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

321 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
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  0.52
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  0.52
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  0.72
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  0.72
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  0.72
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  0.72
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  0.4
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
2018 Yuan L, Guo LH, Yuan CA, Zhang YH, Han K, Nandi A, Honig B, Huang DS. Integration of Multi-omics Data for Gene Regulatory Network Inference and Application to Breast Cancer. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30137012 DOI: 10.1109/Tcbb.2018.2866836  0.36
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  0.72
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  0.72
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  0.72
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  0.72
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  0.8
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, Mueller U. Cis-dimeric architecture of Pcdh15 critical for mechanotransduction Neuron. DOI: 10.2210/Pdb6Cv7/Pdb  0.8
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  0.8
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  0.52
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  0.72
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  0.4
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  0.72
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  0.36
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  0.72
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  0.72
2017 Kostyrko K, Simpson D, Broyde J, Kelly M, Califano A, Honig B, Jackson P, Sweet-Cordero A. Abstract A27: Identification of novel KRAS-synthetic lethal targets for treatment of KRAS-dependent Non-Small Cell Lung Cancer Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-A27  0.8
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  0.8
2017 Ahmad R, Azad T, Barreto C, Begum K, Butt M, Gruffat D, Jerliu A, Kwiat J, Murph M, Gómez KAR, Honig B, Califano A, Singh S, Murray D. Abstract 2609: Columbia University’s Center for Cancer Systems Therapeutics (CaST) 2017 Scholars Program: A synergistic partnership with students from Brooklyn College, CUNY Cancer Research. 77: 2609-2609. DOI: 10.1158/1538-7445.Am2017-2609  0.8
2017 Shen Z, Zhang Y, Han K, Nandi AK, Honig B, Huang D. miRNA-Disease Association Prediction with Collaborative Matrix Factorization Complexity. 2017: 1-9. DOI: 10.1155/2017/2498957  0.8
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  0.72
2016 Deng C, Lipstein MR, Scotto L, Jirau Serrano XO, Mangone MA, Li S, Vendome J, Hao Y, Xu X, Deng SX, Realubit RB, Tatonetti NP, Karan C, Lentzsch S, Fruman DA, ... Honig B, et al. Silencing c-Myc translation as a therapeutic strategy through targeting PI3K delta and CK1 epsilon in hematological malignancies. Blood. PMID 27784673 DOI: 10.1182/Blood-2016-08-731240  0.48
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  0.72
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  0.52
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  0.96
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  0.4
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  0.44
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  0.96
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  0.96
2016 Westphalen CB, Takemoto Y, Tanaka T, Macchini M, Jiang Z, Renz BW, Chen X, Ormanns S, Nagar K, Tailor Y, May R, Cho Y, Asfaha S, Worthley DL, Hayakawa Y, ... ... Honig B, et al. Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis. Cell Stem Cell. 18: 441-455. PMID 27058937 DOI: 10.1016/J.Stem.2016.03.016  0.96
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  0.96
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  0.8
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  0.8
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  0.8
2016 Deng C, Lipstein M, Scotto L, Serrano XOJ, Mangone M, Li S, Vendome J, Hao Y, Xu X, Liu X, Pal I, Deng S, Tatonetti NP, Lentzsch S, Honig B, et al. Silencing c-Myc Translation As a Therapeutic Strategy through Targeting PI3K Delta and CK1 Epsilon in Hematological Malignancies Blood. 128: 291-291. DOI: 10.1182/Blood.V128.22.291.291  0.8
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  0.96
2015 Barrows D, Schoenfeld SM, Hodakoski C, Silkov A, Honig B, Couvillon A, Shymanets A, Nuernberg B, Asara JM, Parsons R. PAK kinases mediate the phosphorylation of PREX2 to initiate feedback inhibition of Rac1. The Journal of Biological Chemistry. PMID 26438819 DOI: 10.1074/Jbc.M115.668244  0.96
