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Barry Honig

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Fabian Dey; Qiangfeng Cliff Zhang; Donald Petrey; Barry Honig
Toward a "structural BLAST": using structural relationships to infer function.
Yinghao Wu; Barry Honig; Avinoam Ben-Shaul
Theory and simulations of adhesion receptor dimerization on membrane surfaces.
Qiangfeng Cliff Zhang; Donald Petrey; Lei Deng; José Ignacio Garzón; Barry Honig
PrePPI: a structure-informed database of protein-protein interactions.

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All Publications

2013: Fabian Dey; Qiangfeng Cliff Zhang; Donald Petrey; Barry Honig
Toward a "structural BLAST": using structural relationships to infer function.
Protein science : a publication of the Protein Society 2013;22(4):359-66.
2013: Yinghao Wu; Barry Honig; Avinoam Ben-Shaul
Theory and simulations of adhesion receptor dimerization on membrane surfaces.
Biophysical journal 2013;104(6):1221-9.
2013: Qiangfeng Cliff Zhang; Donald Petrey; Lei Deng; José Ignacio Garzón; Barry Honig
PrePPI: a structure-informed database of protein-protein interactions.
Nucleic acids research 2013;41(Database issue):D828-33.
2012: Qiangfeng Cliff Zhang; Domenico Accili; Brygida Bisikirska; Andrea Califano; Lei Deng; Tony Hunter; Celine Lefebvre; Tom Maniatis; Donald Petrey; Li Qiang; Yu Shi; Chan Aye Thu; Barry Honig
Structure-based prediction of protein-protein interactions on a genome-wide scale.
Nature 2012;490(7421):556-60.
2012: Oliver J Harrison; Soonjin Hong; Barry Honig; Xiangshu Jin; Phinikoula S Katsamba; Goran Ahlsen; Julia Brasch; Regina B Troyanovsky; Sergey M Troyanovsky; Jeremie Vendome; Lawrence Shapiro
Nectin ectodomain structures reveal a canonical adhesive interface.
Nature structural & molecular biology 2012;19(9):906-15.
2012: Julia Brasch; Oliver J Harrison; Barry Honig; Lawrence Shapiro
Thinking outside the cell: how cadherins drive adhesion.
Trends in cell biology 2012;22(6):299-310.
2012: Yong Chen; Nitin Bhardwaj; Randy A Hall; Barry Honig; Morten Källberg; Svetlana Kurilova; Hui Lu; Ren Sheng; Antonina Silkov; Moe P Tun; Wonhwa Cho
Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions.
Molecular cell 2012;46(2):226-37.
2012: Alexander Eletsky; John K Everett; Barry Honig; Hsiau-Wei Lee; Gaetano T Montelione; Donald Petrey; James H Prestegard; Rong Xiao; Qiangfeng Cliff Zhang; Thomas B Acton; Thomas Szyperski
Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771.
Journal of structural and functional genomics 2012;13(1):1-7.
2012: Aris Floratos; Barry Honig; Dana Pe'er; Andrea Califano
Using systems and structure biology tools to dissect cellular phenotypes.
Journal of the American Medical Informatics Association : JAMIA 2012;19(2):171-5.
2012: Xiangshu Jin; Seetha Mannepalli; Jeremie Vendome; Melissa A Walker; Goran Ahlsen; Fabiana Bahna; Filip Cosmanescu; Klára Felsövályi; Barry Honig; Lawrence Shapiro
Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca²+-free interdomain linkers.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(3):E127-34.
2011: Andrew Kuziemko; Barry Honig; Donald Petrey
Using structure to explore the sequence alignment space of remote homologs.
PLoS computational biology 2011;7(10):e1002175.
2011: Yinghao Wu; Avinoam Ben-Shaul; Lawrence Shapiro; Jeremie Vendome; Barry Honig
Transforming binding affinities from three dimensions to two with application to cadherin clustering.
Nature 2011;475(7357):510-3.
2011: Markus Fischer; Barry Honig; Brian Y Chen; Fabian Dey; Qiangfeng Cliff Zhang; Donald Petrey
MarkUs: a server to navigate sequence-structure-function space.
Nucleic acids research 2011;39(Web Server issue):W357-61.
