Barry H. Honig - Publications

Affiliations: 
Biochemistry and Molecular Biophysics Columbia University, New York, NY 
Area:
computational biophysics and bioinformatics
Website:
http://cpmcnet.columbia.edu/dept/gsas/biochem/faculty/honig.html

284 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Boni N, Shapiro L, Honig B, Wu Y, Rubinstein R. On the formation of ordered protein assemblies in cell-cell interfaces. Proceedings of the National Academy of Sciences of the United States of America. 119: e2206175119. PMID 35969779 DOI: 10.1073/pnas.2206175119  0.67
2022 Xu S, Sergeeva AP, Katsamba PS, Mannepalli S, Bahna F, Bimela J, Zipursky SL, Shapiro L, Honig B, Zinn K. Affinity requirements for control of synaptic targeting and neuronal cell survival by heterophilic IgSF cell adhesion molecules. Cell Reports. 39: 110618. PMID 35385751 DOI: 10.1016/j.celrep.2022.110618  0.714
2022 Goodman KM, Katsamba PS, Rubinstein R, Ahlsén G, Bahna F, Mannepalli S, Dan H, Sampogna RV, Shapiro L, Honig B. How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition. Elife. 11. PMID 35253643 DOI: 10.7554/eLife.72416  0.512
2021 Blockus H, Rolotti SV, Szoboszlay M, Peze-Heidsieck E, Ming T, Schroeder A, Apostolo N, Vennekens KM, Katsamba PS, Bahna F, Mannepalli S, Ahlsen G, Honig B, Shapiro L, de Wit J, et al. Synaptogenic activity of the axon guidance molecule Robo2 underlies hippocampal circuit function. Cell Reports. 37: 109828. PMID 34686348 DOI: 10.1016/j.celrep.2021.109828  0.439
2021 Troyanovsky RB, Sergeeva AP, Indra I, Chen CS, Kato R, Shapiro L, Honig B, Troyanovsky SM. Sorting of cadherin-catenin-associated proteins into individual clusters. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34272290 DOI: 10.1073/pnas.2105550118  0.699
2021 Koss H, Honig B, Shapiro L, Palmer AG. Dimerization of Cadherin-11 involves multi-site coupled unfolding and strand swapping. Structure (London, England : 1993). PMID 34166612 DOI: 10.1016/j.str.2021.06.006  0.485
2021 Murray D, Petrey D, Honig B. Integrating 3D structural information into systems biology. The Journal of Biological Chemistry. 100562. PMID 33744294 DOI: 10.1016/j.jbc.2021.100562  0.706
2020 Broyde J, Simpson DR, Murray D, Paull EO, Chu BW, Tagore S, Jones SJ, Griffin AT, Giorgi FM, Lachmann A, Jackson P, Sweet-Cordero EA, Honig B, Califano A. Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. Nature Biotechnology. PMID 32929263 DOI: 10.1038/S41587-020-0652-7  0.37
2020 Ganapathi M, Argyriou L, Martínez-Azorín F, Morlot S, Yigit G, Lee TM, Auber B, von Gise A, Petrey DS, Thiele H, Cyganek L, Sabater-Molina M, Ahimaz P, Cabezas-Herrera J, Sorlí-García M, ... ... Honig B, et al. Bi-allelic missense disease-causing variants in RPL3L associate neonatal dilated cardiomyopathy with muscle-specific ribosome biogenesis. Human Genetics. PMID 32514796 DOI: 10.1007/S00439-020-02188-6  0.71
2020 Honig B, Shapiro L. Adhesion Protein Structure, Molecular Affinities, and Principles of Cell-Cell Recognition Cell. 181: 520-535. PMID 32359436 DOI: 10.1016/J.Cell.2020.04.010  0.593
2020 Sergeeva AP, Katsamba PS, Cosmanescu F, Brewer JJ, Ahlsen G, Mannepalli S, Shapiro L, Honig B. DIP/Dpr interactions and the evolutionary design of specificity in protein families. Nature Communications. 11: 2125. PMID 32358559 DOI: 10.1038/S41467-020-15981-8  0.774
2020 Indra I, Troyanovsky RB, Shapiro L, Honig B, Troyanovsky SM. Sensing Actin Dynamics through Adherens Junctions. Cell Reports. 30: 2820-2833.e3. PMID 32101754 DOI: 10.1016/J.Celrep.2020.01.106  0.504
2020 Harrison OJ, Brasch J, Katsamba PS, Ahlsen G, Noble AJ, Dan H, Sampogna RV, Potter CS, Carragher B, Honig B, Shapiro L. Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered δ-Protocadherins. Cell Reports. 30: 2655-2671.e7. PMID 32101743 DOI: 10.1016/J.Celrep.2020.02.003  0.572
2019 Lasso G, Mayer SV, Winkelmann ER, Chu T, Elliot O, Patino-Galindo JA, Park K, Rabadan R, Honig B, Shapira SD. A Structure-Informed Atlas of Human-Virus Interactions. Cell. PMID 31474372 DOI: 10.1016/J.Cell.2019.08.005  0.316
2019 Generous AR, Harrison OJ, Troyanovsky RB, Mateo M, Navaratnarajah CK, Donohue RC, Pfaller CK, Alekhina O, Sergeeva AP, Indra I, Thornburg T, Kochetkova I, Billadeau DD, Taylor MP, Troyanovsky SM, ... Honig B, et al. Trans-endocytosis elicited by nectins transfers cytoplasmic cargo including infectious material between cells. Journal of Cell Science. PMID 31331966 DOI: 10.1242/Jcs.235507  0.723
2019 Brasch J, Goodman KM, Noble AJ, Rapp M, Mannepalli S, Bahna F, Dandey VP, Bepler T, Berger B, Maniatis T, Potter CS, Carragher B, Honig B, Shapiro L. Visualization of clustered protocadherin neuronal self-recognition complexes. Nature. PMID 30971825 DOI: 10.1038/s41586-019-1089-3  0.544
2018 Cosmanescu F, Katsamba PS, Sergeeva AP, Ahlsen G, Patel SD, Brewer JJ, Tan L, Xu S, Xiao Q, Nagarkar-Jaiswal S, Nern A, Bellen HJ, Zipursky SL, Honig B, Shapiro L. Neuron-Subtype-Specific Expression, Interaction Affinities, and Specificity Determinants of DIP/Dpr Cell Recognition Proteins. Neuron. PMID 30467080 DOI: 10.1016/J.Neuron.2018.10.046  0.756
2018 Xu S, Xiao Q, Cosmanescu F, Sergeeva AP, Yoo J, Lin Y, Katsamba PS, Ahlsen G, Kaufman J, Linaval NT, Lee PT, Bellen HJ, Shapiro L, Honig B, Tan L, et al. Interactions between the Ig-Superfamily Proteins DIP-α and Dpr6/10 Regulate Assembly of Neural Circuits. Neuron. PMID 30467079 DOI: 10.1016/J.Neuron.2018.11.001  0.755
2018 Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG, Shapiro L, Honig B, Mann RS. Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites. Cell Reports. 24: 2221-2230. PMID 30157419 DOI: 10.1016/J.Celrep.2018.07.100  0.567
2018 Dionne G, Qiu X, Rapp M, Liang X, Zhao B, Peng G, Katsamba PS, Ahlsen G, Rubinstein R, Potter CS, Carragher B, Honig B, Müller U, Shapiro L. Mechanotransduction by PCDH15 Relies on a Novel cis-Dimeric Architecture. Neuron. PMID 30057206 DOI: 10.1016/J.Neuron.2018.07.006  0.556
2018 Brasch J, Katsamba PS, Harrison OJ, Ahlsén G, Troyanovsky RB, Indra I, Kaczynska A, Kaeser B, Troyanovsky S, Honig B, Shapiro L. Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior. Cell Reports. 23: 1840-1852. PMID 29742438 DOI: 10.1016/J.Celrep.2018.04.012  0.584
2018 Indra I, Choi J, Chen CS, Troyanovsky RB, Shapiro L, Honig B, Troyanovsky SM. Spatial and temporal organization of cadherin in punctate adherens junctions. Proceedings of the National Academy of Sciences of the United States of America. PMID 29691319 DOI: 10.1073/Pnas.1720826115  0.525
2018 Evangelista F, Roth AJ, Prisayanh P, Temple BR, Li N, Qian Y, Culton DA, Liu Z, Harrison OJ, Brasch J, Honig B, Shapiro L, Diaz LA. Pathogenic IgG4 autoantibodies from endemic pemphigus foliaceus recognize a desmoglein-1 conformational epitope. Journal of Autoimmunity. PMID 29307589 DOI: 10.1016/J.Jaut.2017.12.017  0.566
2018 Cosmanescu F, Katsamba PS, Sergeeva AP, Ahlsen G, Patel SD, Brewer JJ, Tan L, Xu S, Xiao Q, Nagarkar-Jaiswal S, Bellen H, Zipursky SL, Honig B, Shapiro L. Quantitative interactome for DIP/Dpr Immunoglubin Superfamily Cell Recognition Proteins Neuron. DOI: 10.2210/Pdb6Efy/Pdb  0.745
2018 Murray D, Begum KN, Califano A, Honig B. Abstract 3300: Network analysis of the human protein-protein interactome: Tumorigenic signaling mechanisms Cancer Research. 78: 3300-3300. DOI: 10.1158/1538-7445.Am2018-3300  0.399
2018 Prisayanh P, Evangelista F, Roth A, Temple B, Li N, Qian Y, Culton D, Liu Z, Harrison O, Brasch J, Honig B, Shapiro L, Diaz L. 039 Pathogenic IgG4 anti-Dsg1 autoantibodies from endemic pemphigus foliaceus inhibit the heterophilic Dsg1/Dsc1 adhesive interactions Journal of Investigative Dermatology. 138: S7. DOI: 10.1016/J.Jid.2018.03.043  0.501
2018 Cosmanescu F, Katsamba PS, Sergeeva AP, Ahlsen G, Patel S, Brewer J, Tan L, Xu S, Xiao Q, Zipursky SL, Honig B, Shapiro L. Family-Wide Biophysical Analysis of Dpr-DIP Interactions Biophysical Journal. 114: 154a. DOI: 10.1016/J.Bpj.2017.11.865  0.715