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  0.96
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  0.96
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  0.52
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  0.52
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  0.52
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  0.8
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  0.96
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  0.36
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  0.96
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  0.96
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  0.96
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  0.8
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  0.96
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  0.72
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  0.96
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  0.96
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  0.96
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  0.96
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  0.72
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  0.96
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  0.96
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  0.96
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  0.96
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  0.52
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  0.96
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  0.72
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  0.96
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  0.96
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  0.96
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  0.96
2011 Honig B, Rohs R. Biophysics: Flipping Watson and Crick Nature. 470: 472-473. PMID 21350476 DOI: 10.1038/470472A  0.96
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  0.96
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  0.96
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  0.8
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.52
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  0.52
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  0.4
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  0.96
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  0.96
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  0.96
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  0.96
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  0.56
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  0.56
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  0.96
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  0.96
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  0.52
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  0.96
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  0.4
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  0.96
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  0.96
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  0.96
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  0.8
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.52
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.4
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.6
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  0.4
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  0.96
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  0.96
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  0.96
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  0.68
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.52
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  0.96
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  0.96
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  0.96
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  0.96
2005 Wildonger J, Sosinsky A, Honig B, Mann RS. Lozenge directly activates argos and klumpfuss to regulate programmed cell death. Genes & Development. 19: 1034-9. PMID 15879554 DOI: 10.1101/Gad.1298105  0.96
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  0.96
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  0.96
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  0.96
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  0.4
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  0.96
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  0.96
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  0.96
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  0.96
