Search Results - "Honig, Barry"

Structure-based prediction of ligand–protein interactions on a genome-wide scale by Hwang, Howook, Dey, Fabian, Petrey, Donald, Honig, Barry

“…We report a template-based method, LT-scanner, which scans the human proteome using protein structural alignment to identify proteins that are likely to bind…”
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Thinking outside the cell: how cadherins drive adhesion by Brasch, Julia, Harrison, Oliver J, Honig, Barry, Shapiro, Lawrence

“…Cadherins are a superfamily of cell surface glycoproteins whose ectodomains contain multiple repeats of β-sandwich extracellular cadherin (EC) domains that…”
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Acetylation-regulated interaction between p53 and SET reveals a widespread regulatory mode by Wang, Donglai, Kon, Ning, Lasso, Gorka, Jiang, Le, Leng, Wenchuan, Zhu, Wei-Guo, Qin, Jun, Honig, Barry, Gu, Wei

“…The acidic domain of SET binds and represses unacetylated p53, but this interaction is prevented by cellular-stress-induced p53 CTD acetylation. Acetylation in…”
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On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites by Nayal, Murad, Honig, Barry

“…In this article we introduce a new method for the identification and the accurate characterization of protein surface cavities. The method is encoded in the…”
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PrePPI: a structure-informed database of protein-protein interactions by Zhang, Qiangfeng Cliff, Petrey, Donald, Garzón, José Ignacio, Deng, Lei, Honig, Barry

“…PrePPI (http://bhapp.c2b2.columbia.edu/PrePPI) is a database that combines predicted and experimentally determined protein-protein interactions (PPIs) using a…”
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The role of DNA shape in protein-DNA recognition by Liu, Peng, Honig, Barry, Mann, Richard S, Rohs, Remo, West, Sean M, Sosinsky, Alona

“…The recognition of specific DNA sequences by proteins is thought to depend on two types of mechanism: one that involves the formation of hydrogen bonds with…”
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Structure-based prediction of protein–protein interactions on a genome-wide scale by Zhang, Qiangfeng Cliff, Petrey, Donald, Deng, Lei, Qiang, Li, Shi, Yu, Thu, Chan Aye, Bisikirska, Brygida, Lefebvre, Celine, Accili, Domenico, Hunter, Tony, Maniatis, Tom, Califano, Andrea, Honig, Barry

“…Protein–protein interactions, essential for understanding how a cell functions, are predicted using a new method that combines protein structure with other…”
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Structural basis of adhesive binding by desmocollins and desmogleins by Harrison, Oliver J., Brasch, Julia, Lasso, Gorka, Katsamba, Phinikoula S., Ahlsen, Goran, Honig, Barry, Shapiro, Lawrence

“…Desmosomes are intercellular adhesive junctions that impart strength to vertebrate tissues. Their dense, ordered intercellular attachments are formed by…”
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Origins of specificity in protein-DNA recognition by Rohs, Remo, Jin, Xiangshu, West, Sean M, Joshi, Rohit, Honig, Barry, Mann, Richard S

“…Specific interactions between proteins and DNA are fundamental to many biological processes. In this review, we provide a revised view of protein-DNA…”
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A Structure-Informed Atlas of Human-Virus Interactions by Lasso, Gorka, Mayer, Sandra V., Winkelmann, Evandro R., Chu, Tim, Elliot, Oliver, Patino-Galindo, Juan Angel, Park, Kernyu, Rabadan, Raul, Honig, Barry, Shapira, Sagi D.