2017 Hwang H, Dey F, Petrey D, Honig B. Structure-based prediction of ligand-protein interactions on a genome-wide scale. Proceedings of the National Academy of Sciences of the United States of America. PMID 29229851 DOI: 10.1073/Pnas.1705381114  0.753
2017 Goodman KM, Rubinstein R, Dan H, Bahna F, Mannepalli S, Ahlsén G, Aye Thu C, Sampogna RV, Maniatis T, Honig B, Shapiro L. Protocadherin cis-dimer architecture and recognition unit diversity. Proceedings of the National Academy of Sciences of the United States of America. PMID 29087338 DOI: 10.1073/Pnas.1713449114  0.569
2017 Chiu TP, Rao S, Mann RS, Honig B, Rohs R. Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding. Nucleic Acids Research. PMID 29040720 DOI: 10.1093/Nar/Gkx915  0.405
2017 Larsen ISB, Narimatsu Y, Joshi HJ, Siukstaite L, Harrison OJ, Brasch J, Goodman KM, Hansen L, Shapiro L, Honig B, Vakhrushev SY, Clausen H, Halim A. Discovery of an O-mannosylation pathway selectively serving cadherins and protocadherins. Proceedings of the National Academy of Sciences of the United States of America. PMID 28973932 DOI: 10.1073/Pnas.1708319114  0.493
2017 Bao W, Yuan CA, Zhang Y, Han K, Nandi AK, Honig B, Huang DS. Mutli-features Predction of Protein Translational Modification Sites. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 28961121 DOI: 10.1109/Tcbb.2017.2752703  0.358
2017 Rubinstein R, Goodman KM, Maniatis T, Shapiro L, Honig B. Structural origins of clustered protocadherin-mediated neuronal barcoding. Seminars in Cell & Developmental Biology. PMID 28743640 DOI: 10.1016/J.Semcdb.2017.07.023  0.539
2017 Larsen ISB, Narimatsu Y, Joshi HJ, Yang Z, Harrison OJ, Brasch J, Shapiro L, Honig B, Vakhrushev SY, Clausen H, Halim A. Mammalian O-mannosylation of Cadherins and Plexins is Independent of Protein O-mannosyltransferase 1 and 2. The Journal of Biological Chemistry. PMID 28512129 DOI: 10.1074/Jbc.M117.794487  0.506
2017 Lopez-Rivera E, Liu YP, Verbitsky M, Anderson BR, Capone VP, Otto EA, Yan Z, Mitrotti A, Martino J, Steers NJ, Fasel DA, Vukojevic K, Deng R, Racedo SE, Liu Q, ... ... Honig B, et al. Genetic Drivers of Kidney Defects in the DiGeorge Syndrome. The New England Journal of Medicine. PMID 28121514 DOI: 10.1056/Nejmoa1609009  0.665
2017 Broyde J, Simpson D, Murray D, Lachmann A, Giorgi FM, Honig B, Sweet-Cordero AE, Califano A. Abstract LB-289: Computational detection of oncogene‐centric pathway members Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Lb-289  0.318
2017 Goodman KM, Rubinstein R, Brasch J, Thu CA, Bahna F, Mannepalli S, Dan H, Sampogna RV, Maniatis T, Honig B, Shapiro L. Clustered protocadherin molecular assembly and implications for neuronal self-avoidance Acta Crystallographica Section a Foundations and Advances. 73: a50-a50. DOI: 10.1107/S0108767317099500  0.485
2016 Clark AJ, Gindin T, Zhang B, Wang L, Abel R, Murret CS, Xu F, Bao A, Lu NJ, Zhou T, Kwong PD, Shapiro L, Honig B, Friesner RA. Free Energy Perturbation Calculation of Relative Binding Free energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1. Journal of Molecular Biology. PMID 27908641 DOI: 10.1016/J.Jmb.2016.11.021  0.659
2016 Goodman KM, Rubinstein R, Thu CA, Mannepalli S, Bahna F, Ahlsén G, Rittenhouse C, Maniatis T, Honig B, Shapiro L. γ-Protocadherin structural diversity and functional implications. Elife. 5. PMID 27782885 DOI: 10.7554/Elife.20930  0.578
2016 Garzón JI, Deng L, Murray D, Shapira S, Petrey D, Honig B. A computational interactome and functional annotation for the human proteome. Elife. 5. PMID 27770567 DOI: 10.7554/Elife.18715  0.737
2016 Goodman KM, Yamagata M, Jin X, Mannepalli S, Katsamba PS, Ahlsén G, Sergeeva AP, Honig B, Sanes JR, Shapiro L. Molecular basis of sidekick-mediated cell-cell adhesion and specificity. Elife. 5. PMID 27644106 DOI: 10.7554/Elife.19058  0.759
2016 Wang D, Kon N, Lasso G, Jiang L, Leng W, Zhu WG, Qin J, Honig B, Gu W. Acetylation-regulated interaction between p53 and SET reveals a widespread regulatory mode. Nature. PMID 27626385 DOI: 10.1038/Nature19759  0.322
2016 Sheng R, Jung DJ, Silkov A, Kim H, Singaram I, Wang ZG, Xin Y, Kim E, Park MJ, Thiagarajan-Rosenkranz P, Smrt S, Honig B, Beak K, Ryu S, Lorieau J, et al. Lipids regulate Lck activity through their interactions with the Lck SH2 domain. The Journal of Biological Chemistry. PMID 27334919 DOI: 10.1074/Jbc.M116.720284  0.332
2016 Harrison OJ, Brasch J, Lasso G, Katsamba PS, Ahlsen G, Honig B, Shapiro L. Structural basis of adhesive binding by desmocollins and desmogleins. Proceedings of the National Academy of Sciences of the United States of America. PMID 27298358 DOI: 10.1073/Pnas.1606272113  0.594
2016 Goodman KM, Rubinstein R, Thu CA, Bahna F, Mannepalli S, Ahlsén G, Rittenhouse C, Maniatis T, Honig B, Shapiro L. Structural Basis of Diverse Homophilic Recognition by Clustered α- and β-Protocadherins. Neuron. PMID 27161523 DOI: 10.1016/J.Neuron.2016.04.004  0.575
2016 Park MJ, Sheng R, Silkov A, Jung DJ, Wang ZG, Xin Y, Kim H, Thiagarajan-Rosenkranz P, Song S, Yoon Y, Nam W, Kim I, Kim E, Lee DG, Chen Y, ... ... Honig B, et al. SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins. Molecular Cell. PMID 27052731 DOI: 10.1016/J.Molcel.2016.01.027  0.358
2016 Goodman KM, Rubinstein R, Thu CA, Mannepalli S, Bahna F, Ahlsén G, Rittenhouse C, Maniatis T, Honig B, Shapiro L. Author response: γ-Protocadherin structural diversity and functional implications Elife. DOI: 10.7554/Elife.20930.064  0.527
2016 Goodman KM, Yamagata M, Jin X, Mannepalli S, Katsamba PS, Ahlsén G, Sergeeva AP, Honig B, Sanes JR, Shapiro L. Author response: Molecular basis of sidekick-mediated cell-cell adhesion and specificity Elife. DOI: 10.7554/Elife.19058.021  0.716
2016 Garzón JI, Deng L, Murray D, Shapira S, Petrey D, Honig B. Author response: A computational interactome and functional annotation for the human proteome Elife. DOI: 10.7554/Elife.18715.074  0.667
2015 Rubinstein R, Thu CA, Goodman KM, Wolcott HN, Bahna F, Mannepalli S, Ahlsen G, Chevee M, Halim A, Clausen H, Maniatis T, Shapiro L, Honig B. Molecular Logic of Neuronal Self-Recognition through Protocadherin Domain Interactions. Cell. 163: 629-42. PMID 26478182 DOI: 10.1016/J.Cell.2015.09.026  0.585
2015 Biswas KH, Hartman KL, Yu CH, Harrison OJ, Song H, Smith AW, Huang WY, Lin WC, Guo Z, Padmanabhan A, Troyanovsky SM, Dustin ML, Shapiro L, Honig B, Zaidel-Bar R, et al. E-cadherin junction formation involves an active kinetic nucleation process. Proceedings of the National Academy of Sciences of the United States of America. 112: 10932-7. PMID 26290581 DOI: 10.1073/Pnas.1513775112  0.54
2015 Chen CS, Hong S, Indra I, Sergeeva AP, Troyanovsky RB, Shapiro L, Honig B, Troyanovsky SM. α-Catenin-mediated cadherin clustering couples cadherin and actin dynamics. The Journal of Cell Biology. PMID 26261181 DOI: 10.1083/Jcb.201412064  0.729
2015 Hwang H, Petrey D, Honig B. A hybrid method for protein-protein interface prediction. Protein Science : a Publication of the Protein Society. PMID 26178156 DOI: 10.1002/Pro.2744  0.757
2015 Chen TS, Petrey D, Garzon JI, Honig B. Predicting peptide-mediated interactions on a genome-wide scale. Plos Computational Biology. 11: e1004248. PMID 25938916 DOI: 10.1371/Journal.Pcbi.1004248  0.746
2015 Petrey D, Chen TS, Deng L, Garzon JI, Hwang H, Lasso G, Lee H, Silkov A, Honig B. Template-based prediction of protein function. Current Opinion in Structural Biology. 32: 33-8. PMID 25678152 DOI: 10.1016/J.Sbi.2015.01.007  0.746
2015 Broyde J, Simpson D, Wah DA, Giorgi FM, Petrey D, Alvarez MJ, Silkov A, Lachmann A, Hill DE, Vidal M, Jackson P, Honig B, Sweet-Cordero A, Califano A. Abstract PR13: Systems and structural biology approaches to elucidate new effectors in KRAS mutant tumors Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Pr13  0.715
2014 Vendome J, Felsovalyi K, Song H, Yang Z, Jin X, Brasch J, Harrison OJ, Ahlsen G, Bahna F, Kaczynska A, Katsamba PS, Edmond D, Hubbell WL, Shapiro L, Honig B. Structural and energetic determinants of adhesive binding specificity in type I cadherins. Proceedings of the National Academy of Sciences of the United States of America. 111: E4175-84. PMID 25253890 DOI: 10.1073/Pnas.1416737111  0.604