2011: Qiangfeng Cliff Zhang; Lei Deng; Markus Fisher; Jihong Guan; Barry Honig; Donald Petrey
PredUs: a web server for predicting protein interfaces using structural neighbors.
Nucleic acids research 2011;39(Web Server issue):W283-7.
2011: Jiang Zhu; Yong Yu; Barry Honig; Ehud Y Isacoff; Ming-hui Li; Maximilian H Ulbrich; Jian Yang
Structural model of the TRPP2/PKD1 C-terminal coiled-coil complex produced by a combined computational and experimental approach.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(25):10133-8.
2011: Jeremie Vendome; Shoshana Posy; Xiangshu Jin; Fabiana Bahna; Goran Ahlsen; Lawrence Shapiro; Barry Honig
Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins.
Nature structural & molecular biology 2011;18(6):693-700.
2011: Julia Brasch; Oliver J Harrison; Goran Ahlsen; Stewart M Carnally; Robert M Henderson; Barry Honig; Lawrence Shapiro
Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin.
Journal of molecular biology 2011;408(1):57-73.
2011: Oliver J Harrison; Xiangshu Jin; Soonjin Hong; Fabiana Bahna; Goran Ahlsen; Julia Brasch; Yinghao Wu; Jeremie Vendome; Klara Felsovalyi; Cheri M Hampton; Regina B Troyanovsky; Avinoam Ben-Shaul; Joachim Frank; Sergey M Troyanovsky; Lawrence Shapiro; Barry Honig
The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins.
Structure (London, England : 1993) 2011;19(2):244-56.
2010: Jesko Koehnke; Phinikoula S Katsamba; Goran Ahlsen; Fabiana Bahna; Jeremie Vendome; Barry Honig; Lawrence Shapiro; Xiangshu Jin
Splice form dependence of beta-neurexin/neuroligin binding interactions.
Neuron 2010;67(1):61-74.
2010: R Norel; Donald Petrey; Barry Honig
PUDGE: a flexible, interactive server for protein structure prediction.
Nucleic acids research 2010;38(Web Server issue):W550-4.
2010: Qiangfeng Cliff Zhang; Donald Petrey; R Norel; Barry Honig
Protein interface conservation across structure space.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(24):10896-901.
2010: Jiang Zhu; Lingpeng Cheng; Qin Fang; Z Hong Zhou; Barry Honig
Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement.
Journal of molecular biology 2010;397(3):835-51.
2010: Hunjoong Lee; Zhaohui Li; Antonina Silkov; Markus Fischer; Donald Petrey; Barry Honig; Diana Murray
High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics.
Journal of structural and functional genomics 2010;11(1):51-9.
2010: Carlo Ciatto; Fabiana Bahna; Niccolò Zampieri; Harper C VanSteenhouse; Phini S Katsamba; Goran Ahlsen; Oliver J Harrison; Julia Brasch; Xiangshu Jin; Shoshana Posy; Jeremie Vendome; Barbara Ranscht; Thomas M Jessell; Barry Honig; Lawrence Shapiro
T-cadherin structures reveal a novel adhesive binding mechanism.
Nature structural & molecular biology 2010;17(3):339-47.
2010: Oliver J Harrison; Fabiana Bahna; Phini S Katsamba; Xiangshu Jin; Julia Brasch; Jeremie Vendome; Goran Ahlsen; Kilpatrick J Carroll; Stephen R Price; Barry Honig; Lawrence Shapiro
Two-step adhesive binding by classical cadherins.
Nature structural & molecular biology 2010;17(3):348-57.
2010: Kiran Kumar Singarapu; Jeffrey L Mills; Rong Xiao; Thomas B Acton; Marco Punta; Markus Fischer; Barry Honig; Burkhard Rost; Gaetano T Montelione; Thomas Szyperski
Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175.
Proteins 2010;78(3):779-84.
2010: Brian Y Chen; Barry Honig
VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity.
PLoS computational biology 2010;6(8):.
2010: Remo Rohs; Xiangshu Jin; Sean M West; Rohit Joshi; Barry Honig; Richard S Mann
Origins of specificity in protein-DNA recognition.
Annual review of biochemistry 2010;79():233-69.
