| Year |
Citation |
Score |
| 2022 |
Fink EA, Xu J, Hübner H, Braz JM, Seemann P, Avet C, Craik V, Weikert D, Schmidt MF, Webb CM, Tolmachova NA, Moroz YS, Huang XP, Kalyanaraman C, Gahbauer S, ... ... Jacobson MP, et al. Structure-based discovery of nonopioid analgesics acting through the α-adrenergic receptor. Science (New York, N.Y.). 377: eabn7065. PMID 36173843 DOI: 10.1126/science.abn7065 |
0.458 |
|
| 2021 |
Lak P, O'Donnell H, Du X, Jacobson MP, Shoichet BK. A Crowding Barrier to Protein Inhibition in Colloidal Aggregates. Journal of Medicinal Chemistry. PMID 33761256 DOI: 10.1021/acs.jmedchem.0c02253 |
0.47 |
|
| 2020 |
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, ... ... Jacobson M, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. PMID 32353859 DOI: 10.1038/S41586-020-2286-9 |
0.617 |
|
| 2019 |
Ali I, Ruiz DG, Ni Z, Johnson JR, Zhang H, Li PC, Khalid MM, Conrad RJ, Guo X, Min J, Greenblatt J, Jacobson M, Krogan NJ, Ott M. Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. Molecular Cell. PMID 31054975 DOI: 10.1016/J.Molcel.2019.04.008 |
0.318 |
|
| 2019 |
Ball KA, Chan LM, Stanley DJ, Tierney E, Thapa S, Ta HM, Burton L, Binning JM, Jacobson MP, Gross JD. Conformational Dynamics of the HIV-Vif Protein Complex. Biophysical Journal. PMID 30961890 DOI: 10.1016/J.Bpj.2019.03.014 |
0.34 |
|
| 2018 |
Aleem A, Tsai WC, Tena J, Alvarez G, Deschamps J, Kalyanaraman C, Jacobson MP, Holman TR. Probing the Electrostatic and Steric Requirements for Substrate Binding in Human Platelet-type 12-Lipoxygenase. Biochemistry. PMID 30565457 DOI: 10.1021/Acs.Biochem.8B01167 |
0.306 |
|
| 2018 |
Tang S, Zhang N, Zhou Y, Cortopassi WA, Jacobson MP, Zhao LJ, Zhong RG. Structure-Based Discovery of Novel CK2α-Binding Cyclic Peptides with Anti-Cancer Activity. Molecular Informatics. PMID 30307134 DOI: 10.1002/Minf.201800089 |
0.337 |
|
| 2018 |
Shao H, Li X, Moses MA, Gilbert LA, Kalyanaraman C, Young ZT, Chernova M, Journey SN, Weissman JS, Hann B, Jacobson MP, Neckers LM, Gestwicki JE. Exploration of Benzothiazole-Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70). Journal of Medicinal Chemistry. PMID 29953808 DOI: 10.1021/Acs.Jmedchem.8B00583 |
0.301 |
|
| 2018 |
Taylor IR, Dunyak BM, Komiyama T, Shao H, Ran X, Assimon VA, Kalyanaraman C, Rauch JN, Jacobson MP, Zuiderweg ERP, Gestwicki JE. High Throughput Screen for Inhibitors of Protein-Protein Interactions in a Reconstituted Heat Shock Protein 70 (Hsp70) Complex. The Journal of Biological Chemistry. PMID 29414793 DOI: 10.1074/Jbc.Ra117.001575 |
0.313 |
|
| 2018 |
Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, ... ... Jacobson MP, et al. Prediction of enzymatic pathways by integrative pathway mapping. Elife. 7. PMID 29377793 DOI: 10.7554/Elife.31097 |
0.624 |
|
| 2017 |
Metcalf B, Chuang C, Dufu K, Patel MP, Silva-Garcia A, Johnson C, Lu Q, Partridge JR, Patskovska L, Patskovsky Y, Almo SC, Jacobson MP, Hua L, Xu Q, Gwaltney SL, et al. Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin. Acs Medicinal Chemistry Letters. 8: 321-326. PMID 28337324 DOI: 10.1021/Acsmedchemlett.6B00491 |
0.7 |
|
| 2017 |
Tran HL, Lexa KW, Julien O, Young TS, Walsh CT, Jacobson MP, Wells JA. SAR and molecular mechanics reveal the importance of ring entropy in the biosynthesis and activity of a natural product. Journal of the American Chemical Society. PMID 28170244 DOI: 10.1021/Jacs.6B10792 |