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  0.4
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  0.96
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  0.4
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  0.96
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  0.96
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  0.96
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  0.96
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  0.4
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  0.96
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  0.96
2003 Tao X, Khayat R, Christendat D, Savchenko A, Xu X, Goldsmith-Fischman S, Honig B, Edwards A, Arrowsmith CH, Tong L. Crystal structures of MTH1187 and its yeast ortholog YBL001c. Proteins. 52: 478-80. PMID 12866058 DOI: 10.1002/Prot.10443  0.96
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  0.96
2003 Sosinsky A, Bonin CP, Mann RS, Honig B. Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Research. 31: 3589-92. PMID 12824372 DOI: 10.1093/Nar/Gkg544  0.96
2002 Rost B, Honig B, Valencia A. Bioinformatics in structural genomics Bioinformatics. 18: 897-898. PMID 12117786 DOI: 10.1093/Bioinformatics/18.7.897  0.96
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  0.96
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  0.96
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  0.96
2002 Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B. 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. 23: 128-37. PMID 11913378 DOI: 10.1002/Jcc.1161  0.96
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  0.96
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  0.8
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  0.96
2001 Murray D, McLaughlin S, Honig B. The Role of Electrostatic Interactions in the Regulation of the Membrane Association of G Protein βγ Heterodimers Journal of Biological Chemistry. 276: 45153-45159. PMID 11557749 DOI: 10.1074/Jbc.M101784200  0.96
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  0.96
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  0.72
2001 Rocchia W, Alexov E, Honig B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions Journal of Physical Chemistry B. 105: 6507-6514. DOI: 10.1021/Jp010454Y  0.96
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  0.8
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  0.96
2000 Ben-Tal N, Honig B, Bagdassarian CK, Ben-Shaul A. Association Entropy in Adsorption Processes Biophysical Journal. 79: 1180-1187. PMID 10968982 DOI: 10.1016/S0006-3495(00)76372-7  0.72
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  0.96
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  0.96
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  0.96
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  0.96
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  0.4
1999 Murray D, Arbuzova A, Hangyás-Mihályné G, Gambhir A, Ben-Tal N, Honig B, McLaughlin S. Electrostatic properties of membranes containing acidic lipids and adsorbed basic peptides: theory and experiment. Biophysical Journal. 77: 3176-88. PMID 10585939 DOI: 10.1016/S0006-3495(99)77148-1  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
1997 Chen SW, Honig B. Monovalent and Divalent Salt Effects on Electrostatic Free Energies Defined by the Nonlinear Poisson−Boltzmann Equation: Application to DNA Binding Reactions Journal of Physical Chemistry B. 101: 9113-9118. DOI: 10.1021/Jp971521K  0.8
1997 Ben-Tal N, Sitkoff D, Topol IA, Yang A, Burt SK, Honig B. Free Energy of Amide Hydrogen Bond Formation in Vacuum, in Water, and in Liquid Alkane Solution Journal of Physical Chemistry B. 101: 450-457. DOI: 10.1021/Jp961825R  0.8
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  0.96
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  0.96
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  0.96
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  0.96
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  0.72
1996 Ben-Tal N, Ben-Shaul A, Nicholls A, Honig B. Free-energy determinants of alpha-helix insertion into lipid bilayers. Biophysical Journal. 70: 1803-1812. PMID 8785340 DOI: 10.1016/S0006-3495(96)79744-8  0.72
1996 Lancaster CR, Michel H, Honig B, Gunner MR. Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis. Biophysical Journal. 70: 2469-92. PMID 8744288 DOI: 10.1016/S0006-3495(96)79820-X  0.36
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  0.96
1996 Misra VK, Honig B. The electrostatic contribution to the B to Z transition of DNA Biochemistry. 35: 1115-1124. PMID 8573566 DOI: 10.1021/Bi951463Y  0.96
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  0.96