2009: Remo Rohs; Sean M West; Alona Sosinsky; Peng Liu; Richard S Mann; Barry Honig
The role of DNA shape in protein-DNA recognition.
Nature 2009;461(7268):1248-53.
2009: Donald Petrey; Markus Fischer; Barry Honig
Structural relationships among proteins with different global topologies and their implications for function annotation strategies.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(41):17377-82.
2009: P Katsamba; K Carroll; G Ahlsen; Fabiana Bahna; J Vendome; Shoshana Posy; M Rajebhosale; S Price; Thomas M Jessell; Avinoam Ben-Shaul; Lawrence Shapiro; Barry Honig
Linking molecular affinity and cellular specificity in cadherin-mediated adhesion.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(28):11594-9.
2009: Donald Petrey; Barry Honig
Is protein classification necessary? Toward alternative approaches to function annotation.
Current opinion in structural biology 2009;19(3):363-8.
2009: Remo Rohs; Sean M West; Peng Liu; Barry Honig
Nuance in the double-helix and its role in protein-DNA recognition.
Current opinion in structural biology 2009;19(2):171-7.
2008: Mickey Kosloff; Emil Alexov; Vadim Y Arshavsky; Barry Honig
Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation.
The Journal of biological chemistry 2008;283(45):31197-207.
2008: Jiang Zhu; Hao Fan; Xavier Periole; Barry Honig; Alan E Mark
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials.
Proteins 2008;72(4):1171-88.
2008: Vesselin Z Miloushev; Fabiana Bahna; Carlo Ciatto; Goran Ahlsen; Barry Honig; Lawrence Shapiro; Arthur G Palmer
Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins.
Structure (London, England : 1993) 2008;16(8):1195-205.
2008: Shoshana Posy; Lawrence Shapiro; Barry Honig
Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface?
Journal of molecular biology 2008;378(4):954-68.
2008: Jesko Koehnke; Xiangshu Jin; Nikola Trbovic; Phinikoula S Katsamba; Julia Brasch; Goran Ahlsen; Peter Scheiffele; Barry Honig; Arthur G Palmer; Lawrence Shapiro
Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4.
Structure (London, England : 1993) 2008;16(3):410-21.
2008: Cinque S Soto; Marc Fasnacht; Jiang Zhu; Lucy R Forrest; Barry Honig
Loop modeling: Sampling, filtering, and scoring.
Proteins 2008;70(3):834-43.
2008: Jesko Koehnke; Xiangshu Jin; Elaine C Budreck; Shoshana Posy; Peter Scheiffele; Barry Honig; Lawrence Shapiro
Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(6):1873-8.
2007: Rohit Joshi; Jonathan M Passner; Remo Rohs; Rinku Jain; Alona Sosinsky; Michael A Crickmore; Vinitha Jacob; Aneel K Aggarwal; Barry Honig; Richard S Mann
Functional specificity of a Hox protein mediated by the recognition of minor groove structure.
Cell 2007;131(3):530-43.
2007: Marc Fasnacht; Jiang Zhu; Barry Honig
Local quality assessment in homology models using statistical potentials and support vector machines.
Protein science : a publication of the Protein Society 2007;16(8):1557-68.
2007: Lucy R Forrest; Sotiria Tavoulari; Yuan-Wei Zhang; Gary Rudnick; Barry Honig
Identification of a chloride ion binding site in Na+/Cl -dependent transporters.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(31):12761-6.
2007: Kiran Kumar Singarapu; Gaohua Liu; Rong Xiao; Claudia Bertonati; Barry Honig; Gaetano T Montelione; Thomas Szyperski
NMR structure of protein yjbR from Escherichia coli reveals 'double-wing' DNA binding motif.
Proteins 2007;67(2):501-4.
2007: Alona Sosinsky; Barry Honig; Richard S Mann; Andrea Califano
Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(15):6305-10.
2007: Claudia Bertonati; Barry Honig; Emil Alexov
Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies.
Biophysical journal 2007;92(6):1891-9.
2007: Christopher L Tang; Emil Alexov; Anna Marie Pyle; Barry Honig
Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.
Journal of molecular biology 2007;366(5):1475-96.
2007: Zhexin Xiang; Peter J Steinbach; Matthew P Jacobson; Richard A Friesner; Barry Honig
Prediction of side-chain conformations on protein surfaces.