0.364 |
|
| 2017 |
Bisignano P, Kalyanaraman C, Ghezzi C, Wright EM, Abramson J, Paz A, Jacobson MP, Friemann R, Grabe M. Structural Insights into Sodium-Dependent Sugar Transporters and their Inhibition Mechanism Biophysical Journal. 112: 128a. DOI: 10.1016/J.Bpj.2016.11.714 |
0.346 |
|
| 2017 |
Ball KA, Gross JD, Jacobson MP. Conformational Flexibility of HIV Vif in Complex with Host Proteins Biophysical Journal. 112: 64a. DOI: 10.1016/J.Bpj.2016.11.384 |
0.663 |
|
| 2016 |
Wang Q, Sciabola S, Barreiro G, Hou X, Bai G, Shapiro MJ, Koehn FE, Villalobos A, Jacobson MP. Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction. Journal of Chemical Information and Modeling. PMID 27731994 DOI: 10.1021/Acs.Jcim.6B00237 |
0.397 |
|
| 2016 |
Armstrong M, van Hoorebeke C, Horn T, Deschamps J, Freedman JC, Kalyanaraman C, Jacobson MP, Holman T. Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency. Bioorganic & Medicinal Chemistry. PMID 27647374 DOI: 10.1016/J.Bmc.2016.08.063 |
0.302 |
|
| 2016 |
de Jesus Cortez F, Suzawa M, Irvy S, Bruning JM, Sablin E, Jacobson MP, Fletterick RJ, Ingraham HA, England PM. Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2). Plos One. 11: e0159316. PMID 27467220 DOI: 10.1371/Journal.Pone.0159316 |
0.328 |
|
| 2016 |
Coutsias EA, Lexa KW, Wester MJ, Pollock SN, Jacobson MP. Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics. Journal of Chemical Theory and Computation. PMID 27447193 DOI: 10.1021/Acs.Jctc.6B00250 |
0.338 |
|
| 2016 |
Ball KA, Johnson JR, Lewinski MK, Guatelli J, Verschueren E, Krogan NJ, Jacobson MP. Non-degradative Ubiquitination of Protein Kinases. Plos Computational Biology. 12: e1004898. PMID 27253329 DOI: 10.1371/Journal.Pcbi.1004898 |
0.665 |
|
| 2016 |
Ball KA, Gross J, Jacobson M. Investigating HIV Vif Interactions with Host Proteins Biophysical Journal. 110: 384a. DOI: 10.1016/J.Bpj.2015.11.2074 |
0.657 |
|
| 2015 |
Chow JY, Tian BX, Ramamoorthy G, Hillerich BS, Seidel RD, Almo SC, Jacobson MP, Poulter CD. Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus. Proceedings of the National Academy of Sciences of the United States of America. 112: 5661-6. PMID 25901324 DOI: 10.1073/Pnas.1505127112 |
0.318 |
|
| 2015 |
Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJ. A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. Journal of Biomolecular Screening. 20: 788-800. PMID 25690569 DOI: 10.1177/1087057115570550 |
0.384 |
|
| 2015 |
Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, ... ... Jacobson MP, et al. Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry. 54: 909-31. PMID 25540822 DOI: 10.1021/Bi501388Y |
0.321 |
|
| 2015 |
Hewitt WM, Leung SS, Pye CR, Ponkey AR, Bednarek M, Jacobson MP, Lokey RS. Cell-permeable cyclic peptides from synthetic libraries inspired by natural products. Journal of the American Chemical Society. 137: 715-21. PMID 25517352 DOI: 10.1021/Ja508766B |
0.312 |
|
| 2014 |
Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. Plos Computational Biology. 10: e1003874. PMID 25299649 DOI: 10.1371/Journal.Pcbi.1003874 |
0.321 |
|
| 2014 |
Krishnan S, Miller RM, Tian B, Mullins RD, Jacobson MP, Taunton J. Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis. Journal of the American Chemical Society. 136: 12624-30. PMID 25153195 DOI: 10.1021/Ja505194W |
0.322 |
|
| 2014 |