1996 Sitkoff D, Ben-Tal aN, Honig B. Calculation of Alkane to Water Solvation Free Energies Using Continuum Solvent Models The Journal of Physical Chemistry. 100: 2744-2752. DOI: 10.1021/Jp952986I  0.8
1996 Friedman RA, Honig B. Response to S. H. Gellman, T. S. Haque, and L. F. Newcomb Biophysical Journal. 71: 3525-3526. DOI: 10.1016/S0006-3495(96)79548-6  0.8
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  0.96
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  0.96
1995 Honig B, Nicholls A. Classical electrostatics in biology and chemistry Science. 268: 1144-1149. PMID 7761829 DOI: 10.1126/Science.7761829  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
1995 Hecht JL, Honig B, Shin YK, Hubbell WL. Electrostatic potentials near the surface of DNA: Comparing theory and experiment Journal of Physical Chemistry. 99: 7782-7786. DOI: 10.1021/J100019A067  0.96
1995 Vorobjev YN, Scheraga HA, Honig B. Theoretical Modeling of Electrostatic Effects of Titratable Side Chain Groups on Protein Conformation in a Polar Ionic Solution. 2. pH-Induced Helix-Coil Transition of Poly(L-lysine) in Water and Methanol Ionic Solutions The Journal of Physical Chemistry. 99: 7180-7187. DOI: 10.1021/J100018A060  0.8
1995 Honig B. Theory and simulation Current Opinion in Structural Biology. 5: 203-204. DOI: 10.1016/0959-440X(95)80076-X  0.8
1995 Bharadwaj R, Windemuth A, Sridharan S, Honig B, Nicholls A. The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems Journal of Computational Chemistry. 16: 898-913. DOI: 10.1002/Jcc.540160707  0.8
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
1994 Sitkoff D, Sharp KA, Honig B. Correlating solvation free energies and surface tensions of hydrocarbon solutes Biophysical Chemistry. 51: 397-409. PMID 7919044 DOI: 10.1016/0301-4622(94)00062-X  0.96
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  0.96
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  0.96
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  0.8
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  0.8
1994 Vorobjev YN, Scheraga HA, Hitz B, Honig B. Theoretical Modeling of Electrostatic Effects of Titratable Side-Chain Groups on Protein Conformation in a Polar Ionic Solution. 1. Potential of Mean Force between Charged Lysine Residues and Titration of Poly(L-lysine) in 95% Methanol Solution The Journal of Physical Chemistry. 98: 10940-10948. DOI: 10.1021/J100093A042  0.8
1994 Sitkoff D, Sharp KA, Honig B. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models The Journal of Physical Chemistry. 98: 1978-1988. DOI: 10.1021/J100058A043  0.8
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  0.96
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  0.96
1993 Honig B, Sharp K, Yang AS. Macroscopic Models of Aqueous Solutions: Biological and Chemical Applications The Journal of Physical Chemistry. 97: 1101-1109. DOI: 10.1021/J100108A002  0.8
1992 Friedman RA, Honig B. The electrostatic contribution to DNA base-stacking interactions Biopolymers. 32: 145-158. PMID 1637989 DOI: 10.1002/Bip.360320205  0.96
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  0.96
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  0.96
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  0.96
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  0.96
1991 Sharp KA, Nicholls A, Fine RF, Honig B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects Science. 252: 106-109. PMID 2011744 DOI: 10.1126/Science.2011744  0.96
1991 Gunner MR, Honig B. 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. 88: 9151-9155. PMID 1924378 DOI: 10.1073/Pnas.88.20.9151  0.96
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  0.44
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  0.96
1991 Honig B. Theory and simulation: Editorial overview Current Opinion in Structural Biology. 1: 169-170. DOI: 10.1016/0959-440X(91)90056-Y  0.8
1991 Nicholls A, Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation Journal of Computational Chemistry. 12: 435-445. DOI: 10.1002/Jcc.540120405  0.8
1990 Sharp KA, Honig B, Harvey SC. Electrical potential of transfer RNAs: codon-anticodon recognition. Biochemistry. 29: 340-6. PMID 2405900 DOI: 10.1021/Bi00454A006  0.96
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  0.96
1990 Sharp KA, Honig B. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation The Journal of Physical Chemistry. 94: 7684-7692. DOI: 10.1021/J100382A068  0.8
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  0.96
1989 Jayaram B, Sharp KA, Honig B. The electrostatic potential of B-DNA Biopolymers. 28: 975-993. PMID 2742988 DOI: 10.1002/Bip.360280506  0.96
1989 Soman K, Yang AS, Honig B, Fletterick R. Electrical potentials in trypsin isozymes Biochemistry. 28: 9918-9926. PMID 2695163 DOI: 10.1021/Bi00452A007  0.96