Proteins 2007;66(4):814-23.
2007: Trevor W Siggers; Barry Honig
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.
Nucleic acids research 2007;35(4):1085-97.
2006: Yu-Chieh Lin; Gaohua Liu; Yang Shen; Claudia Bertonati; Adelinda Yee; Barry Honig; Cheryl H Arrowsmith; Thomas Szyperski
NMR structure of protein PA2021 from Pseudomonas aeruginosa.
Proteins 2006;65(3):767-70.
2006: Jiang Zhu; Li Xie; Barry Honig
Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering.
Proteins 2006;65(2):463-79.
2006: Robert J Johnston; John W Copeland; Marc Fasnacht; John F Etchberger; Jun Liu; Barry Honig; Oliver Hobert
An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision in C. elegans.
Development (Cambridge, England) 2006;133(17):3317-28.
2006: Rachel Kolodny; Barry Honig
VISTAL--a new 2D visualization tool of protein 3D structural alignments.
Bioinformatics (Oxford, England) 2006;22(17):2166-7.
2006: Lucy R Forrest; Christopher L Tang; Barry Honig
On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins.
Biophysical journal 2006;91(2):508-17.
2006: Rachel Kolodny; Donald Petrey; Barry Honig
Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction.
Current opinion in structural biology 2006;16(3):393-8.
2006: Murad Nayal; Barry Honig
On the nature of cavities on protein surfaces: application to the identification of drug-binding sites.
Proteins 2006;63(4):892-906.
2006: Christopher O Ortiz; John F Etchberger; Shoshana Posy; Christian Frøkjaer-Jensen; Shawn R Lockery; Barry Honig; Oliver Hobert
Searching for neuronal left/right asymmetry: genomewide analysis of nematode receptor-type guanylyl cyclases.
Genetics 2006;173(1):131-49.
2006: Saurabh D Patel; Carlo Ciatto; Chien Peter Chen; Fabiana Bahna; Manisha Rajebhosale; Natalie Arkus; Ira Schieren; Thomas M Jessell; Barry Honig; Stephen R Price; Lawrence Shapiro
Type II cadherin ectodomain structures: implications for classical cadherin specificity.
Cell 2006;124(6):1255-68.
2005: Donald Petrey; Barry Honig
Protein structure prediction: inroads to biology.
Molecular cell 2005;20(6):811-9.
2005: Robert Powers; Nebojsa Mirkovic; Sharon Goldsmith-Fischman; Thomas B Acton; Yiwen Chiang; Yuanpeng J Huang; LiChung Ma; PK Rajan; John R Cort; Michael A Kennedy; Jinfeng Liu; Burkhard Rost; Barry Honig; Diana Murray; Gaetano T Montelione
Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes.
Protein science : a publication of the Protein Society 2005;14(11):2849-61.
2005: Lucy R Forrest; Barry Honig
An assessment of the accuracy of methods for predicting hydrogen positions in protein structures.
Proteins 2005;61(2):296-309.
2005: Trevor W Siggers; Tonya Silkov; Barry Honig
Bending in the right direction.
Structure (London, England : 1993) 2005;13(10):1400-1.
2005: Chien Peter Chen; Shoshana Posy; Avinoam Ben-Shaul; Lawrence Shapiro; Barry Honig
Specificity of cell-cell adhesion by classical cadherins: Critical role for low-affinity dimerization through beta-strand swapping.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(24):8531-6.
2005: Jill Wildonger; Alona Sosinsky; Barry Honig; Richard S Mann
Lozenge directly activates argos and klumpfuss to regulate programmed cell death.
Genes & development 2005;19(9):1034-9.
2005: Jiang Zhu; Emil Alexov; Barry Honig
Comparative study of generalized born models: Born radii and peptide folding.
The journal of physical chemistry. B 2005;109(7):3008-22.
2005: Yang Shen; Sharon Goldsmith-Fischman; Hanudatta S Atreya; Thomas B Acton; LiChung Ma; Rong Xiao; Barry Honig; Gaetano T Montelione; Thomas Szyperski
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.
Proteins 2005;58(3):747-50.
2005: Trevor W Siggers; Antonina Silkov; Barry Honig
Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.
