| Year |
Citation |
Score |
| 2024 |
Wang Y, Liu J, Peters MM, Ishii R, Wang D, Chowdhury S, Parker KK, Shakhnovich EI. Entropy-driven Denaturation for Sustainable Regeneration of Protein Waste. Biorxiv : the Preprint Server For Biology. PMID 38915630 DOI: 10.1101/2024.06.12.598657 |
0.809 |
|
| 2023 |
Ranganathan S, Liu J, Shakhnovich E. Enzymatic metabolons dramatically enhance metabolic fluxes of low-efficiency biochemical reactions. Biophysical Journal. PMID 37915170 DOI: 10.1016/j.bpj.2023.10.033 |
0.789 |
|
| 2023 |
Bitran A, Park K, Serebryany E, Shakhnovich EI. Co-translational formation of disulfides guides folding of the SARS-CoV-2 receptor binding domain. Biophysical Journal. PMID 37422697 DOI: 10.1016/j.bpj.2023.07.002 |
0.38 |
|
| 2023 |
Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI. Empowering drug off-target discovery with metabolic and structural analysis. Nature Communications. 14: 3390. PMID 37296102 DOI: 10.1038/s41467-023-38859-x |
0.641 |
|
| 2023 |
Serebryany E, Zhao VY, Park K, Bitran A, Trauger SA, Budnik B, Shakhnovich EI. Systematic conformation-to-phenotype mapping via limited deep sequencing of proteins. Molecular Cell. 83: 1936-1952.e7. PMID 37267908 DOI: 10.1016/j.molcel.2023.05.006 |
0.375 |
|
| 2023 |
Ranganathan S, Dasmeh P, Furniss S, Shakhnovich E. Phosphorylation sites are evolutionary checkpoints against liquid-solid transition in protein condensates. Proceedings of the National Academy of Sciences of the United States of America. 120: e2215828120. PMID 37155880 DOI: 10.1073/pnas.2215828120 |
0.806 |
|
| 2023 |
Ogbunugafor CB, Guerrero RF, Shakhnovich EI, Shoulders MD. Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance. Biorxiv : the Preprint Server For Biology. PMID 37066177 DOI: 10.1101/2023.04.09.535490 |
0.316 |
|
| 2023 |
Serebryany E, Zhao VY, Park K, Bitran A, Trauger SA, Budnik B, Shakhnovich EI. Systematic conformation-to-phenotype mapping via limited deep-sequencing of proteins. Arxiv. PMID 36776823 |
0.375 |
|
| 2022 |
Bitran A, Park K, Serebryany E, Shakhnovich EI. Cotranslational formation of disulfides guides folding of the SARS COV-2 receptor binding domain. Biorxiv : the Preprint Server For Biology. PMID 36380756 DOI: 10.1101/2022.11.10.516025 |
0.313 |
|
| 2022 |
Ranganathan S, Liu J, Shakhnovich E. Different states and the associated fates of biomolecular condensates. Essays in Biochemistry. PMID 36350032 DOI: 10.1042/EBC20220054 |
0.79 |
|
| 2022 |
Serebryany E, Chowdhury S, Woods CN, Thorn DC, Watson NE, McClelland AA, Klevit RE, Shakhnovich EI. A native chemical chaperone in the human eye lens. Elife. 11. PMID 35723573 DOI: 10.7554/eLife.76923 |
0.684 |
|
| 2021 |
Zhang Y, Chowdhury S, Rodrigues JV, Shakhnovich EI. Development of antibacterial compounds that constrain evolutionary pathways to resistance. Elife. 10. PMID 34279221 DOI: 10.7554/eLife.64518 |
0.636 |
|
| 2021 |
Razban RM, Dasmeh P, Serohijos AWR, Shakhnovich EI. Avoidance of protein unfolding constrains protein stability in long-term evolution. Biophysical Journal. PMID 33932438 DOI: 10.1016/j.bpj.2021.03.042 |
0.832 |
|
| 2020 |
Bitran A, Jacobs WM, Shakhnovich E. Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins. Plos Computational Biology. 16: e1008323. PMID 33196646 DOI: 10.1371/journal.pcbi.1008323 |
0.358 |
|
| 2020 |
Zhao V, Jacobs WM, Shakhnovich EI. Effect of Protein Structure on Evolution of Cotranslational Folding. Biophysical Journal. PMID 32857962 DOI: 10.1016/J.Bpj.2020.06.037 |
0.52 |
|
| 2020 |
Ranganathan S, Shakhnovich EI. Dynamic metastable long-living droplets formed by sticker-spacer proteins. Elife. 9. PMID 32484438 DOI: 10.7554/Elife.56159 |
0.351 |
|
| 2020 |
Razban RM, Shakhnovich EI. Effects of Single Mutations on Protein Stability Are Gaussian Distributed. Biophysical Journal. PMID 32416078 DOI: 10.1016/J.Bpj.2020.04.027 |
0.457 |
|
| 2020 |
Bitran A, Jacobs WM, Zhai X, Shakhnovich E. Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps. Proceedings of the National Academy of Sciences of the United States of America. 117: 1485-1495. PMID 31911473 DOI: 10.1073/Pnas.1913207117 |
0.496 |
|
| 2020 |
Ranganathan S, Shakhnovich EI. Author response: Dynamic metastable long-living droplets formed by sticker-spacer proteins Elife. DOI: 10.7554/Elife.56159.Sa2 |
0.351 |
|
| 2020 |
Thai J, Serebryany E, Shakhnovich E. Elucidating the Structure of Aggregation-Prone Intermediate Conformations in Diverse Point Mutants of Human γD-Crystallin Biophysical Journal. 118: 40a. DOI: 10.1016/J.Bpj.2019.11.397 |
0.328 |
|
| 2019 |
Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, et al. Common activation mechanism of class A GPCRs. Elife. 8. PMID 31855179 DOI: 10.7554/Elife.50279 |
0.674 |
|
| 2019 |
Chen Q, Xiao Y, Shakhnovich EI, Zhang W, Mu W. Semi-rational design and molecular dynamics simulations study of the thermostability enhancement of cellobiose 2-epimerases. International Journal of Biological Macromolecules. PMID 31733243 DOI: 10.1016/J.Ijbiomac.2019.11.015 |
0.386 |
|
| 2019 |
Adkar BV, Bhattacharyya S, Gilson AI, Zhang W, Shakhnovich EI. Substrate inhibition imposes fitness penalty at high protein stability. Proceedings of the National Academy of Sciences of the United States of America. PMID 31097595 DOI: 10.1073/Pnas.1821447116 |
0.339 |
|
| 2019 |
Rodrigues JV, Ogbunugafor CB, Hartl DL, Shakhnovich EI. Chimeric dihydrofolate reductases display properties of modularity and biophysical diversity. Protein Science : a Publication of the Protein Society. 28: 1359-1367. PMID 31095809 DOI: 10.1002/Pro.3646 |
0.439 |
|
| 2019 |
Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu Z, Stevens RC, Lambert NA, Babu MM, Wang M, et al. Author response: Common activation mechanism of class A GPCRs Elife. DOI: 10.7554/Elife.50279.Sa2 |
0.591 |
|
| 2018 |
Serebryany E, Yu S, Trauger SA, Budnik B, Shakhnovich EI. Dynamic disulfide exchange in a crystallin protein in the human eye lens promotes cataract-associated aggregation. The Journal of Biological Chemistry. PMID 30242128 DOI: 10.1074/Jbc.Ra118.004551 |
0.368 |
|
| 2018 |
Jacobs WM, Shakhnovich EI. Accurate Protein-Folding Transition-Path Statistics From a Simple Free-Energy Landscape. The Journal of Physical Chemistry. B. PMID 30091592 DOI: 10.1021/Acs.Jpcb.8B05842 |
0.397 |
|
| 2018 |
Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI. ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. Bioinformatics (Oxford, England). PMID 30010795 DOI: 10.1093/bioinformatics/bty516 |
0.699 |
|
| 2018 |
Rotem A, Serohijos AWR, Chang CB, Wolfe JT, Fischer AE, Mehoke TS, Zhang H, Tao Y, Ung WL, Choi JM, Rodrigues JV, Abimbola OK, Koehler SA, Wu S, Thielen PM, ... ... Shakhnovich EI, et al. Evolution on the biophysical fitness landscape of an RNA virus. Molecular Biology and Evolution. PMID 29955873 DOI: 10.1093/Molbev/Msy131 |
0.703 |
|
| 2018 |
Bhattacharyya S, Jacobs WM, Adkar BV, Yan J, Zhang W, Shakhnovich EI. Accessibility of the Shine-Dalgarno Sequence Dictates N-Terminal Codon Bias in E. coli. Molecular Cell. 70: 894-905.e5. PMID 29883608 DOI: 10.1016/J.Molcel.2018.05.008 |
0.348 |
|
| 2018 |
Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI. ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. Bioinformatics (Oxford, England). PMID 29741573 DOI: 10.1093/Bioinformatics/Bty370 |
0.746 |
|
| 2018 |
Hu R, Rodrigues JV, Waduge P, Yamazaki H, Cressiot B, Chishti Y, Makowski L, Yu D, Shakhnovich E, Zhao Q, Wanunu M. Differential Enzyme Flexibility Probed Using Solid-State Nanopores. Acs Nano. PMID 29630824 DOI: 10.1021/Acsnano.8B00734 |
0.467 |
|
| 2018 |
Manhart M, Adkar BV, Shakhnovich EI. Trade-offs between microbial growth phases lead to frequency-dependent and non-transitive selection. Proceedings. Biological Sciences. 285. PMID 29445020 DOI: 10.1098/Rspb.2017.2459 |
0.308 |
|
| 2018 |