2014 Kim DH, Park MJ, Gwon GH, Silkov A, Xu ZY, Yang EC, Song S, Song K, Kim Y, Yoon HS, Honig B, Cho W, Cho Y, Hwang I. An ankyrin repeat domain of AKR2 drives chloroplast targeting through coincident binding of two chloroplast lipids. Developmental Cell. 30: 598-609. PMID 25203210 DOI: 10.1016/J.Devcel.2014.07.026  0.391
2014 Thu CA, Chen WV, Rubinstein R, Chevee M, Wolcott HN, Felsovalyi KO, Tapia JC, Shapiro L, Honig B, Maniatis T. Single-cell identity generated by combinatorial homophilic interactions between α, β, and γ protocadherins. Cell. 158: 1045-59. PMID 25171406 DOI: 10.1016/J.Cell.2014.07.012  0.58
2014 Petrey D, Honig B. Structural bioinformatics of the interactome Annual Review of Biophysics. 43: 193-210. PMID 24895853 DOI: 10.1146/Annurev-Biophys-051013-022726  0.712
2014 Shazman S, Lee H, Socol Y, Mann RS, Honig B. OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Nucleic Acids Research. 42: D167-71. PMID 24271386 DOI: 10.1093/Nar/Gkt1165  0.336
2014 Wah DA, Giorgi FM, Petrey D, Alvarez MJ, Silkov T, Broyde J, Rieckhof GE, Honig B, Califano A. Abstract PR09: A systems biology approach to elucidate novel drug targets in KRAS mutant tumors Molecular Cancer Research. 12. DOI: 10.1158/1557-3125.Rasonc14-Pr09  0.682
2014 Song H, Yang Z, Felsovalyi K, Hubbell W, Shapiro L, Honig B. Structural and Energetic Determinants of Adhesive Binding Specificity in Type I Cadherins: The Role of Multiple Conformations in Tuning Affinities Biophysical Journal. 106: 464a. DOI: 10.1016/J.Bpj.2013.11.2628  0.612
2013 Li Y, Altorelli NL, Bahna F, Honig B, Shapiro L, Palmer AG. Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion. Proceedings of the National Academy of Sciences of the United States of America. 110: 16462-7. PMID 24067646 DOI: 10.1073/Pnas.1314303110  0.569
2013 Wu Y, Honig B, Ben-Shaul A. Theory and simulations of adhesion receptor dimerization on membrane surfaces. Biophysical Journal. 104: 1221-9. PMID 23528081 DOI: 10.1016/J.Bpj.2013.02.009  0.521
2013 Dey F, Zhang QC, Petrey D, Honig B. Toward a "structural BLAST": Using structural relationships to infer function Protein Science. 22: 359-366. PMID 23349097 DOI: 10.1002/Pro.2225  0.803
2013 Zhang QC, Petrey D, Garzón JI, Deng L, Honig B. PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Research. 41: D828-33. PMID 23193263 DOI: 10.1093/Nar/Gks1231  0.792
2013 Shazman S, Chen J, Lee H, Liu P, Mann R, Honig B. 75 OnTheFly database – structural basis to study TF’s DNA-binding specificity Journal of Biomolecular Structure and Dynamics. 31: 48-49. DOI: 10.1080/07391102.2013.786509  0.377
2013 Zhang QC, Petrey D, Honig B. 180 Integrating structural and systems biology: structure-based prediction of protein–protein interactions on a genome-wide scale Journal of Biomolecular Structure and Dynamics. 31: 116-116. DOI: 10.1080/07391102.2013.786422  0.796
2013 Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Correction: Corrigendum: Structure-based prediction of protein–protein interactions on a genome-wide scale Nature. 495: 127-127. DOI: 10.1038/Nature11977  0.762
2012 Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. 490: 556-60. PMID 23023127 DOI: 10.1038/Nature11503  0.8
2012 Harrison OJ, Vendome J, Brasch J, Jin X, Hong S, Katsamba PS, Ahlsen G, Troyanovsky RB, Troyanovsky SM, Honig B, Shapiro L. Nectin ectodomain structures reveal a canonical adhesive interface. Nature Structural & Molecular Biology. 19: 906-15. PMID 22902367 DOI: 10.1038/Nsmb.2366  0.613
2012 Brasch J, Harrison OJ, Honig B, Shapiro L. Thinking outside the cell: how cadherins drive adhesion. Trends in Cell Biology. 22: 299-310. PMID 22555008 DOI: 10.1016/J.Tcb.2012.03.004  0.567
2012 Chen Y, Sheng R, Källberg M, Silkov A, Tun MP, Bhardwaj N, Kurilova S, Hall RA, Honig B, Lu H, Cho W. Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions. Molecular Cell. 46: 226-37. PMID 22445486 DOI: 10.1016/J.Molcel.2012.02.012  0.376
2012 Eletsky A, Petrey D, Zhang QC, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Honig B, Montelione GT, Szyperski T. 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. 13: 1-7. PMID 22223187 DOI: 10.1007/S10969-011-9121-3  0.796
2012 Jin X, Walker MA, Felsövályi K, Vendome J, Bahna F, Mannepalli S, Cosmanescu F, Ahlsen G, Honig B, Shapiro L. 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. 109: E127-34. PMID 22171007 DOI: 10.1073/Pnas.1117538108  0.573
2012 Floratos A, Honig B, Pe'er D, Califano A. Using systems and structure biology tools to dissect cellular phenotypes. Journal of the American Medical Informatics Association : Jamia. 19: 171-5. PMID 22081223 DOI: 10.1136/Amiajnl-2011-000490  0.309
2011 Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell. 147: 1270-82. PMID 22153072 DOI: 10.1016/J.Cell.2011.10.053  0.409
2011 Kuziemko A, Honig B, Petrey D. Using structure to explore the sequence alignment space of remote homologs. Plos Computational Biology. 7: e1002175. PMID 21998567 DOI: 10.1371/Journal.Pcbi.1002175  0.776
2011 Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. Acs Chemical Biology. 6: 1314-20. PMID 21967305 DOI: 10.1021/Cb200155T  0.381
2011 Wu Y, Vendome J, Shapiro L, Ben-Shaul A, Honig B. Transforming binding affinities from three dimensions to two with application to cadherin clustering. Nature. 475: 510-3. PMID 21796210 DOI: 10.1038/Nature10183  0.685
2011 Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D. MarkUs: a server to navigate sequence-structure-function space. Nucleic Acids Research. 39: W357-61. PMID 21672961 DOI: 10.1093/Nar/Gkr468  0.774
2011 Zhu J, Yu Y, Ulbrich MH, Li MH, Isacoff EY, Honig B, Yang J. 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. 108: 10133-8. PMID 21642537 DOI: 10.1073/Pnas.1017669108  0.345
2011 Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Research. 39: W283-7. PMID 21609948 DOI: 10.1093/Nar/Gkr311  0.789
2011 Vendome J, Posy S, Jin X, Bahna F, Ahlsen G, Shapiro L, Honig B. Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins. Nature Structural & Molecular Biology. 18: 693-700. PMID 21572446 DOI: 10.1038/Nsmb.2051  0.793
2011 Harrison OJ, Jin X, Hong S, Bahna F, Ahlsen G, Brasch J, Wu Y, Vendome J, Felsovalyi K, Hampton CM, Troyanovsky RB, Ben-Shaul A, Frank J, Troyanovsky SM, Shapiro L, ... Honig B, et al. The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure (London, England : 1993). 19: 244-56. PMID 21300292 DOI: 10.1016/J.Str.2010.11.016  0.674
2011 Brasch J, Harrison OJ, Ahlsen G, Carnally SM, Henderson RM, Honig B, Shapiro L. Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin. Journal of Molecular Biology. 408: 57-73. PMID 21269602 DOI: 10.1016/J.Jmb.2011.01.031  0.576
2011 Zhu J, Yu Y, Ulbrich MH, Li M, Isacoff EY, Honig B, Yang J. A Structural Model of the TRPP2/PKD1 C-Terminal Coiled Coil Complex Obtained by a Combination of Computational and Experimental Approaches Biophysical Journal. 100: 106a. DOI: 10.1016/J.Bpj.2010.12.787  0.382
2011 Wu Y, Shapiro L, Ben-Shaul A, Honig B. Multiscale Simulation of Cadherin-Mediated Cell Adhesion Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.324  0.692
2010 Wu Y, Jin X, Harrison O, Shapiro L, Honig BH, Ben-Shaul A. Cooperativity between trans and cis interactions in cadherin-mediated junction formation. Proceedings of the National Academy of Sciences of the United States of America. 107: 17592-7. PMID 20876147 DOI: 10.1073/Pnas.1011247107  0.666
2010 Chen BY, Honig B. VASP: A volumetric analysis of surface properties yields insights into protein-ligand binding specificity Plos Computational Biology. 6. PMID 20814581 DOI: 10.1371/Journal.Pcbi.1000881  0.403
2010 Love J, Mancia F, Shapiro L, Punta M, Rost B, Girvin M, Wang DN, Zhou M, Hunt JF, Szyperski T, Gouaux E, MacKinnon R, McDermott A, Honig B, Inouye M, et al. The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins. Journal of Structural and Functional Genomics. 11: 191-9. PMID 20690043 DOI: 10.1007/S10969-010-9094-7  0.591
