| Year |
Citation |
Score |
| 2024 |
Zipursky S, Lee J, Sergeeva A, Ahlsen G, Mannepalli S, Bahna F, Goodman K, Khakh B, Weiner J, Shapiro L, Honig B. Astrocyte morphogenesis requires self-recognition. Research Square. PMID 38463964 DOI: 10.21203/rs.3.rs-3932947/v1 |
0.468 |
|
| 2023 |
Zhao H, Murray D, Petrey D, Honig B. ZEPPI: proteome-scale sequence-based evaluation of protein-protein interaction models. Research Square. PMID 37790387 DOI: 10.21203/rs.3.rs-3289791/v1 |
0.81 |
|
| 2023 |
Nagendra K, Izzet A, Judd NB, Zakine R, Friedman L, Harrison OJ, Pontani LL, Shapiro L, Honig B, Brujic J. Push-pull mechanics of E-cadherin ectodomains in biomimetic adhesions. Biophysical Journal. PMID 37528581 DOI: 10.1016/j.bpj.2023.07.026 |
0.513 |
|
| 2023 |
Sergeeva AP, Katsamba PS, Liao J, Sampson JM, Bahna F, Mannepalli S, Morano NC, Shapiro L, Friesner RA, Honig B. Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. Journal of Molecular Biology. 435: 168187. PMID 37355034 DOI: 10.1016/j.jmb.2023.168187 |
0.792 |
|
| 2023 |
Su Z, Kon N, Yi J, Zhao H, Zhang W, Tang Q, Li H, Kobayashi H, Li Z, Duan S, Liu Y, Olive KP, Zhang Z, Honig B, Manfredi JJ, et al. Specific regulation of BACH1 by the hotspot mutant p53 reveals a distinct gain-of-function mechanism. Nature Cancer. PMID 36973430 DOI: 10.1038/s43018-023-00532-z |
0.576 |
|
| 2023 |
Petrey D, Zhao H, Trudeau S, Murray D, Honig B. PrePPI: A structure informed proteome-wide database of protein-protein interactions. Journal of Molecular Biology. 168052. PMID 36933822 DOI: 10.1016/j.jmb.2023.168052 |
0.808 |
|
| 2023 |
Petrey D, Zhao H, Trudeau S, Murray D, Honig B. PrePPI: A structure informed proteome-wide database of protein-protein interactions. Biorxiv : the Preprint Server For Biology. PMID 36909476 DOI: 10.1101/2023.02.27.530276 |
0.807 |
|
| 2023 |
Trudeau SJ, Hwang H, Mathur D, Begum K, Petrey D, Murray D, Honig B. PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions. Protein Science : a Publication of the Protein Society. e4594. PMID 36776141 DOI: 10.1002/pro.4594 |
0.721 |
|
| 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 |
0.666 |
|
| 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 |
0.712 |
|
| 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 |
0.507 |
|
| 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 |
0.432 |
|
| 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 |
0.698 |
|
| 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 |
0.478 |
|
| 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 |
0.699 |
|
| 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 |
0.375 |
|
| 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 |
0.704 |
|
| 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 |
0.589 |
|
| 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 |
0.775 |
|
| 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 |
0.499 |
|
| 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 |
0.567 |
|
| 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 |
0.323 |
|
| 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 |
0.721 |
|
| 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 |
0.539 |
|
| 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 |
0.566 |
|
| 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 |
0.551 |
|
| 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 |
0.581 |
|
| 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 |
0.52 |
|
| 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 |
0.564 |
|
| 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 |
0.407 |
|
| 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 |
0.496 |
|
| 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 |
0.713 |
|
| 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 |
0.75 |
|
| 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 |
0.564 |
|
| 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 |
0.409 |
|
| 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 |
0.488 |
|
| 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 |
0.364 |
|
| 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 |
0.533 |
|
| 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 |
0.502 |
|
| 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 |
0.656 |
|
| 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 |
0.323 |
|
| 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 |
0.479 |
|
| 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 |
0.658 |
|
| 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 |
0.573 |
|
| 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 |
0.734 |
|
| 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 |
0.757 |
|
| 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 |
0.328 |
|
| 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 |
0.335 |
|
| 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 |
0.59 |
|
| 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 |
0.572 |
|
| 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 |
0.362 |
|
| 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 |
0.522 |
|
| 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 |
0.713 |
|
| 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 |
0.66 |
|
| 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 |
0.582 |
|
| 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 |
0.533 |
|
| 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 |
0.726 |
|
| 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 |
0.754 |
|
| 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 |
0.742 |
|
| 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 |
0.74 |
|
| 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 |
0.709 |
|
| 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 |
0.602 |
|
| 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 |
0.396 |
|
| 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 |
0.576 |
|
| 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 |
0.705 |
|
| 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 |
0.339 |
|
| 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 |
0.676 |
|
| 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 |
0.609 |
|
| 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 |
0.565 |
|
| 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 |
0.517 |
|
| 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 |
0.8 |
|
| 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 |
0.789 |
|
| 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 |