Klein EY, Blumenkrantz D, Serohijos A, Shakhnovich E, Choi JM, Rodrigues JV, Smith BD, Lane AP, Feldman A, Pekosz A. Stability of the Influenza Virus Hemagglutinin Protein Correlates with Evolutionary Dynamics. Msphere. 3. PMID 29299534 DOI: 10.1128/mSphereDirect.00554-17 |
0.81 |
|
| 2017 |
Valleau S, Studer RA, Häse F, Kreisbeck C, Saer RG, Blankenship RE, Shakhnovich EI, Aspuru-Guzik A. Absence of Selection for Quantum Coherence in the Fenna-Matthews-Olson Complex: A Combined Evolutionary and Excitonic Study. Acs Central Science. 3: 1086-1095. PMID 29104925 DOI: 10.1021/Acscentsci.7B00269 |
0.322 |
|
| 2017 |
Jacobs WM, Shakhnovich EI. Evidence of evolutionary selection for cotranslational folding. Proceedings of the National Academy of Sciences of the United States of America. 114: 11434-11439. PMID 29073068 DOI: 10.1073/Pnas.1705772114 |
0.465 |
|
| 2017 |
Adkar BV, Manhart M, Bhattacharyya S, Tian J, Musharbash M, Shakhnovich EI. Optimization of lag phase shapes the evolution of a bacterial enzyme. Nature Ecology & Evolution. 1: 149. PMID 28812634 DOI: 10.1038/S41559-017-0149 |
0.3 |
|
| 2017 |
Loureiro RJS, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PFN. A tale of two tails: the importance of unstructured termini in the aggregation pathway of β2-microglobulin. Proteins. PMID 28745031 DOI: 10.1002/Prot.25358 |
0.411 |
|
| 2017 |
Chéron N, Shakhnovich EI. Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations. Journal of Computational Chemistry. PMID 28568844 DOI: 10.1002/Jcc.24839 |
0.334 |
|
| 2017 |
Gilson AI, Marshall-Christensen A, Choi JM, Shakhnovich EI. The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution. Biophysical Journal. 112: 1350-1365. PMID 28402878 DOI: 10.1016/J.Bpj.2017.02.029 |
0.761 |
|
| 2017 |
Choi JM, Gilson AI, Shakhnovich EI. Graph's Topology and Free Energy of a Spin Model on the Graph. Physical Review Letters. 118: 088302. PMID 28282198 DOI: 10.1103/Physrevlett.118.088302 |
0.673 |
|
| 2017 |
Debroise T, Shakhnovich EI, Chéron N. A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016. Journal of Chemical Information and Modeling. PMID 28191941 DOI: 10.1021/Acs.Jcim.6B00610 |
0.345 |
|
| 2017 |
Zhou Q, Sun X, Xia X, Fan Z, Luo Z, Zhao S, Shakhnovich EI, Liang H. Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighbourhoods in Sequence Space. The Journal of Physical Chemistry Letters. PMID 28045264 DOI: 10.1021/Acs.Jpclett.6B02769 |
0.732 |
|
| 2016 |
Bhattacharyya S, Bershtein S, Yan J, Argun T, Gilson AI, Trauger SA, Shakhnovich EI. Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity. Elife. 5. PMID 27938662 DOI: 10.7554/Elife.20309 |
0.422 |
|
| 2016 |
Bershtein S, Serohijos AW, Shakhnovich EI. Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations. Current Opinion in Structural Biology. 42: 31-40. PMID 27810574 DOI: 10.1016/J.Sbi.2016.10.013 |
0.807 |
|
| 2016 |
Jacobs WM, Shakhnovich EI. Structure-Based Prediction of Protein-Folding Transition Paths. Biophysical Journal. 111: 925-36. PMID 27602721 DOI: 10.1016/J.Bpj.2016.06.031 |
0.461 |
|
| 2016 |
Serebryany E, Woodard JC, Adkar BV, Shabab M, King JA, Shakhnovich EI. An internal disulfide locks a misfolded aggregation-prone intermediate in cataract-linked mutants of human γD-crystallin. The Journal of Biological Chemistry. PMID 27417136 DOI: 10.1074/Jbc.M116.735977 |
0.327 |
|
| 2016 |
Woodard JC, Dunatunga S, Shakhnovich EI. A Simple Model of Protein Domain Swapping in Crowded Cellular Environments. Biophysical Journal. 110: 2367-2376. PMID 27276255 DOI: 10.1016/J.Bpj.2016.04.033 |
0.415 |
|
| 2016 |
Jacquin H, Gilson A, Shakhnovich E, Cocco S, Monasson R. Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models. Plos Computational Biology. 12: e1004889. PMID 27177270 DOI: 10.1371/Journal.Pcbi.1004889 |
0.459 |
|
| 2016 |
Chéron N, Serohijos AW, Choi JM, Shakhnovich EI. Evolutionary dynamics of viral escape under antibodies stress: A biophysical model. Protein Science : a Publication of the Protein Society. PMID 26939576 DOI: 10.1002/Pro.2915 |
0.78 |
|
| 2016 |
Rodrigues JV, Bershtein S, Li A, Lozovsky ER, Hartl DL, Shakhnovich EI. Biophysical principles predict fitness landscapes of drug resistance. Proceedings of the National Academy of Sciences of the United States of America. PMID 26929328 DOI: 10.1073/Pnas.1601441113 |
0.35 |
|
| 2016 |
Bhattacharyya S, Bershtein S, Yan J, Argun T, Gilson AI, Trauger SA, Shakhnovich EI. Author response: Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity Elife. DOI: 10.7554/Elife.20309.026 |
0.375 |
|
| 2016 |
Zhou Q, Liang H, Shakhnovich E. Virtual Screening of Human O-GlcNAc Transferase Inhibitors Chinese Journal of Chemical Physics. 29: 374-380. DOI: 10.1063/1674-0068/29/Cjcp1510211 |
0.69 |
|
| 2015 |
Zhou Q, Xia X, Luo Z, Liang H, Shakhnovich E. Searching the Sequence Space for Potent Aptamers Using SELEX in Silico. Journal of Chemical Theory and Computation. 11: 5939-46. PMID 26642994 DOI: 10.1021/Acs.Jctc.5B00707 |
0.722 |
|
| 2015 |
Bershtein S, Serohijos AW, Bhattacharyya S, Manhart M, Choi JM, Mu W, Zhou J, Shakhnovich EI. Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria. Plos Genetics. 11: e1005612. PMID 26484862 DOI: 10.1371/Journal.Pgen.1005612 |
0.797 |
|
| 2015 |
Chéron N, Jasty N, Shakhnovich EI. OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. Journal of Medicinal Chemistry. PMID 26356253 DOI: 10.1021/Acs.Jmedchem.5B00886 |
0.332 |
|
| 2015 |
Zhang H, Cockrell SK, Kolawole AO, Rotem A, Serohijos AW, Chang CB, Tao Y, Mehoke TS, Han Y, Lin JS, Giacobbi NS, Feldman AB, Shakhnovich E, Weitz DA, Wobus CE, et al. Isolation and Analysis of Rare Norovirus Recombinants from Coinfected Mice Using Drop-Based Microfluidics. Journal of Virology. 89: 7722-34. PMID 25972549 DOI: 10.1128/Jvi.01137-15 |
0.769 |
|
| 2015 |
Tian J, Woodard JC, Whitney A, Shakhnovich EI. Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences. Plos Computational Biology. 11: e1004207. PMID 25905910 DOI: 10.1371/Journal.Pcbi.1004207 |
0.443 |
|
| 2015 |
Bershtein S, Choi JM, Bhattacharyya S, Budnik B, Shakhnovich E. Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship. Cell Reports. 11: 645-56. PMID 25892240 DOI: 10.1016/J.Celrep.2015.03.051 |
0.687 |
|
| 2015 |
Choi JM, Serohijos AW, Murphy S, Lucarelli D, Lofranco LL, Feldman A, Shakhnovich EI. Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding. Biophysical Journal. 108: 795-8. PMID 25692584 DOI: 10.1016/J.Bpj.2015.01.001 |
0.812 |
|
| 2015 |
Çetinba? M, Shakhnovich EI. Is catalytic activity of chaperones a selectable trait for the emergence of heat shock response? Biophysical Journal. 108: 438-48. PMID 25606691 DOI: 10.1016/J.Bpj.2014.11.3468 |
0.414 |
|
| 2014 |
Dasmeh P, Serohijos AW, Kepp KP, Shakhnovich EI. The influence of selection for protein stability on dN/dS estimations. Genome Biology and Evolution. 6: 2956-67. PMID 25355808 DOI: 10.1093/Gbe/Evu223 |
0.815 |
|
| 2014 |
Peleg O, Choi JM, Shakhnovich EI. Evolution of specificity in protein-protein interactions. Biophysical Journal. 107: 1686-96. PMID 25296322 DOI: 10.1016/J.Bpj.2014.08.004 |
0.743 |
|
| 2014 |
Serohijos AW, Shakhnovich EI. Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics. Current Opinion in Structural Biology. 26: 84-91. PMID 24952216 DOI: 10.1016/J.Sbi.2014.05.005 |
0.812 |
|
| 2014 |
Estácio SG, Krobath H, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PF. A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior. Plos Computational Biology. 10: e1003606. PMID 24809460 DOI: 10.1371/Journal.Pcbi.1003606 |
0.328 |
|
| 2014 |
Klein EY, Serohijos AW, Choi JM, Shakhnovich EI, Pekosz A. Influenza A H1N1 pandemic strain evolution--divergence and the potential for antigenic drift variants. Plos One. 9: e93632. PMID 24699432 DOI: 10.1371/Journal.Pone.0093632 |
0.769 |
|
| 2014 |
Serohijos AW, Shakhnovich EI. Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions. Molecular Biology and Evolution. 31: 165-76. PMID 24124208 DOI: 10.1093/Molbev/Mst189 |