2010 Koehnke J, Katsamba PS, Ahlsen G, Bahna F, Vendome J, Honig B, Shapiro L, Jin X. Splice form dependence of beta-neurexin/neuroligin binding interactions. Neuron. 67: 61-74. PMID 20624592 DOI: 10.1016/J.Neuron.2010.06.001  0.517
2010 Zhang QC, Petrey D, Norel R, Honig BH. Protein interface conservation across structure space. Proceedings of the National Academy of Sciences of the United States of America. 107: 10896-901. PMID 20534496 DOI: 10.1073/Pnas.1005894107  0.8
2010 Norel R, Petrey D, Honig B. PUDGE: a flexible, interactive server for protein structure prediction. Nucleic Acids Research. 38: W550-4. PMID 20525783 DOI: 10.1093/Nar/Gkq475  0.725
2010 Lee H, Li Z, Silkov A, Fischer M, Petrey D, Honig B, Murray D. High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. Journal of Structural and Functional Genomics. 11: 51-9. PMID 20383749 DOI: 10.1007/S10969-010-9086-7  0.753
2010 Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z. Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nature Structural & Molecular Biology. 17: 423-9. PMID 20364130 DOI: 10.1038/Nsmb.1800  0.361
2010 Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annual Review of Biochemistry. 79: 233-69. PMID 20334529 DOI: 10.1146/Annurev-Biochem-060408-091030  0.357
2010 West SM, Rohs R, Mann RS, Honig B. Electrostatic interactions between arginines and the minor groove in the nucleosome. Journal of Biomolecular Structure & Dynamics. 27: 861-6. PMID 20232938 DOI: 10.1080/07391102.2010.10508587  0.363
2010 Ciatto C, Bahna F, Zampieri N, VanSteenhouse HC, Katsamba PS, Ahlsen G, Harrison OJ, Brasch J, Jin X, Posy S, Vendome J, Ranscht B, Jessell TM, Honig B, Shapiro L. T-cadherin structures reveal a novel adhesive binding mechanism. Nature Structural & Molecular Biology. 17: 339-47. PMID 20190755 DOI: 10.1038/Nsmb.1781  0.788
2010 Harrison OJ, Bahna F, Katsamba PS, Jin X, Brasch J, Vendome J, Ahlsen G, Carroll KJ, Price SR, Honig B, Shapiro L. Two-step adhesive binding by classical cadherins. Nature Structural & Molecular Biology. 17: 348-57. PMID 20190754 DOI: 10.1038/Nsmb.1784  0.559
2010 Zhu J, Cheng L, Fang Q, Zhou ZH, Honig B. Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. Journal of Molecular Biology. 397: 835-51. PMID 20109465 DOI: 10.1016/J.Jmb.2010.01.041  0.335
2010 Cheng L, Zhu J, Hui WH, Zhang X, Honig B, Fang Q, Zhou ZH. Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics. Journal of Molecular Biology. 397: 852-63. PMID 20036256 DOI: 10.1016/J.Jmb.2009.12.027  0.372
2010 Singarapu KK, Mills JL, Xiao R, Acton T, Punta M, Fischer M, Honig B, Rost B, Montelione GT, Szyperski T. Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175. Proteins. 78: 779-84. PMID 19927321 DOI: 10.1002/Prot.22630  0.439
2010 Eccles J, Honig B, Schulten K. Spectroscopic determinants in the reaction center of rhodopseudomonas viridis. Biophysical Journal. 53: 137-44. PMID 19431719 DOI: 10.1016/S0006-3495(88)83075-3  0.455
2009 Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature. 461: 1248-53. PMID 19865164 DOI: 10.1038/Nature08473  0.416
2009 Petrey D, Fischer M, Honig B. 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. 106: 17377-82. PMID 19805138 DOI: 10.1073/Pnas.0907971106  0.748
2009 Katsamba P, Carroll K, Ahlsen G, Bahna F, Vendome J, Posy S, Rajebhosale M, Price S, Jessell TM, Ben-Shaul A, Shapiro L, Honig BH. Linking molecular affinity and cellular specificity in cadherin-mediated adhesion. Proceedings of the National Academy of Sciences of the United States of America. 106: 11594-9. PMID 19553217 DOI: 10.1073/Pnas.0905349106  0.793
2009 Rohs R, West SM, Liu P, Honig B. Nuance in the double-helix and its role in protein-DNA recognition. Current Opinion in Structural Biology. 19: 171-7. PMID 19362815 DOI: 10.1016/J.Sbi.2009.03.002  0.468
2009 Petrey D, Honig B. Is protein classification necessary? Toward alternative approaches to function annotation Current Opinion in Structural Biology. 19: 363-368. PMID 19269161 DOI: 10.1016/J.Sbi.2009.02.001  0.739
2009 Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/J.Str.2008.12.014  0.654
2009 Rossi P, Aramini JM, Xiao R, Chen CX, Nwosu C, Owens LA, Maglaqui M, Nair R, Fischer M, Acton TB, Honig B, Rost B, Montelione GT. Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus. Proteins. 74: 515-9. PMID 18951393 DOI: 10.1002/Prot.22267  0.33
2009 Forrest L, Zhang Y, Honig B, Rudnick G. A Role for Topologically-Inverted Structural Repeats in Secondary Active Transport by Membrane Proteins of the LeuT Fold Biophysical Journal. 96: 382a. DOI: 10.1016/J.Bpj.2008.12.2859  0.636
2009 Wu Y, Honig B. Bridging Cadherin-mediated Cell Adhesion to Multicellular Pattern Formation by Multiscale Modeling and Simulation Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.1409  0.552
2008 Kosloff M, Alexov E, Arshavsky VY, Honig B. Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation. The Journal of Biological Chemistry. 283: 31197-207. PMID 18782760 DOI: 10.1074/Jbc.M803799200  0.306
2008 Miloushev VZ, Bahna F, Ciatto C, Ahlsen G, Honig B, Shapiro L, Palmer AG. Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins. Structure (London, England : 1993). 16: 1195-205. PMID 18682221 DOI: 10.1016/J.Str.2008.05.009  0.54
2008 Forrest LR, Zhang YW, Jacobs MT, Gesmonde J, Xie L, Honig BH, Rudnick G. Mechanism for alternating access in neurotransmitter transporters. Proceedings of the National Academy of Sciences of the United States of America. 105: 10338-43. PMID 18647834 DOI: 10.1073/Pnas.0804659105  0.618
2008 Posy S, Shapiro L, Honig B. Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? Journal of Molecular Biology. 378: 954-68. PMID 18395225 DOI: 10.1016/J.Jmb.2008.02.063  0.813
2008 Zhu J, Fan H, Periole X, Honig B, Mark AE. Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins. 72: 1171-88. PMID 18338384 DOI: 10.1002/Prot.22005  0.398
2008 Koehnke J, Jin X, Trbovic N, Katsamba PS, Brasch J, Ahlsen G, Scheiffele P, Honig B, Palmer AG, Shapiro L. Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4. Structure (London, England : 1993). 16: 410-21. PMID 18334216 DOI: 10.1016/J.Str.2007.12.024  0.526
2008 Koehnke J, Jin X, Budreck EC, Posy S, Scheiffele P, Honig B, Shapiro L. Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2. Proceedings of the National Academy of Sciences of the United States of America. 105: 1873-8. PMID 18250328 DOI: 10.1073/Pnas.0711701105  0.818
2008 Soto CS, Fasnacht M, Zhu J, Forrest L, Honig B. Loop modeling: Sampling, filtering, and scoring. Proteins. 70: 834-43. PMID 17729286 DOI: 10.1002/Prot.21612  0.766
2008 Norel R, Sheinerman F, Petrey D, Honig B. Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis. Protein Science. 10: 2147-2161. PMID 11604522 DOI: 10.1110/Ps.12901  0.712
2008 Polticelli F, Ascenzi P, Bolognesi M, Honig B. Structural determinants of trypsin affinity and specificity for cationic inhibitors Protein Science. 8: 2621-2629. PMID 10631977 DOI: 10.1110/Ps.8.12.2621  0.35
2007 Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell. 131: 530-43. PMID 17981120 DOI: 10.1016/J.Cell.2007.09.024  0.364
2007 Forrest LR, Tavoulari S, Zhang YW, Rudnick G, Honig B. 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. 104: 12761-6. PMID 17652169 DOI: 10.1073/Pnas.0705600104  0.596
2007 Fasnacht M, Zhu J, Honig B. Local quality assessment in homology models using statistical potentials and support vector machines. Protein Science : a Publication of the Protein Society. 16: 1557-68. PMID 17600147 DOI: 10.1110/Ps.072856307  0.307
2007 Honig B. Protein structure space is much more than the sum of its folds Nature Structural and Molecular Biology. 14: 458. PMID 17549077 DOI: 10.1038/Nsmb0607-458  0.352
2007 Sosinsky A, Honig B, Mann RS, Califano A. 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. 104: 6305-10. PMID 17395715 DOI: 10.1073/Pnas.0701614104  0.307
2007 Singarapu KK, Liu G, Xiao R, Bertonati C, Honig B, Montelione GT, Szyperski T. NMR structure of protein yjbR from Escherichia coli reveals 'double-wing' DNA binding motif. Proteins. 67: 501-4. PMID 17266124 DOI: 10.1002/Prot.21297  0.372