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  0.96
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  0.96
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  0.96
1988 Gilson MK, Honig BH. Energetics of charge-charge interactions in proteins. Proteins. 3: 32-52. PMID 3287370 DOI: 10.1002/Prot.340030104  0.96
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  0.96
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  0.96
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  0.44
1987 Sharp K, Fine R, Honig B. Computer simulations of the diffusion of a substrate to an active site of an enzyme Science. 236: 1460-1463. PMID 3589666 DOI: 10.1126/Science.3589666  0.96
1987 Gilson MK, Honig BH. Calculation of electrostatic potentials in an enzyme active site. Nature. 330: 84-6. PMID 3313058 DOI: 10.1038/330084A0  0.96
1986 Gilson MK, Honig BH. The dielectric constant of a folded protein. Biopolymers. 25: 2097-119. PMID 3790703 DOI: 10.1002/Bip.360251106  0.96
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  0.96
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  0.4
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  0.96
1986 Honig BH, Hubbell WL, Flewelling RF. Electrostatic interactions in membranes and proteins. Annual Review of Biophysics and Biophysical Chemistry. 15: 163-93. PMID 2424473 DOI: 10.1146/annurev.bb.15.060186.001115  0.96
1986 Rashin AA, Honig B. The Born Model of Ion Solvation Revisited Annals of the New York Academy of Sciences. 482: 143-144. DOI: 10.1111/J.1749-6632.1986.Tb20945.X  0.8
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  0.96
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  0.96
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  0.96
1985 Rashin AA, Honig B. Reevaluation of the Born model of ion hydration The Journal of Physical Chemistry. 89: 5588-5593. DOI: 10.1021/J100272A006  0.8
1984 Rashin AA, Honig B. On the environment of ionizable groups in globular proteins Journal of Molecular Biology. 173: 515-521. PMID 6708109 DOI: 10.1016/0022-2836(84)90394-2  0.96
1984 Honig BH, Hubbell WL. Stability of "salt bridges" in membrane proteins. Proceedings of the National Academy of Sciences of the United States of America. 81: 5412-6. PMID 6591197 DOI: 10.1073/Pnas.81.17.5412  0.96
1984 Doukas AG, Junnarkar MR, Alfano RR, Callender RH, Kakitani T, Honig B. Fluorescence quantum yield of visual pigments: Evidence for subpicosecond isomerization rates Proceedings of the National Academy of Sciences of the United States of America. 81: 4790-4794. PMID 6589626 DOI: 10.1073/Pnas.81.15.4790  0.96
1983 Kakitani H, Kakitani T, Rodman H, Honig B, Callender R. Correlation of vibrational frequencies with absorption maxima in polyenes, rhodopsin, bacteriorhodopsin, and retinal analogues Journal of Physical Chemistry. 87: 3620-3628. DOI: 10.1021/J100242A011  0.96
1982 Kakitani T, Honig B, Crofts AR. Theoretical studies of the electrochromic response of carotenoids in photosynthetic membranes. Biophysical Journal. 39: 57-63. PMID 7104451 DOI: 10.1016/S0006-3495(82)84490-1  0.96
1982 Honig B. Chapter 20 Photochemical Charge Separation and Active Transport in the Purple Membrane Current Topics in Membranes and Transport. 16: 371-382. DOI: 10.1016/S0070-2161(08)60710-8  0.36
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  0.96
1981 Doukas AG, Pande A, Suzuki T, Callender RH, Honig B, Ottolenghi M. On the mechanism of hydrogen-deuterium exchange in bacteriorhodopsin Biophysical Journal. 33: 275-279. PMID 7225508 DOI: 10.1016/S0006-3495(81)84889-8  0.96
1981 Kalisky O, Ottolenghi M, Honig B, Korenstein R. Environmental effects on formation and photoreaction of the M412 photoproduct of bacteriorhodopsin: implications for the mechanism of proton pumping. Biochemistry. 20: 649-655. PMID 7213600 DOI: 10.1021/Bi00506A031  0.56
1981 Honig B. Excited state properties of visual pigments and bacteriorhodopsin Annals of the New York Academy of Sciences. 269-280. PMID 6942755 DOI: 10.1111/J.1749-6632.1981.Tb50573.X  0.96
1981 Dinur U, Honig B, Ottolenghi M. Analysis Of Primary Photochemical Processes In Bacteriorhodopsin Photochemistry and Photobiology. 33: 523-527. DOI: 10.1111/J.1751-1097.1981.Tb05455.X  0.8
1980 Aton B, Doukas AG, Narva D, Callender RH, Dinur U, Honig B. Resonance raman studies of the primary photochemical event in visual pigments Biophysical Journal. 29: 79-94. PMID 7260248 DOI: 10.1016/S0006-3495(80)85119-8  0.96
1980 Dinur U, Honig B. A consistent semiempirical theory for the calculation of ground and excited state properties Journal of Chemical Physics. 72: 1817-1829. DOI: 10.1063/1.439300  0.8
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  0.96
