexin Xiang, 2001 .

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

Fabiana Bahna, Barry Honig, Lawrence Shapiro, 2011, Nature Structural &Molecular Biology.

Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting

Andrea Califano, Barry Honig, Alona Sosinsky, 2007, Proceedings of the National Academy of Sciences.