2007 Siggers TW, Honig B. Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Research. 35: 1085-97. PMID 17264128 DOI: 10.1093/Nar/Gkl1155  0.76
2007 Tang CL, Alexov E, Pyle AM, Honig B. Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. Journal of Molecular Biology. 366: 1475-96. PMID 17223134 DOI: 10.1016/J.Jmb.2006.12.001  0.553
2007 Bertonati C, Honig B, Alexov E. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophysical Journal. 92: 1891-9. PMID 17208980 DOI: 10.1529/Biophysj.106.092122  0.374
2007 Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B. Prediction of side-chain conformations on protein surfaces. Proteins. 66: 814-23. PMID 17206724 DOI: 10.1002/Prot.21099  0.652
2007 Shapiro L, Honig B. Cell-to-cell contact and extracellular matrix Current Opinion in Cell Biology. 19: 493-494. DOI: 10.1016/J.Ceb.2007.09.009  0.495
2006 Zhu J, Xie L, Honig B. Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering. Proteins. 65: 463-79. PMID 16927337 DOI: 10.1002/Prot.21085  0.351
2006 Lin YC, Liu G, Shen Y, Bertonati C, Yee A, Honig B, Arrowsmith CH, Szyperski T. NMR structure of protein PA2021 from Pseudomonas aeruginosa. Proteins. 65: 767-70. PMID 16927296 DOI: 10.1002/Prot.21098  0.361
2006 Johnston RJ, Copeland JW, Fasnacht M, Etchberger JF, Liu J, Honig B, Hobert O. An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision in C. elegans. Development (Cambridge, England). 133: 3317-28. PMID 16887832 DOI: 10.1242/Dev.02494  0.321
2006 Kolodny R, Honig B. VISTAL--a new 2D visualization tool of protein 3D structural alignments. Bioinformatics (Oxford, England). 22: 2166-7. PMID 16837525 DOI: 10.1093/Bioinformatics/Btl353  0.354
2006 Kolodny R, Petrey D, Honig B. Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Current Opinion in Structural Biology. 16: 393-8. PMID 16678402 DOI: 10.1016/J.Sbi.2006.04.007  0.743
2006 Forrest LR, Tang CL, Honig B. On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophysical Journal. 91: 508-17. PMID 16648166 DOI: 10.1529/Biophysj.106.082313  0.729
2006 Patel SD, Ciatto C, Chen CP, Bahna F, Rajebhosale M, Arkus N, Schieren I, Jessell TM, Honig B, Price SR, Shapiro L. Type II cadherin ectodomain structures: implications for classical cadherin specificity. Cell. 124: 1255-68. PMID 16564015 DOI: 10.1016/J.Cell.2005.12.046  0.662
2006 Ortiz CO, Etchberger JF, Posy SL, Frøkjaer-Jensen C, Lockery S, Honig B, Hobert O. Searching for neuronal left/right asymmetry: genomewide analysis of nematode receptor-type guanylyl cyclases. Genetics. 173: 131-49. PMID 16547101 DOI: 10.1534/Genetics.106.055749  0.751
2006 Nayal M, Honig B. On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites Proteins: Structure, Function and Genetics. 63: 892-906. PMID 16477622 DOI: 10.1002/Prot.20897  0.327
2005 Zhu J, Alexov E, Honig B. Comparative study of generalized born models: Born radii and peptide folding. The Journal of Physical Chemistry. B. 109: 3008-22. PMID 16851315 DOI: 10.1021/Jp046307S  0.302
2005 Petrey D, Honig B. Protein structure prediction: Inroads to biology Molecular Cell. 20: 811-819. PMID 16364908 DOI: 10.1016/J.Molcel.2005.12.005  0.746
2005 Powers R, Mirkovic N, Goldsmith-Fischman S, Acton TB, Chiang Y, Huang YJ, Ma L, Rajan PK, Cort JR, Kennedy MA, Liu J, Rost B, Honig B, Murray D, Montelione GT. 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. 14: 2849-61. PMID 16251366 DOI: 10.1110/Ps.051666705  0.408
2005 Murray PS, Li Z, Wang J, Tang CL, Honig B, Murray D. Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle. Structure (London, England : 1993). 13: 1521-31. PMID 16216583 DOI: 10.1016/J.Str.2005.07.010  0.578
2005 Siggers T, Silkov T, Honig B. Bending in the right direction Structure. 13: 1400-1401. PMID 16216570 DOI: 10.1016/J.Str.2005.09.002  0.712
2005 Forrest LR, Honig B. An assessment of the accuracy of methods for predicting hydrogen positions in protein structures Proteins: Structure, Function and Genetics. 61: 296-309. PMID 16114036 DOI: 10.1002/Prot.20601  0.623
2005 Chen CP, Posy S, Ben-Shaul A, Shapiro L, Honig BH. 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. 102: 8531-6. PMID 15937105 DOI: 10.1073/Pnas.0503319102  0.807
2005 Fan H, Mark AE, Zhu J, Honig B. Comparative study of generalized Born models: protein dynamics. Proceedings of the National Academy of Sciences of the United States of America. 102: 6760-4. PMID 15814616 DOI: 10.1073/Pnas.0408857102  0.32
2005 Murray D, Honig B. To B or not to B: PIP2 answers the question Developmental Cell. 8: 138-139. PMID 15691756 DOI: 10.1016/J.Devcel.2005.01.002  0.31
2005 Siggers TW, Silkov A, Honig B. Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity. Journal of Molecular Biology. 345: 1027-45. PMID 15644202 DOI: 10.1016/J.Jmb.2004.11.010  0.754
2005 Shen Y, Goldsmith-Fischman S, Atreya HS, Acton T, Ma L, Xiao R, Honig B, Montelione GT, Szyperski T. 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. 58: 747-50. PMID 15616961 DOI: 10.1002/Prot.20365  0.308
2005 Kuzin AP, Goldsmith-Fishman S, Edstrom WC, Benach J, Shastry R, Xiao R, Acton TB, Honig B, Monterlione GT, Hunt JF. A conserved core in the SufE sulfur-acceptor protein mediates interdomain interactions in variety of redox protein complexes Acta Crystallographica Section a Foundations of Crystallography. 61: c329-c329. DOI: 10.1107/S0108767305085983  0.309
2004 Ramelot TA, Cort JR, Goldsmith-Fischman S, Kornhaber GJ, Xiao R, Shastry R, Acton TB, Honig B, Montelione GT, Kennedy MA. Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site. Journal of Molecular Biology. 344: 567-83. PMID 15522305 DOI: 10.1016/J.Jmb.2004.08.038  0.346
2004 Goldsmith-Fischman S, Kuzin A, Edstrom WC, Benach J, Shastry R, Xiao R, Acton TB, Honig B, Montelione GT, Hunt JF. 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. 344: 549-565. PMID 15522304 DOI: 10.1016/J.Jmb.2004.08.074  0.373
2004 Gimpelev M, Forrest LR, Murray D, Honig B. Helical packing patterns in membrane and soluble proteins. Biophysical Journal. 87: 4075-86. PMID 15465852 DOI: 10.1529/Biophysj.104.049288  0.794
2004 Fleishman SJ, Harrington S, Friesner RA, Honig B, Ben-Tal N. An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophysical Journal. 87: 3448-59. PMID 15339802 DOI: 10.1529/Biophysj.104.046417  0.606
2004 Liu G, Sukumaran DK, Xu D, Chiang Y, Acton T, Goldsmith-Fischman S, Honig B, Montelione GT, Szyperski T. NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis reveals a distinct 5-helix bundle. Proteins. 55: 756-8. PMID 15103637 DOI: 10.1002/Prot.20009  0.404
2004 Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins. 55: 351-67. PMID 15048827 DOI: 10.1002/Prot.10613  0.566
2004 Xu D, Liu G, Xiao R, Acton T, Goldsmith-Fischman S, Honig B, Montelione GT, Szyperski T. NMR structure of the hypothetical protein AQ-1857 encoded by the Y157 gene from Aquifex aeolicus reveals a novel protein fold. Proteins. 54: 794-6. PMID 14997575 DOI: 10.1002/Prot.10424  0.375
2003 Petrey D, Honig B. GRASP2: Visualization, Surface Properties, and Electrostatics of Macromolecular Structures and Sequences Methods in Enzymology. 374: 492-509. PMID 14696386 DOI: 10.1016/S0076-6879(03)74021-X  0.714
2003 Patel SD, Chen CP, Bahna F, Honig B, Shapiro L. Cadherin-mediated cell-cell adhesion: sticking together as a family. Current Opinion in Structural Biology. 13: 690-8. PMID 14675546 DOI: 10.1016/J.Sbi.2003.10.007  0.685
2003 Tang CL, Xie L, Koh IY, Posy S, Alexov E, Honig B. On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. Journal of Molecular Biology. 334: 1043-62. PMID 14643665 DOI: 10.1016/J.Jmb.2003.10.025  0.797
2003 Sheinerman FB, Al-Lazikani B, Honig B. Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains Journal of Molecular Biology. 334: 823-841. PMID 14636606 DOI: 10.1016/J.Jmb.2003.09.075  0.418
2003 Aramini JM, Huang YJ, Cort JR, Goldsmith-Fischman S, Xiao R, Shih LY, Ho CK, Liu J, Rost B, Honig B, Kennedy MA, Acton TB, Montelione GT. Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Science : a Publication of the Protein Society. 12: 2823-30. PMID 14627742 DOI: 10.1110/Ps.03359003  0.406