0.807 |
|
| 2014 |
Gilson AI, Shakhnovich EI. Can a Protein's Evolutionary Fate be Predicted from its Structure? Biophysical Journal. 106: 657a. DOI: 10.1016/J.Bpj.2013.11.3636 |
0.491 |
|
| 2013 |
Cetinba? M, Shakhnovich EI. Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations. Plos Computational Biology. 9: e1003269. PMID 24244114 DOI: 10.1371/Journal.Pcbi.1003269 |
0.488 |
|
| 2013 |
Estácio SG, Shakhnovich EI, Faísca PF. Assessing the effect of loop mutations in the folding space of β2-microglobulin with molecular dynamics simulations. International Journal of Molecular Sciences. 14: 17256-78. PMID 23975166 DOI: 10.3390/Ijms140917256 |
0.423 |
|
| 2013 |
Krobath H, Shakhnovich EI, Faísca PF. Structural and energetic determinants of co-translational folding. The Journal of Chemical Physics. 138: 215101. PMID 23758397 DOI: 10.1063/1.4808044 |
0.445 |
|
| 2013 |
Dasmeh P, Serohijos AW, Kepp KP, Shakhnovich EI. Positively selected sites in cetacean myoglobins contribute to protein stability. Plos Computational Biology. 9: e1002929. PMID 23505347 DOI: 10.1371/Journal.Pcbi.1002929 |
0.794 |
|
| 2013 |
Raoof S, Heo M, Shakhnovich EI. A one-shot germinal center model under protein structural stability constraints. Physical Biology. 10: 025001. PMID 23492682 DOI: 10.1088/1478-3975/10/2/025001 |
0.361 |
|
| 2013 |
Serohijos AW, Lee SY, Shakhnovich EI. Highly abundant proteins favor more stable 3D structures in yeast. Biophysical Journal. 104: L1-3. PMID 23442924 DOI: 10.1016/J.Bpj.2012.11.3838 |
0.836 |
|
| 2013 |
Bershtein S, Mu W, Serohijos AW, Zhou J, Shakhnovich EI. Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness. Molecular Cell. 49: 133-44. PMID 23219534 DOI: 10.1016/J.Molcel.2012.11.004 |
0.822 |
|
| 2013 |
Tricard S, Stan CA, Shakhnovich EI, Whitesides GM. A macroscopic device described by a Boltzmann-like distribution Soft Matter. 9: 4480-4488. DOI: 10.1039/C3Sm27385G |
0.309 |
|
| 2012 |
Mannige RV, Brooks CL, Shakhnovich EI. A universal trend among proteomes indicates an oily last common ancestor. Plos Computational Biology. 8: e1002839. PMID 23300421 DOI: 10.1371/Journal.Pcbi.1002839 |
0.542 |
|
| 2012 |
Xia Z, Das P, Shakhnovich EI, Zhou R. Collapse of unfolded proteins in a mixture of denaturants. Journal of the American Chemical Society. 134: 18266-74. PMID 23057830 DOI: 10.1021/Ja3031505 |
0.497 |
|
| 2012 |
Serohijos AW, Rimas Z, Shakhnovich EI. Protein biophysics explains why highly abundant proteins evolve slowly. Cell Reports. 2: 249-56. PMID 22938865 DOI: 10.1016/J.Celrep.2012.06.022 |
0.827 |
|
| 2012 |
Estácio SG, Fernandes CS, Krobath H, Faísca PF, Shakhnovich EI. Robustness of atomistic Gō models in predicting native-like folding intermediates. The Journal of Chemical Physics. 137: 085102. PMID 22938266 DOI: 10.1063/1.4747492 |
0.47 |
|
| 2012 |
Wylie CS, Shakhnovich EI. Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation. Plos Computational Biology. 8: e1002609. PMID 22876168 DOI: 10.1371/Journal.Pcbi.1002609 |
0.372 |
|
| 2012 |
Krobath H, Estácio SG, Faísca PF, Shakhnovich EI. Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants. Journal of Molecular Biology. 422: 705-22. PMID 22727745 DOI: 10.1016/J.Jmb.2012.06.020 |
0.393 |
|
| 2012 |
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, ... ... Shakhnovich E, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071 |
0.654 |
|
| 2012 |
Huang L, Shakhnovich EI. Is there an en route folding intermediate for Cold shock proteins? Protein Science : a Publication of the Protein Society. 21: 677-85. PMID 22467601 DOI: 10.1002/Pro.2053 |
0.426 |
|
| 2012 |
Bershtein S, Mu W, Wu W, Shakhnovich EI. Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations. Proceedings of the National Academy of Sciences of the United States of America. 109: 4857-62. PMID 22411825 DOI: 10.1073/Pnas.1118157109 |
0.436 |
|
| 2011 |
Lukatsky DB, Afek A, Shakhnovich EI. Sequence correlations shape protein promiscuity. The Journal of Chemical Physics. 135: 065104. PMID 21842953 DOI: 10.1063/1.3624332 |
0.385 |
|
| 2011 |
Nivón LG, Shakhnovich EI. Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations. Journal of Molecular Biology. 411: 1128-44. PMID 21740912 DOI: 10.1016/J.Jmb.2011.06.042 |
0.815 |
|
| 2011 |
Wylie CS, Shakhnovich EI. A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proceedings of the National Academy of Sciences of the United States of America. 108: 9916-21. PMID 21610162 DOI: 10.1073/Pnas.1017572108 |
0.362 |
|
| 2011 |
Afek A, Shakhnovich EI, Lukatsky DB. Multi-scale sequence correlations increase proteome structural disorder and promiscuity. Journal of Molecular Biology. 409: 439-49. PMID 21463640 DOI: 10.1016/J.Jmb.2011.03.056 |
0.438 |
|
| 2011 |
Heo M, Maslov S, Shakhnovich E. Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions Proceedings of the National Academy of Sciences of the United States of America. 108: 4258-4263. PMID 21368118 DOI: 10.1073/Pnas.1009392108 |
0.446 |
|
| 2011 |
Xu J, Huang L, Shakhnovich EI. The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential. Proteins. 79: 1704-14. PMID 21365688 DOI: 10.1002/Prot.22993 |
0.567 |
|
| 2011 |
Shakhnovich E. Protein folding: To knot or not to knot? Nature Materials. 10: 84-6. PMID 21258348 DOI: 10.1038/nmat2953 |
0.367 |
|
| 2011 |
Shakhnovich E. Protein folding: To knot or not to knot? Nature Materials. 10: 84-86. DOI: 10.1038/Nmat2953 |
0.485 |
|
| 2011 |
Kutchukian PS, Lou D, Shakhnovich EI. In silico fragment-based generation of drug-like compounds Acs Symposium Series. 1076: 151-177. DOI: 10.1021/bk-2011-1076.ch008 |
0.648 |
|
| 2011 |
Heo M, Zeldovich KB, Shakhnovich EI. Diversity Against Adversity: How Adaptive Immune System Evolves Potent Antibodies Journal of Statistical Physics. 144: 241-267. DOI: 10.1007/S10955-011-0241-8 |
0.331 |
|
| 2010 |
Kutchukian PS, Shakhnovich EI. De novo design: balancing novelty and confined chemical space. Expert Opinion On Drug Discovery. 5: 789-812. PMID 22827800 DOI: 10.1517/17460441.2010.497534 |
0.687 |
|
| 2010 |
Faísca PF, Nunes A, Travasso RD, Shakhnovich EI. Non-native interactions play an effective role in protein folding dynamics. Protein Science : a Publication of the Protein Society. 19: 2196-209. PMID 20836137 DOI: 10.1002/Pro.498 |
0.442 |
|
| 2010 |
Zhang J, Shakhnovich EI. Optimality of mutation and selection in germinal centers. Plos Computational Biology. 6: e1000800. PMID 20532164 DOI: 10.1371/Journal.Pcbi.1000800 |
0.304 |
|
| 2010 |
Chen P, Shakhnovich EI. Thermal adaptation of viruses and bacteria. Biophysical Journal. 98: 1109-18. PMID 20371310 DOI: 10.1016/J.Bpj.2009.11.048 |
0.662 |
|
| 2010 |
Heo M, Shakhnovich EI. Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response. Plos Computational Biology. 6: e1000710. PMID 20300650 DOI: 10.1371/Journal.Pcbi.1000710 |
0.364 |
|
| 2010 |
Choi PJ, Xie XS, Shakhnovich EI. Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps. Journal of Molecular Biology. 396: 230-44. PMID 19931280 DOI: 10.1016/J.Jmb.2009.11.035 |
0.323 |
|
| 2009 |
Chen P, Shakhnovich EI. Lethal mutagenesis in viruses and bacteria. Genetics. 183: 639-50. PMID 19620390 DOI: 10.1534/Genetics.109.106492 |
0.685 |
|
| 2009 |
Shakhnovich E. Protein folding roller coaster, one molecule at a time Proceedings of the National Academy of Sciences of the United States of America. 106: 11823-11824. PMID 19617547 DOI: 10.1073/Pnas.0906228106 |
0.436 |
|
| 2009 |
Kutchukian PS, Lou D, Shakhnovich EI. FOG: Fragment Optimized Growth algorithm for the de novo generation of molecules occupying druglike chemical space. Journal of Chemical Information and Modeling. 49: 1630-42. PMID 19527020 DOI: 10.1021/Ci9000458 |
0.685 |
|
| 2009 |