0.371 |
|
| 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 |
0.793 |
|
| 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 |
0.757 |
|
| 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 |
0.797 |
|
| 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 |
0.61 |
|
| 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 |
0.561 |
|
| 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 |
0.381 |
|
| 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 |
0.791 |
|
| 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 |
0.568 |
|
| 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 |
0.31 |
|
| 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 |
0.406 |
|
| 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 |
0.778 |
|
| 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 |
0.375 |
|
| 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 |
0.681 |
|
| 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 |
0.769 |
|
| 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 |
0.35 |
|
| 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 |
0.785 |
|
| 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 |
0.794 |
|
| 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 |
0.669 |
|
| 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 |
0.572 |
|
| 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 |
0.386 |
|
| 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 |
0.689 |
|
| 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 |
0.661 |
|
| 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 |
0.409 |
|
| 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 |
0.589 |
|
| 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 |
0.513 |
|
| 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 |
0.798 |
|
| 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 |
0.72 |
|
| 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 |
0.748 |
|
| 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 |
0.364 |
|
| 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 |
0.36 |
|
| 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 |
0.364 |
|
| 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 |
0.789 |
|
| 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 |
0.556 |
|
| 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 |
0.337 |
|
| 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 |
0.444 |
|
| 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 |
0.456 |
|
| 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 |
0.411 |
|
| 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 |
0.745 |
|
| 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 |
0.794 |
|
| 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 |
0.465 |
|
| 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 |
0.735 |
|
| 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 |
0.651 |
|
| 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 |
0.634 |
|
| 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 |
0.548 |
|
| 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 |
0.307 |
|
| 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 |
0.534 |
|
| 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 |
0.615 |
|
| 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 |
0.401 |
|
| 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 |
0.522 |
|
| 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 |
0.819 |
|
| 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 |
0.765 |
|
| 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 |
0.706 |
|
| 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 |
0.353 |
|
| 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 |
0.365 |
|
| 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 |
0.595 |
|
| 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 |
0.309 |
|
| 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 |
0.356 |
|
| 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 |
0.376 |
|
| 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 |
0.756 |
|
| 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 |
0.552 |
|
| 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 |
0.38 |
|
| 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 |
0.489 |
|
| 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 |
0.366 |
|
| 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 |
0.323 |
|
| 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 |
0.356 |
|
| 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 |
0.738 |
|
| 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 |
0.658 |
|
| 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 |
0.333 |
|
| 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 |
0.303 |
|
| 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 |
0.741 |
|
| 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 |
0.412 |
|
| 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 |
0.579 |
|
| 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 |
0.704 |
|
| 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 |
0.808 |
|
| 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 |
0.323 |
|
| 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 |
0.312 |
|
| 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 |
0.748 |
|
| 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 |
0.31 |
|
| 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 |
0.375 |
|
| 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 |
0.796 |
|
| 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 |
0.607 |
|
| 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 |
0.408 |
|
| 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 |
0.381 |
|
| 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 |
0.706 |
|
| 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 |
0.681 |
|
| 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 |
0.798 |
|
| 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 |
0.423 |
|
| 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 |
0.408 |
|
| 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 |
0.789 |
|
| 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 |
0.394 |
|
| 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 |
0.474 |
|
| 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 |
0.383 |
|
| 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 |
0.306 |
|
| 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 |
0.361 |
|
| 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 |