Jacobson MP, Kalyanaraman C, Zhao S, Tian B. Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. Trends in Biochemical Sciences. 39: 363-71. PMID 24998033 DOI: 10.1016/J.Tibs.2014.05.006 |
0.346 |
|
| 2014 |
Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. Prediction of substrates for glutathione transferases by covalent docking. Journal of Chemical Information and Modeling. 54: 1687-99. PMID 24802635 DOI: 10.1021/Ci5001554 |
0.645 |
|
| 2014 |
Lexa KW, Dolghih E, Jacobson MP. A structure-based model for predicting serum albumin binding. Plos One. 9: e93323. PMID 24691448 DOI: 10.1371/Journal.Pone.0093323 |
0.344 |
|
| 2014 |
Peng LX, Hsu MT, Bonomi M, Agard DA, Jacobson MP. The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery. Plos Computational Biology. 10: e1003464. PMID 24516374 DOI: 10.1371/Journal.Pcbi.1003464 |
0.375 |
|
| 2013 |
Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature. 502: 698-702. PMID 24056934 DOI: 10.1038/Nature12576 |
0.338 |
|
| 2013 |
Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD. Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2. Structure (London, England : 1993). 21: 1571-80. PMID 23911090 DOI: 10.1016/J.Str.2013.06.021 |
0.336 |
|
| 2013 |
Tian B, Wallrapp F, Kalyanaraman C, Zhao S, Eriksson LA, Jacobson MP. Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase. Biochemistry. 52: 5511-3. PMID 23901785 DOI: 10.1021/Bi400546J |
0.315 |
|
| 2013 |
Kim J, Xiao H, Bonanno JB, Kalyanaraman C, Brown S, Tang X, Al-Obaidi NF, Patskovsky Y, Babbitt PC, Jacobson MP, Lee YS, Almo SC. Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature. 498: 123-6. PMID 23676670 DOI: 10.1038/Nature12180 |
0.348 |
|
| 2013 |
Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD. Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proceedings of the National Academy of Sciences of the United States of America. 110: E1196-202. PMID 23493556 DOI: 10.1073/Pnas.1300632110 |
0.352 |
|
| 2013 |
Schönichen A, Webb BA, Jacobson MP, Barber DL. Considering protonation as a posttranslational modification regulating protein structure and function. Annual Review of Biophysics. 42: 289-314. PMID 23451893 DOI: 10.1146/Annurev-Biophys-050511-102349 |
0.354 |
|
| 2013 |
Dolghih E, Jacobson MP. Predicting efflux ratios and blood-brain barrier penetration from chemical structure: combining passive permeability with active efflux by P-glycoprotein. Acs Chemical Neuroscience. 4: 361-7. PMID 23421687 DOI: 10.1021/Cn3001922 |
0.312 |
|
| 2013 |
Choy JW, Bryant C, Calvet CM, Doyle PS, Gunatilleke SS, Leung SS, Ang KK, Chen S, Gut J, Oses-Prieto JA, Johnston JB, Arkin MR, Burlingame AL, Taunton J, Jacobson MP, et al. Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein Journal of Organic Chemistry. 9: 15-25. PMID 23400640 DOI: 10.3762/Bjoc.9.3 |
0.316 |
|
| 2013 |
Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJ, Jacobson MP, Kortemme T. Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. Structure (London, England : 1993). 21: 54-64. PMID 23159126 DOI: 10.1016/J.Str.2012.10.007 |
0.312 |
|
| 2012 |
McClendon CL, Hua L, Barreiro A, Jacobson MP. Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion. Journal of Chemical Theory and Computation. 8: 2115-2126. PMID 23316121 DOI: 10.1021/Ct300008D |
0.743 |
|
| 2012 |