Roland CB, Hatch KA, Prentiss M, Shakhnovich EI. DNA unzipping phase diagram calculated via replica theory. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 79: 051923. PMID 19518496 DOI: 10.1103/Physreve.79.051923 |
0.633 |
|
| 2009 |
Kutchukian PS, Yang JS, Verdine GL, Shakhnovich EI. All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples. Journal of the American Chemical Society. 131: 4622-7. PMID 19334772 DOI: 10.1021/Ja805037P |
0.732 |
|
| 2009 |
Lee JW, Zemojtel T, Shakhnovich E. Systems-level evidence of transcriptional co-regulation of yeast protein complexes Journal of Computational Biology. 16: 331-339. PMID 19193150 DOI: 10.1089/Cmb.2008.17Tt |
0.341 |
|
| 2009 |
Heo M, Kang L, Shakhnovich EI. Emergence of species in evolutionary "simulated annealing". Proceedings of the National Academy of Sciences of the United States of America. 106: 1869-74. PMID 19164759 DOI: 10.1073/Pnas.0809852106 |
0.343 |
|
| 2009 |
Donald JE, Shakhnovich EI. SDR: a database of predicted specificity-determining residues in proteins. Nucleic Acids Research. 37: D191-4. PMID 18927118 DOI: 10.1093/Nar/Gkn716 |
0.803 |
|
| 2008 |
Faísca PF, Travasso RD, Ball RC, Shakhnovich EI. Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis. The Journal of Chemical Physics. 129: 095108. PMID 19044896 DOI: 10.1063/1.2973624 |
0.419 |
|
| 2008 |
Zhang J, Shakhnovich EI. Sensitivity-dependent model of protein-protein interaction networks. Physical Biology. 5: 036011. PMID 18824789 DOI: 10.1088/1478-3975/5/3/036011 |
0.405 |
|
| 2008 |
Zhang J, Maslov S, Shakhnovich EI. Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Molecular Systems Biology. 4: 210. PMID 18682700 DOI: 10.1038/Msb.2008.48 |
0.399 |
|
| 2008 |
Shakhnovich BE, Shakhnovich EI. Improvisation in evolution of genes and genomes: whose structure is it anyway? Current Opinion in Structural Biology. 18: 375-81. PMID 18487041 DOI: 10.1016/J.Sbi.2008.02.007 |
0.372 |
|
| 2008 |
Lukatsky DB, Shakhnovich EI. Statistically enhanced promiscuity of structurally correlated patterns. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 020901. PMID 18351980 DOI: 10.1103/Physreve.77.020901 |
0.356 |
|
| 2008 |
Yang JS, Wallin S, Shakhnovich EI. Universality and diversity of folding mechanics for three-helix bundle proteins. Proceedings of the National Academy of Sciences of the United States of America. 105: 895-900. PMID 18195374 DOI: 10.1073/Pnas.0707284105 |
0.498 |
|
| 2008 |
Zeldovich KB, Shakhnovich EI. Understanding protein evolution: from protein physics to Darwinian selection. Annual Review of Physical Chemistry. 59: 105-27. PMID 17937598 DOI: 10.1146/Annurev.Physchem.58.032806.104449 |
0.451 |
|
| 2008 |
Pereira de Araújo AF, Gomes AL, Bursztyn AA, Shakhnovich EI. Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins. Proteins. 70: 971-83. PMID 17847091 DOI: 10.1002/Prot.21571 |
0.392 |
|
| 2007 |
Zeldovich KB, Chen P, Shakhnovich EI. Protein stability imposes limits on organism complexity and speed of molecular evolution. Proceedings of the National Academy of Sciences of the United States of America. 104: 16152-7. PMID 17913881 DOI: 10.1073/Pnas.0705366104 |
0.685 |
|
| 2007 |
Lam AR, Borreguero JM, Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich E. Parallel folding pathways in the SH3 domain protein. Journal of Molecular Biology. 373: 1348-60. PMID 17900612 DOI: 10.1016/J.Jmb.2007.08.032 |
0.644 |
|
| 2007 |
Deeds EJ, Ashenberg O, Gerardin J, Shakhnovich EI. Robust protein protein interactions in crowded cellular environments. Proceedings of the National Academy of Sciences of the United States of America. 104: 14952-7. PMID 17848524 DOI: 10.1073/Pnas.0702766104 |
0.708 |
|
| 2007 |
Zeldovich KB, Chen P, Shakhnovich BE, Shakhnovich EI. A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds. Plos Computational Biology. 3: e139. PMID 17630830 DOI: 10.1371/Journal.Pcbi.0030139 |
0.71 |
|
| 2007 |
Perlstein EO, Deeds EJ, Ashenberg O, Shakhnovich EI, Schreiber SL. Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations. Proceedings of the National Academy of Sciences of the United States of America. 104: 10553-8. PMID 17566105 DOI: 10.1073/Pnas.0704037104 |
0.654 |
|
| 2007 |
Berezovsky IN, Zeldovich KB, Shakhnovich EI. Positive and negative design in stability and thermal adaptation of natural proteins. Plos Computational Biology. 3: e52. PMID 17381236 DOI: 10.1371/Journal.Pcbi.0030052 |
0.435 |
|
| 2007 |
Wallin S, Zeldovich KB, Shakhnovich EI. The folding mechanics of a knotted protein. Journal of Molecular Biology. 368: 884-93. PMID 17368671 DOI: 10.1016/J.Jmb.2007.02.035 |
0.481 |
|
| 2007 |
Kleiner A, Shakhnovich E. The mechanical unfolding of ubiquitin through all-atom Monte Carlo simulation with a Go-type potential. Biophysical Journal. 92: 2054-61. PMID 17293405 DOI: 10.1529/Biophysj.106.081257 |
0.453 |
|
| 2007 |
Donald JE, Chen WW, Shakhnovich EI. Energetics of protein-DNA interactions. Nucleic Acids Research. 35: 1039-47. PMID 17259221 DOI: 10.1093/Nar/Gkl1103 |
0.803 |
|
| 2007 |
Yang JS, Chen WW, Skolnick J, Shakhnovich EI. All-atom ab initio folding of a diverse set of proteins. Structure (London, England : 1993). 15: 53-63. PMID 17223532 DOI: 10.1016/J.Str.2006.11.010 |
0.663 |
|
| 2007 |
Zeldovich KB, Berezovsky IN, Shakhnovich EI. Protein and DNA sequence determinants of thermophilic adaptation. Plos Computational Biology. 3: e5. PMID 17222055 DOI: 10.1371/Journal.Pcbi.0030005 |
0.344 |
|
| 2007 |
Chen WW, Yang JS, Shakhnovich EI. A knowledge-based move set for protein folding. Proteins. 66: 682-8. PMID 17143895 DOI: 10.1002/Prot.21237 |
0.617 |
|
| 2007 |
Lukatsky DB, Shakhnovich BE, Mintseris J, Shakhnovich EI. Structural similarity enhances interaction propensity of proteins. Journal of Molecular Biology. 365: 1596-606. PMID 17141268 DOI: 10.1016/J.Jmb.2006.11.020 |
0.466 |
|
| 2007 |
Deeds EJ, Shakhnovich EI. A structure-centric view of protein evolution, design, and adaptation. Advances in Enzymology and Related Areas of Molecular Biology. 75: 133-91, xi-xii. PMID 17124867 DOI: 10.1002/9780471224464.Ch2 |
0.758 |
|
| 2007 |
Roland CB, Shakhnovich EI. Divergent evolution of a structural proteome: phenomenological models. Biophysical Journal. 92: 701-16. PMID 17071665 DOI: 10.1529/Biophysj.106.081265 |
0.662 |
|
| 2006 |
Lukatsky DB, Zeldovich KB, Shakhnovich EI. Statistically enhanced self-attraction of random patterns. Physical Review Letters. 97: 178101. PMID 17155509 DOI: 10.1103/Physrevlett.97.178101 |
0.351 |
|
| 2006 |
Hubner IA, Deeds EJ, Shakhnovich EI. Understanding ensemble protein folding at atomic detail. Proceedings of the National Academy of Sciences of the United States of America. 103: 17747-52. PMID 17095606 DOI: 10.1073/Pnas.0605580103 |
0.84 |
|
| 2006 |
Shakhnovich E. Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet Chemical Reviews. 106: 1559-1588. PMID 16683745 DOI: 10.1021/Cr040425U |
0.506 |
|
| 2006 |
Hubner IA, Lindberg M, Haglund E, Oliveberg M, Shakhnovich EI. Common motifs and topological effects in the protein folding transition state. Journal of Molecular Biology. 359: 1075-85. PMID 16678203 DOI: 10.1016/J.Jmb.2006.04.015 |
0.816 |
|
| 2006 |
Lindberg MO, Haglund E, Hubner IA, Shakhnovich EI, Oliveberg M. Identification of the minimal protein-folding nucleus through loop-entropy perturbations. Proceedings of the National Academy of Sciences of the United States of America. 103: 4083-8. PMID 16505376 DOI: 10.1073/Pnas.0508863103 |
0.835 |
|
| 2006 |
Zeldovich KB, Berezovsky IN, Shakhnovich EI. Physical origins of protein superfamilies. Journal of Molecular Biology. 357: 1335-43. PMID 16483605 DOI: 10.1016/J.Jmb.2006.01.081 |
0.508 |
|
| 2006 |
Zhang Y, Hubner IA, Arakaki AK, Shakhnovich E, Skolnick J. On the origin and highly likely completeness of single-domain protein structures. Proceedings of the National Academy of Sciences of the United States of America. 103: 2605-10. PMID 16478803 DOI: 10.1073/Pnas.0509379103 |