2003 Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A, Koh IY, Alexov E, Honig B. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins. 53: 430-5. PMID 14579332 DOI: 10.1002/Prot.10550  0.787
2003 Goldsmith-Fischman S, Honig B. Structural genomics: Computational methods for structure analysis Protein Science. 12: 1813-1821. PMID 12930981 DOI: 10.1110/Ps.0242903  0.358
2003 Ramelot TA, Ni S, Goldsmith-Fischman S, Cort JR, Honig B, Kennedy MA. Solution structure of Vibrio cholerae protein VC0424: a variation of the ferredoxin-like fold. Protein Science : a Publication of the Protein Society. 12: 1556-61. PMID 12824501 DOI: 10.1110/Ps.03108103  0.391
2002 Honig B. Combining Bioinformatics and Biophysics to Understand Protein-Protein and Protein-Ligand Interactions. The Scientific World Journal. 2: 43-44. PMID 29973796 DOI: 10.1100/Tsw.2002.22  0.466
2002 Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side-chain conformations. Journal of Molecular Biology. 320: 597-608. PMID 12096912 DOI: 10.1016/S0022-2836(02)00470-9  0.661
2002 Sheinerman FB, Honig B. On the role of electrostatic interactions in the design of protein-protein interfaces Journal of Molecular Biology. 318: 161-177. PMID 12054776 DOI: 10.1016/S0022-2836(02)00030-X  0.379
2002 Xiang Z, Soto CS, Honig B. 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. 99: 7432-7. PMID 12032300 DOI: 10.1073/Pnas.102179699  0.725
2002 Murray D, Honig B. Electrostatic control of the membrane targeting of C2 domains Molecular Cell. 9: 145-154. PMID 11804593 DOI: 10.1016/S1097-2765(01)00426-9  0.305
2002 Murray D, Arbuzova A, Honig B, McLaughlint S. The role of electrostatic and nonpolar interactions in the association of peripheral proteins with membranes Current Topics in Membranes. 52: 277-307. DOI: 10.1016/S1063-5823(02)52012-3  0.358
2001 Al-Lazikani B, Sheinerman FB, Honig B. 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. 98: 14796-14801. PMID 11752426 DOI: 10.1073/Pnas.011577898  0.387
2001 Xiang Z, Honig B. Extending the accuracy limits of prediction for side-chain conformations Journal of Molecular Biology. 311: 421-430. PMID 11478870 DOI: 10.1006/Jmbi.2001.4865  0.54
2001 Al-Lazikani B, Jung J, Xiang Z, Honig B. Protein structure prediction Current Opinion in Chemical Biology. 5: 51-56. PMID 11166648 DOI: 10.1016/S1367-5931(00)00164-2  0.624
2001 Xiang Z, Honig B. CorrigendumExtending the accuracy limits of prediction for side-chain conformations Journal of Molecular Biology. 312. DOI: 10.1006/Jmbi.2001.4985  0.512
2000 Petrey D, Honig B. Free energy determinants of tertiary structure and the evaluation of protein models Protein Science. 9: 2181-2191. PMID 11152128 DOI: 10.1110/Ps.9.11.2181  0.74
2000 Yang AS, Honig B. 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. 301: 691-711. PMID 10966778 DOI: 10.1006/Jmbi.2000.3975  0.442
2000 Yang AS, Honig B. 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. 301: 679-689. PMID 10966777 DOI: 10.1006/Jmbi.2000.3974  0.396
2000 Yang AS, Honig B. 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. 301: 665-678. PMID 10966776 DOI: 10.1006/Jmbi.2000.3973  0.44
2000 Arbuzova A, Wang L, Wang J, Hangyás-Mihályné G, Murray D, Honig B, McLaughlin S. Membrane binding of peptides containing both basic and aromatic residues. Experimental studies with peptides corresponding to the scaffolding region of caveolin and the effector region of MARCKS. Biochemistry. 39: 10330-9. PMID 10956022 DOI: 10.1021/Bi001039J  0.301
2000 Sheinerman FB, Norel R, Honig B. Electrostatic aspects of protein-protein interactions. Current Opinion in Structural Biology. 10: 153-159. PMID 10753808 DOI: 10.1016/S0959-440X(00)00065-8  0.38
1999 Honig B. Protein folding: From the levinthal paradox to structure prediction Journal of Molecular Biology. 293: 283-293. PMID 10550209 DOI: 10.1006/Jmbi.1999.3006  0.432
1999 Chin K, Sharp KA, Honig B, Pyle AM. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function. Nature Structural Biology. 6: 1055-61. PMID 10542099 DOI: 10.1038/14940  0.314
1999 Yang AS, Honig B. Sequence to structure alignment in comparative modeling using PrISM Proteins: Structure, Function and Genetics. 37: 66-72. PMID 10526354 DOI: 10.1002/(Sici)1097-0134(1999)37:3+<66::Aid-Prot10>3.0.Co;2-K  0.393
1999 Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC. Improving macromolecular electrostatics calculations. Protein Engineering. 12: 657-62. PMID 10469826 DOI: 10.1093/Protein/12.8.657  0.302
1999 Xiao L, Honig B. Electrostatic contributions to the stability of hyperthermophilic proteins Journal of Molecular Biology. 289: 1435-1444. PMID 10373377 DOI: 10.1006/Jmbi.1999.2810  0.384
1999 Nayal M, Hitz BC, Honig B. GRASS: A server for the graphical representation and analysis of structures Protein Science. 8: 676-679. PMID 10091670 DOI: 10.1110/Ps.8.3.676  0.334
1998 Misra VK, Hecht JL, Yang AS, Honig B. Electrostatic contributions to the binding free energy of the λcl repressor to DNA Biophysical Journal. 75: 2262-2273. PMID 9788922 DOI: 10.1016/S0006-3495(98)77671-4  0.366
1998 Murray D, Hermida-Matsumoto L, Buser CA, Tsang J, Sigal CT, Ben-Tal N, Honig B, Resh MD, McLaughlin S. Electrostatics and the membrane association of Src: Theory and experiment Biochemistry. 37: 2145-2159. PMID 9485361 DOI: 10.1021/Bi972012B  0.322
1997 Ben-Tal N, Honig B, Miller C, McLaughlin S. Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles Biophysical Journal. 73: 1717-1727. PMID 9336168 DOI: 10.1016/S0006-3495(97)78203-1  0.34
1997 Murray D, Ben-Tal N, Honig B, McLaughlin S. Electrostatic interaction of myristoylated proteins with membranes: Simple physics, complicated biology Structure. 5: 985-989. PMID 9309215 DOI: 10.1016/S0969-2126(97)00251-7  0.336
1997 Froloff N, Windemuth A, Honig B. On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions Protein Science. 6: 1293-1301. PMID 9194189 DOI: 10.1002/Pro.5560060617  0.347
1996 Honig B, Cohen FE. Adding backbone to protein folding: Why proteins are polypeptides Folding and Design. 1. PMID 9079357 DOI: 10.1016/S1359-0278(96)00005-3  0.404
1996 Ben-Tal N, Honig B. Helix-helix interactions in lipid bilayers Biophysical Journal. 71: 3046-3050. PMID 8968575 DOI: 10.1016/S0006-3495(96)79498-5  0.352
1996 Sampogna RV, Honig B. Electrostatic coupling between retinal isomerization and the ionization state of Glu-204: A general mechanism for proton release in bacteriorhodopsin Biophysical Journal. 71: 1165-1171. PMID 8873990 DOI: 10.1016/S0006-3495(96)79320-7  0.342
1996 Ben-Tal N, Honig B, Peitzsch RM, Denisov G, McLaughlin S. Binding of small basic peptides to membranes containing acidic lipids: Theoretical models and experimental results Biophysical Journal. 71: 561-575. PMID 8842196 DOI: 10.1016/S0006-3495(96)79280-9  0.316
1996 Ben-Shaul A, Ben-Tal N, Honig B. Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes Biophysical Journal. 71: 130-137. PMID 8804596 DOI: 10.1016/S0006-3495(96)79208-1  0.354
1996 Yang AS, Hitz B, Honig B. Free energy determinants of secondary structure formation: III. β-turns and their role in protein folding Journal of Molecular Biology. 259: 873-882. PMID 8683589 DOI: 10.1006/Jmbi.1996.0364  0.385
1996 Sharp KA, Kumar S, Rossky PJ, Friedman RA, Honig B. Size dependence of transfer free energies. 2. Hard sphere models Journal of Physical Chemistry. 100: 14166-14177. DOI: 10.1021/Jp960668T  0.508
1996 Marten B, Kim K, Cortis C, Friesner RA, Murphy RB, Ringnalda MN, Sitkoff D, Honig B. New Model for Calculation of Solvation Free Energies:  Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects The Journal of Physical Chemistry. 100: 11775-11788. DOI: 10.1021/Jp953087X  0.491
1996 Gunner MR, Nicholls A, Honig B. Electrostatic Potentials inRhodopseudomonas viridisReaction Centers:  Implications for the Driving Force and Directionality of Electron Transfer† The Journal of Physical Chemistry. 100: 4277-4291. DOI: 10.1021/Jp9519070  0.3