Kuroda D, Shirai H, Jacobson MP, Nakamura H. Computer-aided antibody design. Protein Engineering, Design & Selection : Peds. 25: 507-21. PMID 22661385 DOI: 10.1093/Protein/Gzs024 |
0.342 |
|
| 2012 |
Leung SS, Mijalkovic J, Borrelli K, Jacobson MP. Testing physical models of passive membrane permeation. Journal of Chemical Information and Modeling. 52: 1621-36. PMID 22621168 DOI: 10.1021/Ci200583T |
0.301 |
|
| 2012 |
Kumar P, Chimenti MS, Pemble H, Schönichen A, Thompson O, Jacobson MP, Wittmann T. Multisite phosphorylation disrupts arginine-glutamate salt bridge networks required for binding of cytoplasmic linker-associated protein 2 (CLASP2) to end-binding protein 1 (EB1). The Journal of Biological Chemistry. 287: 17050-64. PMID 22467876 DOI: 10.1074/Jbc.M111.316661 |
0.357 |
|
| 2012 |
Rafi SB, Hearn BR, Vedantham P, Jacobson MP, Renslo AR. Predicting and improving the membrane permeability of peptidic small molecules. Journal of Medicinal Chemistry. 55: 3163-9. PMID 22394492 DOI: 10.1021/Jm201634Q |
0.313 |
|
| 2012 |
Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, ... ... Jacobson MP, et al. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proceedings of the National Academy of Sciences of the United States of America. 109: 4122-7. PMID 22392983 DOI: 10.1073/Pnas.1112081109 |
0.334 |
|
| 2012 |
Gerlt JA, Babbitt PC, Jacobson MP, Almo SC. Divergent evolution in enolase superfamily: strategies for assigning functions. The Journal of Biological Chemistry. 287: 29-34. PMID 22069326 DOI: 10.1074/Jbc.R111.240945 |
0.322 |
|
| 2011 |
Narayanan A, LeClaire LL, Barber DL, Jacobson MP. Phosphorylation of the Arp2 subunit relieves auto-inhibitory interactions for Arp2/3 complex activation. Plos Computational Biology. 7: e1002226. PMID 22125478 DOI: 10.1371/Journal.Pcbi.1002226 |
0.306 |
|
| 2011 |
MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA. Assessment of protein structure refinement in CASP9. Proteins. 79: 74-90. PMID 22069034 DOI: 10.1002/Prot.23131 |
0.736 |
|
| 2011 |
Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV. The Enzyme Function Initiative. Biochemistry. 50: 9950-62. PMID 21999478 DOI: 10.1021/Bi201312U |
0.632 |
|
| 2011 |
Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP. A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series. Journal of Chemical Information and Modeling. 51: 2082-9. PMID 21780805 DOI: 10.1021/Ci200033N |
0.398 |
|
| 2011 |
Nilmeier J, Hua L, Coutsias EA, Jacobson MP. Assessing protein loop flexibility by hierarchical Monte Carlo sampling. Journal of Chemical Theory and Computation. 7: 1564-1574. PMID 21743800 DOI: 10.1021/Ct1006696 |
0.781 |
|
| 2011 |
Dolghih E, Bryant C, Renslo AR, Jacobson MP. Predicting binding to p-glycoprotein by flexible receptor docking. Plos Computational Biology. 7: e1002083. PMID 21731480 DOI: 10.1371/Journal.Pcbi.1002083 |
0.321 |
|
| 2011 |
Cossins BP, Jacobson MP, Guallar V. A new view of the bacterial cytosol environment. Plos Computational Biology. 7: e1002066. PMID 21695225 DOI: 10.1371/Journal.Pcbi.1002066 |
0.355 |
|
| 2011 |
Sadowsky JD, Burlingame MA, Wolan DW, McClendon CL, Jacobson MP, Wells JA. Turning a protein kinase on or off from a single allosteric site via disulfide trapping. Proceedings of the National Academy of Sciences of the United States of America. 108: 6056-61. PMID 21430264 DOI: 10.1073/Pnas.1102376108 |
0.324 |
|
| 2011 |