1980 Dinur U, Honig B. A Consistent Semiempirical Theory For The Calculation Of Ground And Excited State Properties Cheminform. 11. DOI: 10.1002/Chin.198023077  0.8
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  0.8
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  0.96
1979 Honig B, Ebrey T, Callender RH, Dinur U, Ottolenghi M. Photoisomerization, energy storage, and charge separation: A model for light energy transduction in visual pigments and bacteriorhodopsin Proceedings of the National Academy of Sciences of the United States of America. 76: 2503-2507. PMID 288039 DOI: 10.1073/Pnas.76.6.2503  0.96
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  0.8
1979 Dinur U, Honig B. Natural orbitals of s-cis-butadiene and their relation to photochemical cyclization Chemical Physics Letters. 64: 588-592. DOI: 10.1016/0009-2614(79)80252-3  0.96
1978 Honig B, Stein WD. Design principles for active transport systems Journal of Theoretical Biology. 75: 299-305. PMID 745445 DOI: 10.1016/0022-5193(78)90336-3  0.96
1978 Aton B, Callender RH, Honig B. Photochemical cis-trans isomerisation of bovine rhodopsin at liquid helium temperatures Nature. 273: 784-786. PMID 661987 DOI: 10.1038/273784A0  0.96
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  0.96
1978 Honig B. Light Energy Transduction in Visual Pigments and Bacteriorhodopsin Annual Review of Physical Chemistry. 29: 31-57. DOI: 10.1146/Annurev.Pc.29.100178.000335  0.8
1978 Doukas AG, Aton B, Callender RH, Honig B. Resonance Raman excitation profiles of all-trans retinal: theoretical implications Chemical Physics Letters. 56: 248-252. DOI: 10.1016/0009-2614(78)80232-2  0.96
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  0.96
1977 Stein WD, Honig B. Models for the active transport of cations ⋯ The steady-state analysis Molecular and Cellular Biochemistry. 15: 27-44. PMID 865483 DOI: 10.1007/Bf01731287  0.96
1977 Ebrey TG, Honig B. New wavelength dependent visual pigment nomograms Vision Research. 17: 147-151. PMID 855199 DOI: 10.1016/0042-6989(77)90213-9  0.96
1977 Hurley JB, Ebrey TG, Honig B, Ottolenghi M. Temperature and wavelength effects on the photochemistry of rhodopsin, isorhodopsin, bacteriorhodopsin and their photoproducts Nature. 270: 540-542. PMID 593379 DOI: 10.1038/270540A0  0.96
1977 Rosenfeld T, Honig B, Ottolenghi M, Hurley J, Ebrey TG. Cis-Trans Isomerization in the Photochemistry of Vision Pure and Applied Chemistry. 49: 341-351. DOI: 10.1351/Pac197749030341  0.96
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  0.96
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  0.96
1975 Greenberg AD, Honig B, Ebrey TG. Wavelength dependence of the bandwidths of visual pigment spectra Nature. 257: 823-824. PMID 1186873 DOI: 10.1038/257823A0  0.96
1975 Alchalel A, Honig B, Ottolenghi M, Rosenfeld T. Triplet-sensitized cis-trans isomerization of the protonated schiff base of retinal isomers. Journal of the American Chemical Society. 97: 2161-2166. PMID 1133410 DOI: 10.1021/Ja00841A029  0.56
1975 Ebrey TG, Honig B. Molecular aspects of photoreceptor function Quarterly Reviews of Biophysics. 8: 129-184. PMID 127191 DOI: 10.1017/S0033583500001785  0.96
1975 Honig B, Warshel A, Karplus M. Theoretical studies of the visual chromophore Accounts of Chemical Research. 8: 92-100. DOI: 10.1021/Ar50087A003  0.84
1975 Alchalel A, Honig B, Ottolenghi M, Rosenfeld T. Triplet-Sensitized Cis-Trans Isomerization Of The Protonated Schiff Base Of Retinal Isomers Cheminform. 6. DOI: 10.1002/Chin.197526144  0.8
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  0.96
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  0.8
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  0.96
1973 Honig B, Kahn P, Ebrey TG. Intrinsic optical activity of retinal isomers. Implications for the circular dichroism spectrum of rhodopsin Biochemistry. 12: 1637-1643. PMID 4699992 DOI: 10.1021/Bi00732A027  0.96
1972 Ebrey TG, Honig B. Ultraviolet chromophore transitions in the rhodopsin spectrum Proceedings of the National Academy of Sciences of the United States of America. 69: 1897-1899. PMID 4505668 DOI: 10.1073/Pnas.69.7.1897  0.96
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  0.96
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  0.96
1970 Sharf B, Honig B. Comments on vibronic intensity borrowing Chemical Physics Letters. 7: 132-136. DOI: 10.1016/0009-2614(70)80267-6  0.96
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  0.8
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  0.8
1964 Turner AG, Honig BH, Parr RG, Hoyland JR. Off-center hydrogen atom calculations The Journal of Chemical Physics. 40: 3216-3220.  0.96
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