1995 Friedman RA, Honig B. A free energy analysis of nucleic acid base stacking in aqueous solution Biophysical Journal. 69: 1528-1535. PMID 8534823 DOI: 10.1016/S0006-3495(95)80023-8  0.334
1995 Honig B, Yang AS. Free energy balance in protein folding Advances in Protein Chemistry. 46: 27-58. PMID 7771321 DOI: 10.1016/S0065-3233(08)60331-9  0.355
1995 Honig B, Nicholls A. Classical electrostatics in biology and chemistry Science. 268: 1144-1149. PMID 7761829 DOI: 10.1126/Science.7761829  0.338
1995 Misra VK, Honig B. On the magnitude of the electrostatic contribution to ligand-DNA interactions Proceedings of the National Academy of Sciences of the United States of America. 92: 4691-4695. PMID 7753866 DOI: 10.1073/Pnas.92.10.4691  0.319
1995 Sharp KA, Honig B. Salt effects on nucleic acids Current Opinion in Structural Biology. 5: 323-328. PMID 7583630 DOI: 10.1016/0959-440X(95)80093-X  0.323
1995 Yang AS, Honig B. Free energy determinants of secondary structure formation: II. Antiparallel β-sheets Journal of Molecular Biology. 252: 366-376. PMID 7563057 DOI: 10.1006/Jmbi.1995.0503  0.339
1995 Yang AS, Honig B. Free Energy Determinants of Secondary Structure Formation: I. α-Helices Journal of Molecular Biology. 252: 351-365. PMID 7563056 DOI: 10.1006/Jmbi.1995.0502  0.342
1995 Sharp KA, Friedman RA, Misra V, Hecht J, Honig B. Salt effects on polyelectrolyte–ligand binding: Comparison of Poisson–Boltzmann, and limiting law/counterion binding models Biopolymers. 36: 245-262. PMID 7492748 DOI: 10.1002/Bip.360360211  0.335
1995 Kumar SK, Szleifer I, Sharp K, Rossky PJ, Friedman R, Honig B. Size dependence of transfer free energies. 1. A Flory-Huggins approach Journal of Physical Chemistry. 99: 8382-8391. DOI: 10.1021/J100020A076  0.475
1995 Honig B, Ottolenghi M, Sheves M. Acid-Base Equilibria and the Proton Pump in Bacteriorhodopsin Israel Journal of Chemistry. 35: 429-446. DOI: 10.1002/Ijch.199500041  0.305
1994 Monge A, Friesner RA, Honig B. 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. 91: 5027-9. PMID 8197177 DOI: 10.1073/Pnas.91.11.5027  0.56
1994 Smith KC, Honig B. Evaluation of the conformational free energies of loops in proteins Proteins: Structure, Function and Genetics. 18: 119-132. PMID 8159662 DOI: 10.1002/Prot.340180205  0.374
1994 Misra VK, Hecht JL, Sharp KA, Friedman RA, Honig B. Salt effects on protein-DNA interactions: The λcI repressor and EcoRI endonuclease Journal of Molecular Biology. 238: 264-280. PMID 8158653 DOI: 10.1006/Jmbi.1994.1286  0.364
1994 Yang AS, Honig B. Structural origins of pH and ionic strength effects on protein stability: Acid denaturation of sperm whale apomyoglobin Journal of Molecular Biology. 237: 602-614. PMID 8158640 DOI: 10.1006/Jmbi.1994.1258  0.318
1994 Sampogna RV, Honig B. Environmental effects on the protonation states of active site residues in bacteriorhodopsin Biophysical Journal. 66: 1341-1352. PMID 8061190 DOI: 10.1016/S0006-3495(94)80925-7  0.326
1994 Scott DL, Mandel AM, Sigler PB, Honig B. The electrostatic basis for the interfacial binding of secretory phospholipases A2. Biophysical Journal. 67: 493-504. PMID 7948668 DOI: 10.1016/S0006-3495(94)80546-6  0.333
1994 Sitkoff D, Lockhart DJ, Sharp KA, Honig B. Calculation of electrostatic effects at the amino terminus of an α helix Biophysical Journal. 67: 2251-2260. PMID 7696466 DOI: 10.1016/S0006-3495(94)80709-X  0.322
1994 Misra VK, Sharp KA, Friedman RA, Honig B. Salt effects on ligand-DNA binding: Minor groove binding antibiotics Journal of Molecular Biology. 238: 245-263. PMID 7512653 DOI: 10.1006/Jmbi.1994.1285  0.305
1994 Tannor DJ, Marten B, Murphy R, Friesner RA, Sitkoff D, Nicholls A, Honig B, Ringnalda M, Goddard WA. Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory Journal of the American Chemical Society. 116: 11875-11882. DOI: 10.1021/Ja00105A030  0.469
1994 Rajasekaran E, Jayaram B, Honig B. Electrostatic Interactions In Aliphatic Dicarboxylic Acids : A Computational Route To The Determination Of Pka Shifts Journal of the American Chemical Society. 116: 8238-8240. DOI: 10.1021/Ja00097A033  0.61
1993 Yang AS, Honig B. On the pH dependence of protein stability Journal of Molecular Biology. 231: 459-474. PMID 8510157 DOI: 10.1006/Jmbi.1993.1294  0.317
1993 Yang AS, Gunner MR, Sampogna R, Sharp K, Honig B. On the calculation of pK(a)s in proteins Proteins: Structure, Function and Genetics. 15: 252-265. PMID 7681210 DOI: 10.1002/Prot.340150304  0.327
1992 Friedman RA, Honig B. The electrostatic contribution to DNA base-stacking interactions Biopolymers. 32: 145-158. PMID 1637989 DOI: 10.1002/Bip.360320205  0.344
1992 McGrath ME, Vásquez JR, Craik CS, Yang AS, Honig B, Fletterick RJ. Perturbing the polar environment of Asp102 in trypsin: consequences of replacing conserved Ser214. Biochemistry. 31: 3059-64. PMID 1554694 DOI: 10.1021/Bi00127A005  0.312
1992 Yang AS, Sharp KA, Honig B. Analysis of the heat capacity dependence of protein folding Journal of Molecular Biology. 227: 889-900. PMID 1404393 DOI: 10.1016/0022-2836(92)90229-D  0.351
1992 Yang A, Honig B. Electrostatic effects on protein stability Current Biology. 2: 82. DOI: 10.1016/0960-9822(92)90213-T  0.314
1992 Yang AS, Honig B. Electrostatic effects on protein stability. Current Opinion in Structural Biology 1992, 2:40...-45 Current Opinion in Structural Biology. 2: 40-45. DOI: 10.1016/0959-440X(92)90174-6  0.359
1991 Gilson MK, Honig B. The inclusion of electrostatic hydration energies in molecular mechanics calculations Journal of Computer-Aided Molecular Design. 5: 5-20. PMID 2072125 DOI: 10.1007/Bf00173467  0.55
1991 Sharp KA, Nicholls A, Friedman R, Honig B. Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. Biochemistry. 30: 9686-9697. PMID 1911756 DOI: 10.1021/Bi00104A017  0.339
1991 Nicholls A, Sharp KA, Honig B. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons Proteins: Structure, Function and Genetics. 11: 281-296. PMID 1758883 DOI: 10.1002/Prot.340110407  0.397
1990 Koutalos Y, Ebrey TG, Gilson HR, Honig B. Octopus photoreceptor membranes. Surface charge density and pK of the Schiff base of the pigments. Biophysical Journal. 58: 493-501. PMID 2207250 DOI: 10.1016/S0006-3495(90)82394-8  0.302
1990 Jayaram B, Swaminathan S, Beveridge DL, Sharp K, Honig B. Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model Macromolecules. 23: 3156-3165. DOI: 10.1021/Ma00214A021  0.687
1989 Gilson MK, Honig B. Destabilization of an alpha-helix-bundle protein by helix dipoles Proceedings of the National Academy of Sciences of the United States of America. 86: 1524-1528. PMID 2922396 DOI: 10.1073/Pnas.86.5.1524  0.587
1989 Jayaram B, Sharp KA, Honig B. The electrostatic potential of B-DNA Biopolymers. 28: 975-993. PMID 2742988 DOI: 10.1002/Bip.360280506  0.595
1989 Chen JG, Nakamura T, Ebrey TG, Ok H, Konno K, Derguini F, Nakanishi K, Honig B. Wavelength regulation in iodopsin, a cone pigment. Biophysical Journal. 55: 725-9. PMID 2524224 DOI: 10.1016/S0006-3495(89)82871-1  0.42
1989 Jayaram B, Fine R, Sharp K, Honig B. Free energy calculations of ion hydration: an analysis of the Born model in terms of microscopic simulations The Journal of Physical Chemistry. 93: 4320-4327. DOI: 10.1021/J100347A081  0.562
1988 Gilson HS, Honig BH, Croteau A, Zarrilli G, Nakanishi K. Analysis of the factors that influence the C=N stretching frequency of polyene Schiff bases. Implications for bacteriorhodopsin and rhodopsin. Biophysical Journal. 53: 261-9. PMID 3345334 DOI: 10.1016/S0006-3495(88)83087-X  0.41
1988 Lanyi JK, Zimányi L, Nakanishi K, Derguini F, Okabe M, Honig B. Chromophore/protein and chromophore/anion interactions in halorhodopsin. Biophysical Journal. 53: 185-91. PMID 3345330 DOI: 10.1016/S0006-3495(88)83080-7  0.488
1988 Gilson MK, Honig BH. Energetics of charge-charge interactions in proteins. Proteins. 3: 32-52. PMID 3287370 DOI: 10.1002/Prot.340030104  0.587
1988 Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis Proteins. 4: 7-18. PMID 3186692 DOI: 10.1002/Prot.340040104  0.578