0.389 |
|
| 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 |
0.541 |
|
| 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 |
0.627 |
|
| 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 |
0.513 |
|
| 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 |
0.735 |
|
| 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 |
0.301 |
|
| 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 |
0.446 |
|
| 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 |
0.399 |
|
| 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 |
0.445 |
|
| 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 |
0.303 |
|
| 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 |
0.386 |
|
| 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 |
0.439 |
|
| 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 |
0.396 |
|
| 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 |
0.305 |
|
| 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 |
0.388 |
|
| 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 |
0.335 |
|
| 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 |
0.371 |
|
| 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 |
0.323 |
|
| 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 |
0.343 |
|
| 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 |
0.339 |
|
| 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 |
0.353 |
|
| 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 |
0.302 |
|
| 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 |
0.407 |
|
| 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 |
0.345 |
|
| 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 |
0.317 |
|
| 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 |
0.357 |
|
| 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 |
0.386 |
|
| 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 |
0.507 |
|
| 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 |
0.489 |
|
| 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 |
0.303 |
|
| 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 |
0.361 |
|
| 1995 |
Honig B, Nicholls A. Classical electrostatics in biology and chemistry Science. 268: 1144-1149. PMID 7761829 DOI: 10.1126/Science.7761829 |
0.339 |
|
| 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 |
0.321 |
|
| 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 |
0.324 |
|
| 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 |
0.341 |
|
| 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 |
0.473 |
|
| 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 |
0.306 |
|
| 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 |
0.376 |
|
| 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 |
0.368 |
|
| 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 |
0.32 |
|
| 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 |
0.329 |
|
| 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 |
0.336 |
|
| 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 |
0.321 |
|
| 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 |
0.306 |
|
| 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 |
0.467 |
|
| 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 |
0.572 |
|
| 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 |
0.3 |
|
| 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 |
0.321 |
|
| 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 |
0.331 |
|
| 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 |
0.31 |
|
| 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 |
0.357 |
|
| 1992 |
Yang A, Honig B. Electrostatic effects on protein stability Current Biology. 2: 82. DOI: 10.1016/0960-9822(92)90213-T |
0.322 |
|
| 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 |
0.363 |
|
| 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 |
0.547 |
|
| 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 |
0.343 |
|
| 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 |
0.403 |
|
| 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 |
0.663 |
|
| 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 |
0.585 |
|
| 1989 |
Jayaram B, Sharp KA, Honig B. The electrostatic potential of B-DNA Biopolymers. 28: 975-993. PMID 2742988 DOI: 10.1002/Bip.360280506 |
0.555 |
|
| 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 |
0.517 |
|
| 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 |
0.49 |
|
| 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 |
0.576 |
|
| 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 |
0.348 |
|
| 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 |
0.532 |
|
| 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 |
0.371 |
|
| 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 |
0.324 |
|
| 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 |
0.328 |
|
| 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 |
0.52 |
|
| 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 |
0.435 |
|
| 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 |
0.34 |
|
| 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 |
0.302 |
|
| 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 |
0.41 |
|
| 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 |
0.386 |
|
| 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 |
0.39 |
|
| 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 |
0.393 |
|
| 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 |
0.388 |
|
| 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 |
0.388 |
|
| 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 |
0.388 |
|
| 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 |
0.414 |
|
| 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 |
0.358 |
|
| 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 |
0.685 |
|
| 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 |
0.314 |
|
| 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 |
0.372 |
|
| 1975 |
Honig B, Warshel A, Karplus M. Theoretical studies of the visual chromophore Accounts of Chemical Research. 8: 92-100. DOI: 10.1021/Ar50087A003 |
0.524 |
|
| 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 |
0.376 |
|
| 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 |
0.377 |
|
| 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 |
0.634 |
|
| 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 |
0.409 |
|
| 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 |
0.408 |
|
| 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 |
0.425 |
|
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