“…While knowledge of protein-protein interactions (PPIs) is critical for understanding virus-host relationships, limitations on the scalability of…”
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Structural Bioinformatics of the Interactome by Petrey, Donald, Honig, Barry

“…The past decade has seen a dramatic expansion in the number and range of techniques available to obtain genome-wide information and to analyze this information…”
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Protein interface conservation across structure space by Zhang, Qiangfeng Cliff, Petrey, Donald, Norel, Raquel, Honig, Barry H

“…With the advent of Systems Biology, the prediction of whether two proteins form a complex has become a problem of increased importance. A variety of…”
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Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins by Slattery, Matthew, Riley, Todd, Liu, Peng, Abe, Namiko, Gomez-Alcala, Pilar, Dror, Iris, Zhou, Tianyin, Rohs, Remo, Honig, Barry, Bussemaker, Harmen J., Mann, Richard S.

“…Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. Transcription factors often…”
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Mechanism for alternating access in neurotransmitter transporters by Forrest, Lucy R, Zhang, Yuan-Wei, Jacobs, Miriam T, Gesmonde, Joan, Xie, Li, Honig, Barry H, Rudnick, Gary

“…Crystal structures of LeuT, a bacterial homologue of mammalian neurotransmitter transporters, show a molecule of bound substrate that is essentially exposed to…”
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Cooperativity between trans and cis interactions in cadherin-mediated junction formation by Wu, Yinghao, Jin, Xiangshu, Harrison, Oliver, Shapiro, Lawrence, Honig, Barry H., Ben-Shaul, Avinoam

“…Intercellullar junctions formed by cadherins, including desmosomes and adherens junctions, comprise two dimensional arrays of "trans" dimers formed between…”
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Visualization of clustered protocadherin neuronal self-recognition complexes by Brasch, Julia, Goodman, Kerry M., Noble, Alex J., Rapp, Micah, Mannepalli, Seetha, Bahna, Fabiana, Dandey, Venkata P., Bepler, Tristan, Berger, Bonnie, Maniatis, Tom, Potter, Clinton S., Carragher, Bridget, Honig, Barry, Shapiro, Lawrence

“…Neurite self-recognition and avoidance are fundamental properties of all nervous systems 1 . These processes facilitate dendritic arborization 2 , 3 , prevent…”
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Molecular Logic of Neuronal Self-Recognition through Protocadherin Domain Interactions by Rubinstein, Rotem, Thu, Chan Aye, Goodman, Kerry Marie, Wolcott, Holly Noelle, Bahna, Fabiana, Mannepalli, Seetha, Ahlsen, Goran, Chevee, Maxime, Halim, Adnan, Clausen, Henrik, Maniatis, Tom, Shapiro, Lawrence, Honig, Barry

“…Self-avoidance, a process preventing interactions of axons and dendrites from the same neuron during development, is mediated in vertebrates through the…”
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Discovery of an O-mannosylation pathway selectively serving cadherins and protocadherins by Larsen, Ida Signe Bohse, Narimatsu, Yoshiki, Joshi, Hiren Jitendra, Siukstaite, Lina, Harrison, Oliver J., Brasch, Julia, Goodman, Kerry M., Hansen, Lars, Shapiro, Lawrence, Honig, Barry, Vakhrushev, Sergey Y., Clausen, Henrik, Halim, Adnan

“…The cadherin (cdh) superfamily of adhesion molecules carry O-linked mannose (O-Man) glycans at highly conserved sites localized to specific β-strands of their…”
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Structural origins of clustered protocadherin-mediated neuronal barcoding by Rubinstein, Rotem, Goodman, Kerry Marie, Maniatis, Tom, Shapiro, Lawrence, Honig, Barry

“…Clustered protocadherins mediate neuronal self-recognition and non-self discrimination—neuronal “barcoding”—which underpin neuronal self-avoidance in…”
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Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1 by Clark, Anthony J., Gindin, Tatyana, Zhang, Baoshan, Wang, Lingle, Abel, Robert, Murret, Colleen S., Xu, Fang, Bao, Amy, Lu, Nina J., Zhou, Tongqing, Kwong, Peter D., Shapiro, Lawrence, Honig, Barry, Friesner, Richard A.

“…Direct calculation of relative binding affinities between antibodies and antigens is a long-sought goal. However, despite substantial efforts, no generally…”
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