0.842 |
|
| 2006 |
von Grotthuss M, Plewczynski D, Ginalski K, Rychlewski L, Shakhnovich EI. PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. Bmc Bioinformatics. 7: 53. PMID 16460560 DOI: 10.1186/1471-2105-7-53 |
0.435 |
|
| 2006 |
Oliveberg M, Shakhnovich EI. Folding and binding: the conformational repertoire of proteins: folding, aggregation and structural recognition. Current Opinion in Structural Biology. 16: 68-70. PMID 16443362 DOI: 10.1016/J.Sbi.2006.01.015 |
0.431 |
|
| 2006 |
Deeds EJ, Ashenberg O, Shakhnovich EI. A simple physical model for scaling in protein-protein interaction networks. Proceedings of the National Academy of Sciences of the United States of America. 103: 311-6. PMID 16384916 DOI: 10.1073/Pnas.0509715102 |
0.694 |
|
| 2006 |
Shakhnovich E. Monte-Carlo methods in studies of protein folding and evolution Lecture Notes in Physics. 704: 563-593. DOI: 10.1007/3-540-35284-8_21 |
0.342 |
|
| 2005 |
Hubner IA, Deeds EJ, Shakhnovich EI. High-resolution protein folding with a transferable potential. Proceedings of the National Academy of Sciences of the United States of America. 102: 18914-9. PMID 16365306 DOI: 10.1073/Pnas.0502181102 |
0.833 |
|
| 2005 |
Berezovsky IN, Chen WW, Choi PJ, Shakhnovich EI. Entropic stabilization of proteins and its proteomic consequences. Plos Computational Biology. 1: e47. PMID 16201009 DOI: 10.1371/Journal.Pcbi.0010047 |
0.622 |
|
| 2005 |
Hubner IA, Shakhnovich EI. Geometric and physical considerations for realistic protein models. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 022901. PMID 16196617 DOI: 10.1103/Physreve.72.022901 |
0.815 |
|
| 2005 |
Berezovsky IN, Shakhnovich EI. Physics and evolution of thermophilic adaptation. Proceedings of the National Academy of Sciences of the United States of America. 102: 12742-7. PMID 16120678 DOI: 10.1073/Pnas.0503890102 |
0.449 |
|
| 2005 |
Donald JE, Shakhnovich EI. Predicting specificity-determining residues in two large eukaryotic transcription factor families. Nucleic Acids Research. 33: 4455-65. PMID 16085755 DOI: 10.1093/Nar/Gki755 |
0.794 |
|
| 2005 |
Chen WW, Shakhnovich EI. Lessons from the design of a novel atomic potential for protein folding. Protein Science : a Publication of the Protein Society. 14: 1741-52. PMID 15987903 DOI: 10.1110/Ps.051440705 |
0.59 |
|
| 2005 |
Ding F, Guo W, Dokholyan NV, Shakhnovich EI, Shea JE. Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. Journal of Molecular Biology. 350: 1035-50. PMID 15982666 DOI: 10.1016/J.Jmb.2005.05.017 |
0.621 |
|
| 2005 |
Hubner IA, Edmonds KA, Shakhnovich EI. Nucleation and the transition state of the SH3 domain. Journal of Molecular Biology. 349: 424-34. PMID 15890206 DOI: 10.1016/J.Jmb.2005.03.050 |
0.824 |
|
| 2005 |
Deeds EJ, Shakhnovich EI. The emergence of scaling in sequence-based physical models of protein evolution. Biophysical Journal. 88: 3905-11. PMID 15805176 DOI: 10.1529/Biophysj.104.051433 |
0.724 |
|
| 2005 |
Donald JE, Shakhnovich EI. Determining functional specificity from protein sequences. Bioinformatics (Oxford, England). 21: 2629-35. PMID 15797914 DOI: 10.1093/Bioinformatics/Bti396 |
0.794 |
|
| 2005 |
Donald JE, Hubner IA, Rotemberg VM, Shakhnovich EI, Mirny LA. CoC: a database of universally conserved residues in protein folds. Bioinformatics (Oxford, England). 21: 2539-40. PMID 15746286 DOI: 10.1093/Bioinformatics/Bti360 |
0.812 |
|
| 2005 |
Deeds EJ, Hennessey H, Shakhnovich EI. Prokaryotic phylogenies inferred from protein structural domains. Genome Research. 15: 393-402. PMID 15741510 DOI: 10.1101/Gr.3033805 |
0.716 |
|
| 2005 |
Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Research. 15: 385-92. PMID 15741509 DOI: 10.1101/Gr.3133605 |
0.72 |
|
| 2004 |
Nivón LG, Shakhnovich EI. All-atom Monte Carlo simulation of GCAA RNA folding. Journal of Molecular Biology. 344: 29-45. PMID 15504400 DOI: 10.1016/J.Jmb.2004.09.041 |
0.805 |
|
| 2004 |
Geissler PL, Shakhnovich EI, Grosberg AY. Solvation versus freezing in a heteropolymer globule. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 021802. PMID 15447508 DOI: 10.1103/Physreve.70.021802 |
0.67 |
|
| 2004 |
Dominy BN, Shakhnovich EI. Native atom types for knowledge-based potentials: application to binding energy prediction. Journal of Medicinal Chemistry. 47: 4538-58. PMID 15317465 DOI: 10.1021/Jm0498046 |
0.723 |
|
| 2004 |
Tiana G, Dokholyan NV, Broglia RA, Shakhnovich EI. The evolution dynamics of model proteins. The Journal of Chemical Physics. 121: 2381-9. PMID 15260793 DOI: 10.1063/1.1768513 |
0.661 |
|
| 2004 |
Tannenbaum E, Deeds EJ, Shakhnovich EI. Semiconservative replication in the quasispecies model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 061916. PMID 15244626 DOI: 10.1103/Physreve.69.061916 |
0.653 |
|
| 2004 |
Liu Z, Dominy BN, Shakhnovich EI. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. Journal of the American Chemical Society. 126: 8515-28. PMID 15238009 DOI: 10.1021/Ja032018Q |
0.755 |
|
| 2004 |
Hubner IA, Oliveberg M, Shakhnovich EI. Simulation, experiment, and evolution: understanding nucleation in protein S6 folding. Proceedings of the National Academy of Sciences of the United States of America. 101: 8354-9. PMID 15150413 DOI: 10.1073/Pnas.0401672101 |
0.835 |
|
| 2004 |
Hubner IA, Shimada J, Shakhnovich EI. Commitment and nucleation in the protein G transition state. Journal of Molecular Biology. 336: 745-61. PMID 15095985 DOI: 10.1016/J.Jmb.2003.12.032 |
0.833 |
|
| 2004 |
Deeds EJ, Shakhnovich B, Shakhnovich EI. Proteomic traces of speciation. Journal of Molecular Biology. 336: 695-706. PMID 15095981 DOI: 10.1016/J.Jmb.2003.12.066 |
0.718 |
|
| 2004 |
Tiana G, Shakhnovich BE, Dokholyan NV, Shakhnovich EI. Imprint of evolution on protein structures. Proceedings of the National Academy of Sciences of the United States of America. 101: 2846-51. PMID 14970345 DOI: 10.1073/Pnas.0306638101 |
0.643 |
|
| 2004 |
Morrissey MP, Ahmed Z, Shakhnovich EI. The role of cotranslation in protein folding: A lattice model study Polymer. 45: 557-571. DOI: 10.1016/J.Polymer.2003.10.090 |
0.492 |
|
| 2003 |
Dokholyan NV, Borreguero JM, Buldyrev SV, Ding F, Stanley HE, Shakhnovich EI. Identifying importance of amino acids for protein folding from crystal structures. Methods in Enzymology. 374: 616-38. PMID 14696390 DOI: 10.1016/S0076-6879(03)74025-7 |
0.642 |
|
| 2003 |
Deeds EJ, Dokholyan NV, Shakhnovich EI. Protein evolution within a structural space. Biophysical Journal. 85: 2962-72. PMID 14581198 DOI: 10.1016/S0006-3495(03)74716-X |
0.749 |
|
| 2003 |
Tannenbaum E, Deeds EJ, Shakhnovich EI. Equilibrium distribution of mutators in the single fitness peak model. Physical Review Letters. 91: 138105. PMID 14525341 DOI: 10.1103/Physrevlett.91.138105 |
0.67 |
|
| 2003 |
Pei J, Dokholyan NV, Shakhnovich EI, Grishin NV. Using protein design for homology detection and active site searches. Proceedings of the National Academy of Sciences of the United States of America. 100: 11361-6. PMID 12975528 DOI: 10.1073/Pnas.2034878100 |
0.546 |
|
| 2003 |
Shakhnovich BE, Harvey JM, Comeau S, Lorenz D, DeLisi C, Shakhnovich E. ELISA: Structure-function inferences based on statistically significant and evolutionarily inspired observations Bmc Bioinformatics. 4. PMID 12952559 DOI: 10.1186/1471-2105-4-34 |
0.378 |
|
| 2003 |
England JL, Shakhnovich BE, Shakhnovich EI. Natural selection of more designable folds: a mechanism for thermophilic adaptation. Proceedings of the National Academy of Sciences of the United States of America. 100: 8727-31. PMID 12843403 DOI: 10.1073/Pnas.1530713100 |
0.448 |
|
| 2003 |
Kussell E, Shimada J, Shakhnovich EI. Side-chain dynamics and protein folding. Proteins. 52: 303-21. PMID 12833553 DOI: 10.1002/Prot.10426 |
0.794 |
|
| 2003 |
England JL, Shakhnovich EI. Structural determinant of protein designability. Physical Review Letters. 90: 218101. PMID 12786593 DOI: 10.1103/Physrevlett.90.218101 |