Journal of molecular biology 2005;345(5):1027-45.
2004: Marina Gimpelev; Lucy R Forrest; Diana Murray; Barry Honig
Helical packing patterns in membrane and soluble proteins.
Biophysical journal 2004;87(6):4075-86.
2004: Theresa A Ramelot; John R Cort; Sharon Goldsmith-Fischman; Gregory J Kornhaber; Rong Xiao; Ritu Shastry; Thomas B Acton; Barry Honig; Gaetano T Montelione; Michael A Kennedy
Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site.
Journal of molecular biology 2004;344(2):567-83.
2004: Sharon Goldsmith-Fischman; Alexandre Kuzin; William C Edstrom; Jordi Benach; Ritu Shastry; Rong Xiao; Thomas B Acton; Barry Honig; Gaetano T Montelione; John F Hunt
The SufE sulfur-acceptor protein contains a conserved core structure that mediates interdomain interactions in a variety of redox protein complexes.
Journal of molecular biology 2004;344(2):549-65.
2004: Gaohua Liu; Dinesh K Sukumaran; Duanxiang Xu; Yiwen Chiang; Thomas B Acton; Sharon Goldsmith-Fischman; Barry Honig; Gaetano T Montelione; Thomas Szyperski
NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis reveals a distinct 5-helix bundle.
Proteins 2004;55(3):756-8.
2004: Matthew P Jacobson; David L Pincus; Chaya S Rapp; Tyler J F Day; Barry Honig; David E Shaw; Richard A Friesner
A hierarchical approach to all-atom protein loop prediction.
Proteins 2004;55(2):351-67.
2004: Duanxiang Xu; Gaohua Liu; Rong Xiao; Thomas B Acton; Sharon Goldsmith-Fischman; Barry Honig; Gaetano T Montelione; Thomas Szyperski
NMR structure of the hypothetical protein AQ-1857 encoded by the Y157 gene from Aquifex aeolicus reveals a novel protein fold.
Proteins 2004;54(4):794-6.
2003: Christopher L Tang; Lei Xie; Ingrid Y Y Koh; Shoshana Posy; Emil Alexov; Barry Honig
On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles.
Journal of molecular biology 2003;334(5):1043-62.
2003: Felix B Sheinerman; Bissan Al-Lazikani; Barry Honig
Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains.
Journal of molecular biology 2003;334(4):823-41.
2003: Saurabh D Patel; Chien Peter Chen; Fabiana Bahna; Barry Honig; Lawrence Shapiro
Cadherin-mediated cell-cell adhesion: sticking together as a family.
Current opinion in structural biology 2003;13(6):690-8.
2003: James M Aramini; Yuanpeng J Huang; John R Cort; Sharon Goldsmith-Fischman; Rong Xiao; Liang-Yu Shih; Chi K Ho; Jinfeng Liu; Burkhard Rost; Barry Honig; Michael A Kennedy; Thomas B Acton; Gaetano T Montelione
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii.
Protein science : a publication of the Protein Society 2003;12(12):2823-30.
2003: Sharon Goldsmith-Fischman; Barry Honig
Structural genomics: computational methods for structure analysis.
Protein science : a publication of the Protein Society 2003;12(9):1813-21.
2003: Xiao Tao; Reza Khayat; Dinesh Christendat; Alexei Savchenko; Xiaohui Xu; Sharon Goldsmith-Fischman; Barry Honig; Aled Edwards; Cheryl H Arrowsmith; Liang Tong
Crystal structures of MTH1187 and its yeast ortholog YBL001c.
Proteins 2003;52(3):478-80.
2003: Theresa A Ramelot; Shuisong Ni; Sharon Goldsmith-Fischman; John R Cort; Barry Honig; Michael A Kennedy
Solution structure of Vibrio cholerae protein VC0424: a variation of the ferredoxin-like fold.
Protein science : a publication of the Protein Society 2003;12(7):1556-61.
2003: Alona Sosinsky; Christopher P Bonin; Richard S Mann; Barry Honig
Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors.
Nucleic acids research 2003;31(13):3589-92.
2003: Donald Petrey; Barry Honig
GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences.
Methods in enzymology 2003;374():492-509.