Wong SE, Sellers BD, Jacobson MP. Effects of somatic mutations on CDR loop flexibility during affinity maturation. Proteins. 79: 821-9. PMID 21287614 DOI: 10.1002/Prot.22920 |
0.69 |
|
| 2010 |
Morcos F, Chatterjee S, McClendon CL, Brenner PR, López-Rendón R, Zintsmaster J, Ercsey-Ravasz M, Sweet CR, Jacobson MP, Peng JW, Izaguirre JA. Modeling conformational ensembles of slow functional motions in Pin1-WW. Plos Computational Biology. 6: e1001015. PMID 21152000 DOI: 10.1371/Journal.Pcbi.1001015 |
0.373 |
|
| 2010 |
Shimazu T, Hirschey MD, Hua L, Dittenhafer-Reed KE, Schwer B, Lombard DB, Li Y, Bunkenborg J, Alt FW, Denu JM, Jacobson MP, Verdin E. SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production. Cell Metabolism. 12: 654-61. PMID 21109197 DOI: 10.1016/J.Cmet.2010.11.003 |
0.704 |
|
| 2010 |
Sellers BD, Nilmeier JP, Jacobson MP. Antibodies as a model system for comparative model refinement. Proteins. 78: 2490-505. PMID 20602354 DOI: 10.1002/Prot.22757 |
0.773 |
|
| 2010 |
Wilbur JD, Hwang PK, Ybe JA, Lane M, Sellers BD, Jacobson MP, Fletterick RJ, Brodsky FM. Conformation switching of clathrin light chain regulates clathrin lattice assembly. Developmental Cell. 18: 841-8. PMID 20493816 DOI: 10.1016/J.Devcel.2010.04.007 |
0.729 |
|
| 2010 |
Kalyanaraman C, Jacobson MP. Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway. Biochemistry. 49: 4003-5. PMID 20415432 DOI: 10.1021/Bi100445G |
0.317 |
|
| 2010 |
Huang N, Jacobson MP. Binding-site assessment by virtual fragment screening. Plos One. 5: e10109. PMID 20404926 DOI: 10.1371/Journal.Pone.0010109 |
0.647 |
|
| 2010 |
Rafi SB, McClendon CL, Jacobson MP. Using Statistically Significant Correlated Motions of Residues in a MD Based Approach to Investigate Allostery in Ubiquitin Conjugating Protein Biophysical Journal. 98: 388a. DOI: 10.1016/J.Bpj.2009.12.2091 |
0.352 |
|
| 2010 |
Chimenti MS, Kelly MJ, Barber DL, Jacobson MP. Molecular Dynamics Simulations Predict A pH-Dependent Conformational Change in the C-Helix of Cell Cycle Checkpoint Kinase Wee1 Biophysical Journal. 98: 232a. DOI: 10.1016/J.Bpj.2009.12.1254 |
0.321 |
|
| 2009 |
Nilmeier J, Jacobson MP. Monte Carlo Sampling with Hierarchical Move Sets: POSH Monte Carlo. Journal of Chemical Theory and Computation. 5: 1968-84. PMID 26613140 DOI: 10.1021/Ct8005166 |
0.77 |
|
| 2009 |
McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP. Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. Journal of Chemical Theory and Computation. 5: 2486-2502. PMID 20161451 DOI: 10.1021/Ct9001812 |
0.354 |
|
| 2009 |
Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis . Biochemistry. 48: 11546-58. PMID 19883118 DOI: 10.1021/Bi901731C |
0.321 |
|
| 2009 |
MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in CASP8. Proteins. 77: 66-80. PMID 19714776 DOI: 10.1002/Prot.22538 |
0.744 |
|
| 2009 |
Farady CJ, Sellers BD, Jacobson MP, Craik CS. Improving the species cross-reactivity of an antibody using computational design. Bioorganic & Medicinal Chemistry Letters. 19: 3744-7. PMID 19477127 DOI: 10.1016/J.Bmcl.2009.05.005 |
0.718 |
|
| 2009 |
Rapp CS, Schonbrun C, Jacobson MP, Kalyanaraman C, Huang N. Automated site preparation in physics-based rescoring of receptor ligand complexes. Proteins. 77: 52-61. PMID 19382204 DOI: 10.1002/Prot.22415 |
0.65 |
|
| 2009 |