0.433 |
|
| 2003 |
Chen W, Mirny L, Shakhnovich EI. Fold recognition with minimal gaps. Proteins. 51: 531-43. PMID 12784212 DOI: 10.1002/Prot.10402 |
0.697 |
|
| 2003 |
Li L, Shakhnovich EI, Mirny LA. Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proceedings of the National Academy of Sciences of the United States of America. 100: 4463-8. PMID 12679523 DOI: 10.1073/Pnas.0737647100 |
0.802 |
|
| 2003 |
Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI. Functional fingerprints of folds: evidence for correlated structure-function evolution. Journal of Molecular Biology. 326: 1-9. PMID 12547186 DOI: 10.1016/S0022-2836(02)01362-1 |
0.511 |
|
| 2002 |
Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Direct molecular dynamics observation of protein folding transition state ensemble. Biophysical Journal. 83: 3525-32. PMID 12496119 DOI: 10.1016/S0006-3495(02)75352-6 |
0.638 |
|
| 2002 |
Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. Journal of Molecular Biology. 324: 851-7. PMID 12460582 DOI: 10.1016/S0022-2836(02)01112-9 |
0.589 |
|
| 2002 |
Kussell E, Shakhnovich EI. Glassy dynamics of side-chain ordering in a simple model of protein folding. Physical Review Letters. 89: 168101. PMID 12398757 DOI: 10.1103/Physrevlett.89.168101 |
0.723 |
|
| 2002 |
Dokholyan NV, Shakhnovich B, Shakhnovich EI. Expanding protein universe and its origin from the biological Big Bang. Proceedings of the National Academy of Sciences of the United States of America. 99: 14132-6. PMID 12384571 DOI: 10.1073/Pnas.202497999 |
0.6 |
|
| 2002 |
Shimada J, Shakhnovich EI. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proceedings of the National Academy of Sciences of the United States of America. 99: 11175-80. PMID 12165568 DOI: 10.1073/Pnas.162268099 |
0.641 |
|
| 2002 |
Dokholyan NV, Li L, Ding F, Shakhnovich EI. Topological determinants of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 99: 8637-41. PMID 12084924 DOI: 10.1073/Pnas.122076099 |
0.8 |
|
| 2002 |
Ishchenko AV, Shakhnovich EI. SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. Journal of Medicinal Chemistry. 45: 2770-80. PMID 12061879 DOI: 10.1021/Jm0105833 |
0.637 |
|
| 2002 |
Geissler PL, Shakhnovich EI. Reversible stretching of random heteropolymers. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 056110. PMID 12059650 DOI: 10.1103/Physreve.65.056110 |
0.596 |
|
| 2002 |
Borreguero JM, Dokholyan NV, Buldyrev SV, Shakhnovich EI, Stanley HE. Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. Journal of Molecular Biology. 318: 863-76. PMID 12054829 DOI: 10.1016/S0022-2836(02)00136-5 |
0.638 |
|
| 2002 |
Grzybowski BA, Ishchenko AV, Shimada J, Shakhnovich EI. From knowledge-based potentials to combinatorial lead design in silico. Accounts of Chemical Research. 35: 261-9. PMID 12020163 DOI: 10.1021/Ar970146B |
0.711 |
|
| 2002 |
Kussell E, Shimada J, Shakhnovich EI. A structure-based method for derivation of all-atom potentials for protein folding. Proceedings of the National Academy of Sciences of the United States of America. 99: 5343-8. PMID 11943859 DOI: 10.1073/Pnas.072665799 |
0.795 |
|
| 2002 |
Grzybowski BA, Ishchenko AV, Kim CY, Topalov G, Chapman R, Christianson DW, Whitesides GM, Shakhnovich EI. Combinatorial computational method gives new picomolar ligands for a known enzyme. Proceedings of the National Academy of Sciences of the United States of America. 99: 1270-3. PMID 11818565 DOI: 10.1073/Pnas.032673399 |
0.583 |
|
| 2002 |
Geissler PL, Shakhnovich EI. Reversible stretching of random heteropolymers Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 65: 056110/1-056110/4. DOI: 10.1103/PhysRevE.65.056110 |
0.468 |
|
| 2002 |
Geissler PL, Shakhnovich EI. Mechanical response of random heteropolymers Macromolecules. 35: 4429-4436. DOI: 10.1021/Ma012008E |
0.636 |
|
| 2002 |
Shimada J, Ekins S, Elkin C, Shakhnovich EI, Wery JP. Integrating computer-based de novo drug design and multidimensional filtering for desirable drugs Drug Discovery Today: Targets. 1: 196-205. DOI: 10.1016/S1477-3627(02)02274-2 |
0.51 |
|
| 2002 |
Dokholyan NV, Mirny LA, Shakhnovich EI. Understanding conserved amino acids in proteins Physica a: Statistical Mechanics and Its Applications. 314: 600-606. DOI: 10.1016/S0378-4371(02)01079-8 |
0.705 |
|
| 2001 |
Tiana G, Broglia RA, Shakhnovich EI. Energy profile of the space of model protein sequences. Journal of Biological Physics. 27: 147-59. PMID 23345740 DOI: 10.1023/A:1013151530254 |
0.305 |
|
| 2001 |
Li L, Shakhnovich EI. Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proceedings of the National Academy of Sciences of the United States of America. 98: 13014-8. PMID 11606790 DOI: 10.1073/Pnas.241378398 |
0.733 |
|
| 2001 |
Dokholyan NV, Shakhnovich EI. Understanding hierarchical protein evolution from first principles. Journal of Molecular Biology. 312: 289-307. PMID 11545603 DOI: 10.1006/Jmbi.2001.4949 |
0.627 |
|
| 2001 |
Kussell E, Shimada J, Shakhnovich EI. Excluded volume in protein side-chain packing. Journal of Molecular Biology. 311: 183-93. PMID 11469867 DOI: 10.1006/Jmbi.2001.4846 |
0.785 |
|
| 2001 |
Berriz GF, Shakhnovich EI. Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model. Journal of Molecular Biology. 310: 673-85. PMID 11439031 DOI: 10.1006/Jmbi.2001.4792 |
0.791 |
|
| 2001 |
Mirny L, Shakhnovich E. Protein folding theory: From lattice to all-atom models Annual Review of Biophysics and Biomolecular Structure. 30: 361-396. PMID 11340064 DOI: 10.1146/Annurev.Biophys.30.1.361 |
0.678 |
|
| 2001 |
Mirny L, Shakhnovich E. Evolutionary conservation of the folding nucleus Journal of Molecular Biology. 308: 123-129. PMID 11327757 DOI: 10.1006/Jmbi.2001.4602 |
0.64 |
|
| 2001 |
Shimada J, Kussell EL, Shakhnovich EI. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. Journal of Molecular Biology. 308: 79-95. PMID 11302709 DOI: 10.1006/Jmbi.2001.4586 |
0.802 |
|
| 2001 |
Li L, Shakhnovich EI. Different circular permutations produced different folding nuclei in proteins: a computational study. Journal of Molecular Biology. 306: 121-32. PMID 11178898 DOI: 10.1006/Jmbi.2000.4375 |
0.745 |
|
| 2000 |
Choe SE, Li L, Matsudaira PT, Wagner G, Shakhnovich EI. Differential stabilization of two hydrophobic cores in the transition state of the villin 14T folding reaction. Journal of Molecular Biology. 304: 99-115. PMID 11071813 DOI: 10.1006/Jmbi.2000.4190 |
0.727 |
|
| 2000 |
Vendruscolo M, Mirny LA, Shakhnovich EI, Domany E. Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score. Proteins. 41: 192-201. PMID 10966572 DOI: 10.1002/1097-0134(20001101)41:2<192::Aid-Prot40>3.0.Co;2-3 |
0.592 |
|
| 2000 |
Mirny LA, Finkelstein AV, Shakhnovich EI. Statistical significance of protein structure prediction by threading. Proceedings of the National Academy of Sciences of the United States of America. 97: 9978-83. PMID 10954732 DOI: 10.1073/Pnas.160271197 |
0.62 |
|
| 2000 |
Abkevich VI, Shakhnovich EI. What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis. Journal of Molecular Biology. 300: 975-85. PMID 10891282 DOI: 10.1006/Jmbi.2000.3893 |
0.425 |
|
| 2000 |
Shimada J, Ishchenko AV, Shakhnovich EI. Analysis of knowledge-based protein-ligand potentials using a self-consistent method. Protein Science : a Publication of the Protein Society. 9: 765-75. PMID 10794420 DOI: 10.1110/Ps.9.4.765 |
0.731 |
|
| 2000 |
Li L, Mirny LA, Shakhnovich EI. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nature Structural Biology. 7: 336-42. PMID 10742180 DOI: 10.1038/74111 |
0.822 |
|
| 2000 |
Tiana G, Broglia RA, Shakhnovich EI. Hiking in the energy landscape in sequence space: a bumpy road to good folders. Proteins. 39: 244-51. PMID 10737946 DOI: 10.1002/(Sici)1097-0134(20000515)39:3<244::Aid-Prot70>3.0.Co;2-# |
0.352 |
|
| 2000 |
Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Identifying the protein folding nucleus using molecular dynamics. Journal of Molecular Biology. 296: 1183-8. PMID 10698625 DOI: 10.1006/Jmbi.1999.3534 |
0.641 |
|
| 2000 |
Grzybowski BA, Ishchenko AV, Dewitte RS, Whitesides GM, Shakhnovich EI. Development of a knowledge-based potential for crystals of small organic molecules: Calculation of energy surfaces for C=0⋯H-N hydrogen bonds Journal of Physical Chemistry B. 104: 7293-7298. DOI: 10.1021/Jp000644T |
0.591 |
|
| 2000 |
Shakhnovich E, Kussell E, Shimada J. Folding thermodynamics and kinetics in all-atom simulations Journal of Molecular Graphics and Modelling. 18: 555. DOI: 10.1016/S1093-3263(00)80130-8 |
0.748 |
|
| 1999 |
Finkel'shteĭn AV, Rykunov DS, Lobanov MIu, Badretdinov FIa, Reva BA, Skolnick J, Mirnyĭ LA, Shakhnovich EI. [When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible]. Biofizika. 44: 980-91. PMID 10707272 |
0.345 |
|
| 1999 |
Morrissey MP, Shakhnovich EI. Evidence for the role of PrP(C) helix 1 in the hydrophilic seeding of prion aggregates. Proceedings of the National Academy of Sciences of the United States of America. 96: 11293-8. PMID 10500170 DOI: 10.1073/Pnas.96.20.11293 |
0.351 |
|
| 1999 |
Mirny LA, Shakhnovich EI. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. Journal of Molecular Biology. 291: 177-96. PMID 10438614 DOI: 10.1006/Jmbi.1999.2911 |
0.706 |
|
| 1999 |
Dinner AR, Abkevich V, Shakhnovich E, Karplus M. Factors that affect the folding ability of proteins. Proteins. 35: 34-40. PMID 10090284 DOI: 10.1002/(Sici)1097-0134(19990401)35:1<34::Aid-Prot4>3.0.Co;2-Q |
0.546 |
|
| 1999 |
Shakhnovich EI. Folding by association. Nature Structural Biology. 6: 99-102. PMID 10048934 DOI: 10.1038/5785 |
0.424 |
|
| 1999 |
Kussell EL, Shakhnovich EI. Analytical Approach to the Protein Design Problem Physical Review Letters. 83: 4437-4440. DOI: 10.1103/Physrevlett.83.4437 |
0.712 |
|
| 1999 |
Broglia RA, Tiana G, Roman HE, Vigezzi E, Shakhnovich E. Stability of Designed Proteins against Mutations Physical Review Letters. 82: 4727-4730. DOI: 10.1103/Physrevlett.82.4727 |
0.406 |
|
| 1999 |
Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich E. On the role of conformational geometry in protein folding The Journal of Chemical Physics. 111: 10375-10380. DOI: 10.1063/1.480387 |
0.735 |
|
| 1999 |
Chou JJ, Shakhnovich EI. A study on local-global cooperativity in protein collapse Journal of Physical Chemistry B. 103: 2535-2542. DOI: 10.1021/Jp9839192 |
0.401 |
|
| 1999 |
Berriz GF, Shakhnovich EI. The well-tempered protein Current Opinion in Colloid and Interface Science. 4: 72-82. DOI: 10.1016/S1359-0294(99)00010-2 |
0.81 |
|
| 1999 |
Finkelstein AV, Rykunov DS, Lobanov MY, Badretdinov AY, Reva BA, Skolnick J, Mirny LA, Shakhnovich EI. When and how the homologs can overcome errors in the energy estimates and make the 3D structure prediction possible Biofizika. 44: 990-991. |
0.493 |
|
| 1998 |
Shakhnovich EI. Folding nucleus: specific or multiple? Insights from lattice models and experiments. Folding & Design. 3: R108-11; discussion . PMID 9889170 DOI: 10.1016/S1359-0278(98)00056-X |
0.429 |
|
| 1998 |
Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Discrete molecular dynamics studies of the folding of a protein-like model. Folding & Design. 3: 577-87. PMID 9889167 DOI: 10.1016/S1359-0278(98)00072-8 |
0.609 |
|
| 1998 |
Choe SE, Matsudaira PT, Osterhout J, Wagner G, Shakhnovich EI. Folding kinetics of villin 14T, a protein domain with a central beta-sheet and two hydrophobic cores. Biochemistry. 37: 14508-18. PMID 9772179 DOI: 10.1021/Bi980889K |
0.368 |
|
| 1998 |
Mirny LA, Shakhnovich EI. Protein structure prediction by threading. Why it works and why it does not. Journal of Molecular Biology. 283: 507-26. PMID 9769221 DOI: 10.1006/Jmbi.1998.2092 |
0.627 |
|
| 1998 |
Michnick SW, Shakhnovich E. A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies. Folding & Design. 3: 239-51. PMID 9710570 DOI: 10.1016/S1359-0278(98)00035-2 |
0.695 |
|
| 1998 |
Fersht AR, Shakhnovich EI. Protein folding: think globally, (inter)act locally. Current Biology : Cb. 8: R478-9. PMID 9663379 DOI: 10.1016/S0960-9822(98)70310-0 |
0.473 |
|
| 1998 |
Abkevich VI, Gutin AM, Shakhnovich EI. Theory of kinetic partitioning in protein folding with possible applications to prions. Proteins. 31: 335-44. PMID 9626694 DOI: 10.1002/(Sici)1097-0134(19980601)31:4<335::Aid-Prot1>3.0.Co;2-H |
0.462 |
|
| 1998 |
Shakhnovich EI. Protein design: a perspective from simple tractable models Folding & Design. 3: R45-58. PMID 9562552 DOI: 10.1016/S1359-0278(98)00021-2 |
0.454 |
|
| 1998 |
Gutin AM, Abkevich VI, Shakhnovich EI. A protein engineering analysis of the transition state for protein folding: simulation in the lattice model. Folding & Design. 3: 183-94. PMID 9562547 DOI: 10.1016/S1359-0278(98)00026-1 |
0.443 |
|
| 1998 |
Mirny LA, Abkevich VI, Shakhnovich EI. How evolution makes proteins fold quickly. Proceedings of the National Academy of Sciences of the United States of America. 95: 4976-81. PMID 9560213 DOI: 10.1073/Pnas.95.9.4976 |
0.682 |
|
| 1998 |
Gutin A, Sali A, Abkevich V, Karplus M, Shakhnovich EI. Temperature dependence of the folding rate in a simple protein model: Search for a “glass” transition The Journal of Chemical Physics. 108: 6466-6483. DOI: 10.1063/1.476053 |
0.542 |
|
| 1998 |
Chakraborty AK, Shakhnovich EI, Pande VS. Freezing of compact random heteropolymers with correlated sequence fluctuations The Journal of Chemical Physics. 108: 1683-1687. DOI: 10.1063/1.475539 |
0.509 |
|
| 1998 |
Tiana G, Broglia RA, Roman HE, Vigezzi E, Shakhnovich E. Folding and misfolding of designed proteinlike chains with mutations The Journal of Chemical Physics. 108: 757-761. DOI: 10.1063/1.475435 |
0.426 |
|
| 1997 |
Abkevich VI, Gutin AM, Shakhnovich EI. Computer simulations of prebiotic evolution Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27-38. PMID 9390277 |
0.329 |
|
| 1997 |
Morrissey MP, Shakhnovich EI. Design of proteins with selected thermal properties. Folding & Design. 1: 391-405. PMID 9080185 DOI: 10.1016/S1359-0278(96)00054-5 |
0.41 |
|
| 1997 |
Abkevich VI, Gutin AM, Shakhnovich EI. Improved design of stable and fast-folding model proteins. Folding & Design. 1: 221-30. PMID 9079383 DOI: 10.1016/S1359-0278(96)00033-8 |
0.411 |
|
| 1997 |
Shakhnovich EI. Modeling protein folding: the beauty and power of simplicity. Folding & Design. 1: R50-4. PMID 9079377 DOI: 10.1016/S1359-0278(96)00027-2 |
0.469 |
|
| 1997 |
Shakhnovich EI. Theoretical studies of protein-folding thermodynamics and kinetics Current Opinion in Structural Biology. 7: 29-40. PMID 9032061 DOI: 10.1016/S0959-440X(97)80005-X |
0.482 |
|
| 1997 |
Gutman L, Shakhnovich E. Frozen phases with re-entrant transition for random heteropolymers with composition specific and annealed cross-links The Journal of Chemical Physics. 107: 1247-1258. DOI: 10.1063/1.474136 |
0.353 |
|
| 1997 |
Berriz GF, Gutin AM, Shakhnovich EI. Cooperativity and stability in a Langevin model of proteinlike folding Journal of Chemical Physics. 106: 9276-9285. DOI: 10.1063/1.474039 |
0.77 |
|
| 1997 |
Bratko D, Chakraborty AK, Shakhnovich EI. The structure of a random heteropolymer in a disordered medium: Ensemble growth simulation Journal of Chemical Physics. 106: 1264-1279. DOI: 10.1063/1.473223 |
0.321 |
|
| 1997 |
DeWitte RS, Ishchenko AV, Shakhnovich EI. SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 2. Case studies in molecular design Journal of the American Chemical Society. 119: 4608-4617. DOI: 10.1021/Ja963689+ |
0.578 |
|
| 1997 |
Sfatos CD, Shakhnovich EI. Statistical mechanics of random heteropolymers Physics Report. 288: 77-108. DOI: 10.1016/S0370-1573(97)00022-7 |
0.327 |
|
| 1996 |
Gutin A, Abkevich VV, Shakhnovich E. Chain Length Scaling of Protein Folding Time. Physical Review Letters. 77: 5433-5436. PMID 10062802 DOI: 10.1103/Physrevlett.77.5433 |