2003: Donald Petrey; Zhexin Xiang; Christopher L Tang; Lei Xie; Marina Gimpelev; Therese Mitros; Cinque S Soto; Sharon Goldsmith-Fischman; Andrew Kernytsky; Avner Schlessinger; Ingrid Y Y Koh; Emil Alexov; Barry Honig
Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling.
Proteins 2003;53 Suppl 6():430-5.
2002: Matthew P Jacobson; Richard A Friesner; Zhexin Xiang; Barry Honig
On the role of the crystal environment in determining protein side-chain conformations.
Journal of molecular biology 2002;320(3):597-608.
2002: Zhexin Xiang; Cinque S Soto; Barry Honig
Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(11):7432-7.
2002: Felix B Sheinerman; Barry Honig
On the role of electrostatic interactions in the design of protein-protein interfaces.
Journal of molecular biology 2002;318(1):161-77.
2002: Walter Rocchia; Sundaram Sridharan; Anthony Nicholls; Emil Alexov; Alessandro Chiabrera; Barry Honig
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.
Journal of computational chemistry 2002;23(1):128-37.
2002: Diana Murray; Barry Honig
Electrostatic control of the membrane targeting of C2 domains.
Molecular cell 2002;9(1):145-54.
2001: Bissan Al-Lazikani; Felix B Sheinerman; Barry Honig
Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(26):14796-801.
2001: R Norel; Felix B Sheinerman; Donald Petrey; Barry Honig
Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis.
Protein science : a publication of the Protein Society 2001;10(11):2147-61.
2001: Zhexin Xiang; Barry Honig
Extending the accuracy limits of prediction for side-chain conformations.
Journal of molecular biology 2001;311(2):421-30.
2001: Bissan Al-Lazikani; J Jung; Z Xiang; Barry Honig
Protein structure prediction.
Current opinion in chemical biology 2001;5(1):51-6.
2000: Donald Petrey; Barry Honig
Free energy determinants of tertiary structure and the evaluation of protein models.
Protein science : a publication of the Protein Society 2000;9(11):2181-91.
2000: An-Suei Yang; Barry Honig
An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments.
Journal of molecular biology 2000;301(3):691-711.
2000: An-Suei Yang; Barry Honig
An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence.
Journal of molecular biology 2000;301(3):679-89.
2000: An-Suei Yang; Barry Honig
An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance.
Journal of molecular biology 2000;301(3):665-78.
2000: Felix B Sheinerman; R Norel; Barry Honig
Electrostatic aspects of protein-protein interactions.
Current opinion in structural biology 2000;10(2):153-9.
1999: Fabio Polticelli; P Ascenzi; M Bolognesi; Barry Honig
Structural determinants of trypsin affinity and specificity for cationic inhibitors.
Protein science : a publication of the Protein Society 1999;8(12):2621-9.
1999: K Chin; K A Sharp; Barry Honig; Anna Marie Pyle
Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function.
Nature structural biology 1999;6(11):1055-61.
1999: Barry Honig
Protein folding: from the levinthal paradox to structure prediction.
Journal of molecular biology 1999;293(2):283-93.
1999: L Xiao; Barry Honig
Electrostatic contributions to the stability of hyperthermophilic proteins.
Journal of molecular biology 1999;289(5):1435-44.
1999: M Nayal; B C Hitz; Barry Honig
GRASS: a server for the graphical representation and analysis of structures.
Protein science : a publication of the Protein Society 1999;8(3):676-9.
1999: An-Suei Yang; Barry Honig
Sequence to structure alignment in comparative modeling using PrISM.
Proteins 1999;Suppl 3():66-72.
1998: Vinod K Misra; J L Hecht; An-Suei Yang; Barry Honig
Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA.
Biophysical journal 1998;75(5):2262-73.
1997: N Ben-Tal; Barry Honig; C Miller; S McLaughlin
Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles.
Biophysical journal 1997;73(4):1717-27.
1997: Nicolas FROLOFF; A Windemuth; Barry Honig
On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions.
Protein science : a publication of the Protein Society 1997;6(6):1293-301.
1997: Barry Honig
New challenges in computational biochemistry.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1997;():21-4.
1996: N Ben-Tal; Barry Honig
Helix-helix interactions in lipid bilayers.