1988 Rodman Gilson HS, Honig BH. Analysis of NMR and absorption spectroscopic data in bacteriorhodopsin: Models for protein-chromophore interactions Journal of the American Chemical Society. 110: 1943-1950. DOI: 10.1021/Ja00214A046  0.342
1988 Gilson MK, Sharp KA, Honig BH. Calculating the electrostatic potential of molecules in solution: Method and error assessment Journal of Computational Chemistry. 9: 327-335. DOI: 10.1002/Jcc.540090407  0.535
1987 Gilson MK, Honig BH. Calculation of electrostatic potentials in an enzyme active site. Nature. 330: 84-6. PMID 3313058 DOI: 10.1038/330084A0  0.578
1987 Sharp K, Fine R, Schulten K, Honig B. Brownian dynamics simulation of diffusion to irregular bodies The Journal of Physical Chemistry. 91: 3624-3631. DOI: 10.1021/J100297A032  0.372
1986 Gilson MK, Honig BH. The dielectric constant of a folded protein. Biopolymers. 25: 2097-119. PMID 3790703 DOI: 10.1002/Bip.360251106  0.563
1986 Rashin AA, Iofin M, Honig B. Internal cavities and buried waters in globular proteins Biochemistry. 25: 3619-3625. PMID 3718947 DOI: 10.1021/Bi00360A021  0.32
1986 Klapper I, Hagstrom R, Fine R, Sharp K, Honig B. Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification Proteins. 1: 47-59. PMID 3449851 DOI: 10.1002/Prot.340010109  0.326
1986 Spudich JL, McCain DA, Nakanishi K, Okabe M, Shimizu N, Rodman H, Honig B, Bogomolni RA. Chromophore/protein interaction in bacterial sensory rhodopsin and bacteriorhodopsin Biophysical Journal. 49: 479-483. PMID 2937462 DOI: 10.1016/S0006-3495(86)83657-8  0.517
1985 Gilson MK, Rashin A, Fine R, Honig B. On the calculation of electrostatic interactions in proteins Journal of Molecular Biology. 184: 503-516. PMID 4046024 DOI: 10.1016/0022-2836(85)90297-9  0.591
1985 Schiffmiller R, Callender RH, Waddell WH, Govindjee R, Ebrey TG, Kakitani H, Honig B, Nakanishi K. Resonance Raman studies of bacteriorhodopsin analogues. Photochemistry and Photobiology. 41: 563-7. PMID 4011709 DOI: 10.1111/J.1751-1097.1985.Tb03527.X  0.434
1985 Kakitani H, Kakitani T, Rodman H, Honig B. On the mechanism of wavelength regulation in visual pigments Photochemistry and Photobiology. 41: 471-479. PMID 4011704 DOI: 10.1111/J.1751-1097.1985.Tb03514.X  0.339
1983 Kakitani T, Kakitani H, Honig B, Nakanishi K. Symmetric charge distribution in the bacteriorhodopsin binding site Journal of the American Chemical Society. 105: 648-650. DOI: 10.1021/Ja00341A069  0.409
1982 Honig B, Ebrey TG. [61] Protein- chromophore interactions as spectroscopic and photochemical determinants Methods in Enzymology. 88: 462-470. DOI: 10.1016/0076-6879(82)88064-6  0.336
1981 Balogh-Nair V, Carriker JD, Honig B, Kamat V, Motto MG, Nakanishi K, Sen R, Sheves M, Tanis MA, Tsujimoto K. THE ‘OPSIN SHIFT’ IN BACTERIORHODOPSIN: STUDIES WITH ARTIFICIAL BACTERIORHODOPSINS Photochemistry and Photobiology. 33: 483-488. DOI: 10.1111/J.1751-1097.1981.Tb05449.X  0.424
1980 Nakanishi K, Balogh-Nair V, Arnaboldi M, Tsujimoto K, Honig B. An external point-charge model for bacteriorhodopsin to account for its purple color Journal of the American Chemical Society. 102: 7945-7947. DOI: 10.1021/Ja00547A028  0.387
1980 Honig B, Dinur U, Birge RR, Ebrey TG. The isomer dependence of oscillator strengths in retinal and related molecules. Spectroscopic assignments Journal of the American Chemical Society. 102: 488-494. DOI: 10.1021/Ja00522A008  0.491
1980 Dinur U, Honig B, Schulten K. On the nature of excited electronic states in cyanine dyes: implications for visual pigment spectra Chemical Physics Letters. 72: 493-497. DOI: 10.1016/0009-2614(80)80339-3  0.411
1980 Schulten K, Dinur U, Honig B. The spectra of carbonium ions, cyanine dyes, and protonated Schiff base polyenes The Journal of Chemical Physics. 73: 3927-3935. DOI: 10.1002/Chin.198105044  0.391
1980 SHEVES M, NAKANISHI K, HONIG B. ChemInform Abstract: THROUGH-SPACE ELECTROSTATIC EFFECTS IN ELECTRONIC SPECTRA. EXPERIMENTAL EVIDENCE FOR THE EXTERNAL POINT-CHARGE MODEL OF VISUAL PIGMENTS Chemischer Informationsdienst. 11. DOI: 10.1002/Chin.198007044  0.394
1980 Honig B, Dinur U, Nakanishi K, Balogh-Nair V, Gawinowicz MA, Arnaboldi M, Motto MG. An external point-charge model for wavelength regulation in visual pigments Cheminform. 11. DOI: 10.1002/Chin.198007043  0.389
1979 Nakanishi K, Balogh-Nair V, Gawinowicz MA, Arnaboldi M, Motto M, Honig B. Double point charge model for visual pigments; evidence from dihydrorhodopsins. Photochemistry and Photobiology. 29: 657-60. PMID 451005 DOI: 10.1111/J.1751-1097.1979.Tb07745.X  0.389
1979 Sheves M, Nakanishi K, Honig B. Through-space electrostatic effects in electronic spectra. Experimental evidence for the external point-charge model of visual pigments Journal of the American Chemical Society. 101: 7086-7088. DOI: 10.1021/Ja00517A061  0.394
1979 Honig B, Dinur U, Nakanishi K, Balogh-Nair V, Gawinowicz MA, Arnaboldi M, Motto MG. An external point-charge model for wavelength regulation in visual pigments Journal of the American Chemical Society. 101: 7084-7086. DOI: 10.1021/Ja00517A060  0.389
1978 Hagler AT, Honig B. On the formation of protein tertiary structure on a computer Proceedings of the National Academy of Sciences of the United States of America. 75: 554-558. PMID 273217 DOI: 10.1073/Pnas.75.2.554  0.411
1977 Ebrey TG, Becher B, Mao B, Kilbride P, Honig B. Exciton interactions and chromophore orientation in the purple membrane Journal of Molecular Biology. 112: 377-397. PMID 875024 DOI: 10.1016/S0022-2836(77)80188-5  0.318
1977 Yonath A, Podjarny A, Honig B, Sielecki A, Traub W. Crystallographic studies of protein denaturation and renaturation. 2. Sodium dodecyl sulfate induced structural changes in triclinic lysozyme. Biochemistry. 16: 1418-24. PMID 849424 DOI: 10.1021/Bi00626A028  0.354
1976 Honig B, Ray A, Levinthal C. Conformational flexibility and protein folding: rigid structural fragments connected by flexible joints in subtilisin BPN. Proceedings of the National Academy of Sciences of the United States of America. 73: 1974-8. PMID 1064867 DOI: 10.1073/Pnas.73.6.1974  0.683
1976 Honig B, Greenberg AD, Dinur U, Ebrey TG. Visual-pigment spectra: Implications of the protonation of the retinal Schiff base Biochemistry. 15: 4593-4599. PMID 974079 DOI: 10.1021/Bi00666A008  0.313
1975 Ebrey T, Govindjee R, Honig B, Pollock E, Chan W, Crouch R, Yudd A, Nakanishi K. Properties of several sterically modified retinal analogs and their photosensitive pigments Biochemistry. 14: 3933-3941. DOI: 10.1021/Bi00689A002  0.373
1975 Honig B, Warshel A, Karplus M. Theoretical studies of the visual chromophore Accounts of Chemical Research. 8: 92-100. DOI: 10.1021/Ar50087A003  0.526
1974 Chan WK, Nakanishi K, Ebrey TG, Honig B. Letter: Properties of 14-methylretinal, 13-desmethyl-14-methylretinal, and visual pigments formed therefrom. Journal of the American Chemical Society. 96: 3642-4. PMID 4833721 DOI: 10.1021/Ja00818A045  0.377
1974 Chan WK, Nakanishi K, Ebrey TG, Honig B. Properties Of 14-Methylretinal, 13-Desmethyl-14-Methylretinal, And Visual Pigments Formed Therefrom Cheminform. 5. DOI: 10.1002/Chin.197432417  0.378
1973 Honig B, Kabat EA, Katz L, Levinthal C, Wu TT. Model-building of neurohypophyseal hormones. Journal of Molecular Biology. 80: 277-95. PMID 4763987 DOI: 10.1016/0022-2836(73)90173-3  0.632
1971 Honig B, Hudson B, Sykes BD, Karplus M. Ring orientation in -ionone and retinals Proceedings of the National Academy of Sciences of the United States of America. 68: 1289-1293. PMID 5288377 DOI: 10.1073/Pnas.68.6.1289  0.41
1971 Honig B, Karplus M. Implications of torsional potential of retinal isomers for visual excitation Nature. 229: 558-560. PMID 4925351 DOI: 10.1038/229558A0  0.409
1967 Honig B, Jortner J, Szöke A. Theoretical Studies of Two‐Photon Absorption Processes. I. Molecular Benzene Journal of Chemical Physics. 46: 2714-2727. DOI: 10.1063/1.1841103  0.427
1967 Honig B, Jortner J. Theoretical Studies of Two-Photon Absorption Processes. II. Model Calculations Journal of Chemical Physics. 47: 3698-3703. DOI: 10.1063/1.1701522  0.424
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