0.391 |
|
| 1996 |
Mirny LA, Abkevich V, Shakhnovich EI. Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model. Folding & Design. 1: 103-16. PMID 9079370 DOI: 10.1016/S1359-0278(96)00019-3 |
0.675 |
|
| 1996 |
Mirny LA, Shakhnovich EI. How to derive a protein folding potential? A new approach to an old problem. Journal of Molecular Biology. 264: 1164-79. PMID 9000638 DOI: 10.1006/Jmbi.1996.0704 |
0.669 |
|
| 1996 |
Abkevich VI, Gutin AM, Shakhnovich EI. How the first biopolymers could have evolved. Proceedings of the National Academy of Sciences of the United States of America. 93: 839-44. PMID 8570645 DOI: 10.1073/Pnas.93.2.839 |
0.399 |
|
| 1996 |
Shakhnovich E, Abkevich V, Ptitsyn O. Conserved residues and the mechanism of protein folding. Nature. 379: 96-8. PMID 8538750 DOI: 10.1038/379096A0 |
0.501 |
|
| 1996 |
DeWitte RS, Shakhnovich EI. SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence Journal of the American Chemical Society. 118: 11733-11744. DOI: 10.1021/Ja960751U |
0.346 |
|
| 1995 |
DeWitte RS, Michnick SW, Shakhnovich EI. Exhaustive enumeration of protein conformations using experimental restraints. Protein Science : a Publication of the Protein Society. 4: 1780-91. PMID 8528076 DOI: 10.1002/Pro.5560040913 |
0.686 |
|
| 1995 |
Gutin AM, Abkevich VI, Shakhnovich EI. Is burst hydrophobic collapse necessary for protein folding? Biochemistry. 34: 3066-76. PMID 7893719 DOI: 10.1021/Bi00009A038 |
0.48 |
|
| 1995 |
Gutin AM, Abkevich VI, Shakhnovich EI. Evolution-like selection of fast-folding model proteins. Proceedings of the National Academy of Sciences of the United States of America. 92: 1282-6. PMID 7877968 DOI: 10.1073/Pnas.92.5.1282 |
0.441 |
|
| 1995 |
DeWitte RS, Shakhnovich EI. Pseudodihedrals: simplified protein backbone representation with knowledge-based energy. Protein Science : a Publication of the Protein Society. 3: 1570-81. PMID 7833816 DOI: 10.1002/Pro.5560030922 |
0.414 |
|
| 1995 |
Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI, Dill KA. A test of lattice protein folding algorithms. Proceedings of the National Academy of Sciences of the United States of America. 92: 325-9. PMID 7816842 DOI: 10.1073/Pnas.92.1.325 |
0.421 |
|
| 1995 |
Abkevich VI, Gutin AM, Shakhnovich EI. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. Journal of Molecular Biology. 252: 460-71. PMID 7563065 DOI: 10.1006/Jmbi.1995.0511 |
0.475 |
|
| 1995 |
Abkevich VI, Gutin AM, Shakhnovich EI. Domains in folding of model proteins. Protein Science : a Publication of the Protein Society. 4: 1167-77. PMID 7549881 DOI: 10.1002/Pro.5560040615 |
0.469 |
|
| 1995 |
Karplus M, S˘ali A, Shakhnovich E. Kinetics of protein folding Nature. 373: 665-665. DOI: 10.1038/373665A0 |
0.586 |
|
| 1995 |
Grosberg A, Gutin A, Shakhnovich E. Conformational Entropy of a Branched Polymer Macromolecules. 28: 3718-3727. DOI: 10.1021/Ma00114A028 |
0.532 |
|
| 1995 |
Karplus M, Caflisch A, Săli A, Shakhnovich E. Protein dynamics: From the native to the unfolded state and back again Molecular Engineering. 5: 55-70. DOI: 10.1007/Bf00999578 |
0.572 |
|
| 1994 |
Shakhnovich E. Proteins with selected sequences fold into unique native conformation. Physical Review Letters. 72: 3907-3910. PMID 10056327 DOI: 10.1103/Physrevlett.72.3907 |
0.455 |
|
| 1994 |
Archontis GZ, Shakhnovich EI. Phase Transitions In Heteropolymers With Secondary Structure Physical Review E. 49: 3109-3123. PMID 9961577 DOI: 10.1103/Physreve.49.3109 |
0.31 |
|
| 1994 |
Shakhnovich EI, Gutin AM. A new approach to the design of stable proteins. Protein Engineering. 6: 793-800. PMID 8309926 DOI: 10.1093/Protein/6.8.793 |
0.382 |
|
| 1994 |
Sali A, Shakhnovich E, Karplus M. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. Journal of Molecular Biology. 235: 1614-36. PMID 8107095 DOI: 10.1006/Jmbi.1994.1110 |
0.571 |
|
| 1994 |
Abkevich VI, Gutin AM, Shakhnovich EI. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry. 33: 10026-36. PMID 8060971 DOI: 10.1021/Bi00199A029 |
0.474 |
|
| 1994 |
Sali A, Shakhnovich E, Karplus M. How does a protein fold? Nature. 369: 248-51. PMID 7710478 DOI: 10.1038/369248A0 |
0.556 |
|
| 1994 |
Ramanathan S, Shakhnovich E. Statistical mechanics of proteins with ''evolutionary selected'' sequences Physical Review E. 50: 1303-1312. DOI: 10.1103/Physreve.50.1303 |
0.397 |
|
| 1994 |
Dinner A, Šali A, Karplus M, Shakhnovich E. Phase diagram of a model protein derived by exhaustive enumeration of the conformations The Journal of Chemical Physics. 101: 1444-1451. DOI: 10.1063/1.467769 |
0.569 |
|
| 1994 |
Abkevich VI, Gutin AM, Shakhnovich EI. Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations The Journal of Chemical Physics. 101: 6052-6062. DOI: 10.1063/1.467320 |
0.432 |
|
| 1994 |
Gutin AM, Shakhnovich EI. Statistical mechanics of polymers with distance constraints The Journal of Chemical Physics. 100: 5290-5293. DOI: 10.1063/1.467193 |
0.308 |
|
| 1993 |
Shakhnovich EI, Gutin AM. Engineering of stable and fast-folding sequences of model proteins. Proceedings of the National Academy of Sciences of the United States of America. 90: 7195-9. PMID 8346235 DOI: 10.1073/Pnas.90.15.7195 |
0.507 |
|
| 1993 |
Gutin AM, Grosberg AY, Shakhnovich EI. Globular state of branched random heteropolymers Journal of Physics a: Mathematical and General. 26: 1037-1049. DOI: 10.1088/0305-4470/26/5/023 |
0.566 |
|
| 1993 |
Gutin AM, Shakhnovich EI. Ground state of random copolymers and the discrete random energy model The Journal of Chemical Physics. 98: 8174-8177. DOI: 10.1063/1.464522 |
0.302 |
|
| 1991 |
Shakhnovich E, Farztdinov G, Gutin A, Karplus M. Protein folding bottlenecks: A lattice Monte Carlo simulation. Physical Review Letters. 67: 1665-1668. PMID 10044213 DOI: 10.1103/Physrevlett.67.1665 |
0.566 |
|
| 1991 |
Shakhnovich EI, Gutin AM. Influence of point mutations on protein structure: probability of a neutral mutation. Journal of Theoretical Biology. 149: 537-46. PMID 2062107 DOI: 10.1016/S0022-5193(05)80097-9 |
0.416 |
|
| 1990 |
Fernández A, Shakhnovich EI. Activation-energy landscape for metastable RNA folding. Physical Review A. 42: 3657-3659. PMID 9904458 DOI: 10.1103/Physreva.42.3657 |
0.362 |
|
| 1990 |
Shakhnovich EI, Gutin AM. Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach. Biophysical Chemistry. 34: 187-99. PMID 2611345 DOI: 10.1016/0301-4622(89)80058-4 |
0.429 |
|
| 1990 |
Finkelstein AV, Shakhnovich EI. Theory of cooperative transitions in protein molecules. II. Phase diagram for a protein molecule in solution. Biopolymers. 28: 1681-94. PMID 2597724 DOI: 10.1002/bip.360281004 |
0.304 |
|
| 1990 |
Shakhnovich EI, Finkelstein AV. Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first-order phase transition. Biopolymers. 28: 1667-80. PMID 2597723 DOI: 10.1002/bip.360281003 |
0.338 |
|
| 1990 |
Shakhnovich EI, Gutin AM. Implications of thermodynamics of protein folding for evolution of primary sequences. Nature. 346: 773-5. PMID 2388698 DOI: 10.1038/346773A0 |
0.492 |
|
| 1990 |
Shakhnovich E, Gutin A. Enumeration of all compact conformations of copolymers with random sequence of links The Journal of Chemical Physics. 93: 5967-5971. DOI: 10.1063/1.459480 |
0.409 |
|
| 1989 |
Shakhnovich EI, Gutin AM. The Nonergodic (“Spin-Glass–Like”) Phase of Heteropolymer with Quenched Disordered Sequence of Links Epl. 8: 327-332. DOI: 10.1209/0295-5075/8/4/005 |
0.301 |
|
| 1989 |
Shakhnovich EI, Gutin AM. Frozen states of a disordered globular heteropolymer Journal of Physics A. 22: 1647-1659. DOI: 10.1088/0305-4470/22/10/019 |
0.344 |
|
| 1988 |
Grosberg AY, Nechaev S, Shakhnovich E. The role of topological constraints in the kinetics of collapse of macromolecules Journal De Physique. 49: 2095-2100. DOI: 10.1051/Jphys:0198800490120209500 |
0.589 |
|
| Show low-probability matches. |