Biophysical journal 1996;71(6):3046-50.
1996: R V Sampogna; Barry Honig
Electrostatic coupling between retinal isomerization and the ionization state of Glu-204: a general mechanism for proton release in bacteriorhodopsin.
Biophysical journal 1996;71(3):1165-71.
1996: N Ben-Tal; Barry Honig; Robert Peitzsch; G Denisov; Stuart McLaughlin
Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results.
Biophysical journal 1996;71(2):561-75.
1996: A Ben-Shaul; N Ben-Tal; Barry Honig
Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes.
Biophysical journal 1996;71(1):130-7.
1996: An-Suei Yang; B Hitz; Barry Honig
Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding.
Journal of molecular biology 1996;259(4):873-82.
1996: Roy Lancaster; Hartmut Michel; Barry Honig; M R Gunner
Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis.
Biophysical journal 1996;70(6):2469-92.
1996: N Ben-Tal; A Ben-Shaul; A Nicholls; Barry Honig
Free-energy determinants of alpha-helix insertion into lipid bilayers.
Biophysical journal 1996;70(4):1803-12.
1996: Vinod K Misra; Barry Honig
The electrostatic contribution to the B to Z transition of DNA.
Biochemistry 1996;35(4):1115-24.
1995: R A Friedman; Barry Honig
A free energy analysis of nucleic acid base stacking in aqueous solution.
Biophysical journal 1995;69(4):1528-35.
1995: An-Suei Yang; Barry Honig
Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets.
Journal of molecular biology 1995;252(3):366-76.
1995: An-Suei Yang; Barry Honig
Free energy determinants of secondary structure formation: I. alpha-Helices.
Journal of molecular biology 1995;252(3):351-65.
1995: Kim A Sharp; R A Friedman; Vinod K Misra; J Hecht; Barry Honig
Salt effects on polyelectrolyte-ligand binding: comparison of Poisson-Boltzmann, and limiting law/counterion binding models.
Biopolymers 1995;36(2):245-62.
1995: Kim A Sharp; Barry Honig
Salt effects on nucleic acids.
Current opinion in structural biology 1995;5(3):323-8.
1995: Barry Honig; A Nicholls
Classical electrostatics in biology and chemistry.
Science (New York, N.Y.) 1995;268(5214):1144-9.
1995: Vinod K Misra; Barry Honig
On the magnitude of the electrostatic contribution to ligand-DNA interactions.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(10):4691-5.
1995: Barry Honig; An-Suei Yang
Free energy balance in protein folding.
Advances in protein chemistry 1995;46():27-58.
1994: D Sitkoff; D J Lockhart; Kim A Sharp; Barry Honig
Calculation of electrostatic effects at the amino terminus of an alpha helix.
Biophysical journal 1994;67(6):2251-60.
1994: D Sitkoff; Kim A Sharp; Barry Honig
Correlating solvation free energies and surface tensions of hydrocarbon solutes.
Biophysical chemistry 1994;51(2-3):397-403; discussion 404-9.
1994: A Monge; Richard A Friesner; Barry Honig
An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(11):5027-9.
1994: R V Sampogna; Barry Honig
Environmental effects on the protonation states of active site residues in bacteriorhodopsin.
Biophysical journal 1994;66(5):1341-52.
1994: Vinod K Misra; J L Hecht; Kim A Sharp; R A Friedman; Barry Honig
Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease.
Journal of molecular biology 1994;238(2):264-80.
1994: Vinod K Misra; Kim A Sharp; R A Friedman; Barry Honig
Salt effects on ligand-DNA binding. Minor groove binding antibiotics.
Journal of molecular biology 1994;238(2):245-63.
1994: An-Suei Yang; Barry Honig
Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin.
Journal of molecular biology 1994;237(5):602-14.
1994: K C Smith; Barry Honig
Evaluation of the conformational free energies of loops in proteins.
Proteins 1994;18(2):119-32.
1993: An-Suei Yang; Barry Honig
On the pH dependence of protein stability.
Journal of molecular biology 1993;231(2):459-74.
1993: An-Suei Yang; M R Gunner; R Sampogna; K Sharp; Barry Honig
On the calculation of pKas in proteins.
Proteins 1993;15(3):252-65.
1992: An-Suei Yang; Kim A Sharp; Barry Honig
Analysis of the heat capacity dependence of protein folding.
Journal of molecular biology 1992;227(3):889-900.
1992: M E McGrath; J R Vásquez; Charles S Craik; An-Suei Yang; Barry Honig; Robert J Fletterick
Perturbing the polar environment of Asp102 in trypsin: consequences of replacing conserved Ser214.
Biochemistry 1992;31(12):3059-64.
1992: R A Friedman; Barry Honig
The electrostatic contribution to DNA base-stacking interactions.
Biopolymers 1992;32(2):145-59.
1991: M R Gunner; Barry Honig
Electrostatic control of midpoint potentials in the cytochrome subunit of the Rhodopseudomonas viridis reaction center.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(20):9151-5.
1991: Kim A Sharp; A Nicholls; R Friedman; Barry Honig
Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models.
Biochemistry 1991;30(40):9686-97.
1991: Kim A Sharp; A Nicholls; R F Fine; Barry Honig
Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects.
Science (New York, N.Y.) 1991;252(5002):106-9.
1991: Michael K Gilson; Barry Honig
The inclusion of electrostatic hydration energies in molecular mechanics calculations.
Journal of computer-aided molecular design 1991;5(1):5-20.
1991: A Nicholls; Kim A Sharp; Barry Honig
Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.
Proteins 1991;11(4):281-96.
1990: Kim A Sharp; Barry Honig; Stephen C Harvey
Electrical potential of transfer RNAs: codon-anticodon recognition.
Biochemistry 1990;29(2):340-6.
1990: Kim A Sharp; Barry Honig
Electrostatic interactions in macromolecules: theory and applications.
Annual review of biophysics and biophysical chemistry 1990;19():301-32.
1989: K Soman; An-Suei Yang; Barry Honig; Robert J Fletterick
Electrical potentials in trypsin isozymes.
Biochemistry 1989;28(26):9918-26.
1989: B Jayaram; Kim A Sharp; Barry Honig
The electrostatic potential of B-DNA.
Biopolymers 1989;28(5):975-93.
1989: Michael K Gilson; Barry Honig
Destabilization of an alpha-helix-bundle protein by helix dipoles.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(5):1524-8.
1989: Barry Honig; K Sharp; Michael K Gilson
Electrostatic interactions in proteins.
Progress in clinical and biological research 1989;289():65-74.
1988: H S Gilson; Barry Honig; A Croteau; G Zarrilli; K Nakanishi
Analysis of the factors that influence the C=N stretching frequency of polyene Schiff bases. Implications for bacteriorhodopsin and rhodopsin.
Biophysical journal 1988;53(2):261-9.
1988: Michael K Gilson; Barry Honig
Energetics of charge-charge interactions in proteins.
Proteins 1988;3(1):32-52.
1988: Michael K Gilson; Barry Honig
Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis.
Proteins 1988;4(1):7-18.
1987: Michael K Gilson; Barry Honig
Calculation of electrostatic potentials in an enzyme active site.
Nature 1987;330(6143):84-6.
1987: K Sharp; R Fine; Barry Honig
Computer simulations of the diffusion of a substrate to an active site of an enzyme.
Science (New York, N.Y.) 1987;236(4807):1460-3.
1986: Michael K Gilson; Barry Honig
The dielectric constant of a folded protein.
Biopolymers 1986;25(11):2097-119.
1986: I Klapper; R Hagstrom; R Fine; K Sharp; Barry Honig
Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification.
Proteins 1986;1(1):47-59.
1986: A A Rashin; M Iofin; Barry Honig
Internal cavities and buried waters in globular proteins.
Biochemistry 1986;25(12):3619-25.
1985: Michael K Gilson; A Rashin; R Fine; Barry Honig
On the calculation of electrostatic interactions in proteins.
Journal of molecular biology 1985;184(3):503-16.
1984: A A Rashin; Barry Honig
On the environment of ionizable groups in globular proteins.
Journal of molecular biology 1984;173(4):515-21.
1983: J Eccles; Barry Honig
Charged amino acids as spectroscopic determinants for chlorophyll in vivo.
Proceedings of the National Academy of Sciences of the United States of America 1983;80(16):4959-62.