Narayanan A, Jacobson MP. Computational studies of protein regulation by post-translational phosphorylation. Current Opinion in Structural Biology. 19: 156-63. PMID 19339172 DOI: 10.1016/J.Sbi.2009.02.007 |
0.368 |
|
| 2009 |
Narayanan A, Sellers BD, Jacobson MP. Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains. Journal of Molecular Biology. 388: 941-53. PMID 19324053 DOI: 10.1016/J.Jmb.2009.03.043 |
0.727 |
|
| 2009 |
Tan ES, Naylor JC, Groban ES, Bunzow JR, Jacobson MP, Grandy DK, Scanlan TS. The molecular basis of species-specific ligand activation of trace amine-associated receptor 1 (TAAR(1)). Acs Chemical Biology. 4: 209-20. PMID 19256523 DOI: 10.1021/Cb800304D |
0.34 |
|
| 2009 |
Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, ... ... Jacobson MP, et al. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. Journal of Structural and Functional Genomics. 10: 107-25. PMID 19219566 DOI: 10.1007/S10969-008-9056-5 |
0.517 |
|
| 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, ... ... Jacobson MP, 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 |
0.48 |
|
| 2008 |
Nilmeier J, Jacobson M. Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility. Journal of Chemical Theory and Computation. 4: 835-846. PMID 19119325 DOI: 10.1021/Ct700334A |
0.778 |
|
| 2008 |
Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure (London, England : 1993). 16: 1668-77. PMID 19000819 DOI: 10.1016/J.Str.2008.08.015 |
0.332 |
|
| 2008 |
Tan ES, Groban ES, Jacobson MP, Scanlan TS. Toward deciphering the code to aminergic G protein-coupled receptor drug design. Chemistry & Biology. 15: 343-53. PMID 18420141 DOI: 10.1016/J.Chembiol.2008.03.004 |
0.318 |
|
| 2008 |
Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 72: 959-71. PMID 18300241 DOI: 10.1002/Prot.21990 |
0.789 |
|
| 2008 |
Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. Journal of Molecular Biology. 377: 914-34. PMID 18280498 DOI: 10.1016/J.Jmb.2008.01.049 |
0.582 |
|
| 2008 |
Wong S, Jacobson MP. Conformational selection in silico: loop latching motions and ligand binding in enzymes. Proteins. 71: 153-64. PMID 17932934 DOI: 10.1002/Prot.21666 |
0.735 |
|
| 2007 |
Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes. Journal of Chemical Theory and Computation. 3: 640-8. PMID 26637042 DOI: 10.1021/Ct600129F |
0.504 |
|
| 2007 |
Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nature Chemical Biology. 3: 486-91. PMID 17603539 DOI: 10.1038/Nchembio.2007.11 |
0.382 |
|
| 2007 |
Huang N, Jacobson MP. Physics-based methods for studying protein-ligand interactions. Current Opinion in Drug Discovery & Development. 10: 325-31. PMID 17554859 |
0.605 |
|
| 2007 |
Mandell DJ, Chorny I, Groban ES, Wong SE, Levine E, Rapp CS, Jacobson MP. Strengths of hydrogen bonds involving phosphorylated amino acid side chains. Journal of the American Chemical Society. 129: 820-7. PMID 17243818 DOI: 10.1021/Ja063019W |
0.681 |
|
| 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 |
0.546 |
|
| 2007 |
Li X, Jacobson MP, Zhu K, Zhao S, Friesner RA. Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling. Proteins. 66: 824-37. PMID 17154422 DOI: 10.1002/Prot.21125 |
0.55 |
|
| 2007 |
Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale optimization of a truncated newton minimization algorithm and application to proteins and protein-ligand complexes Journal of Chemical Theory and Computation. 3: 640-648. DOI: 10.1021/ct600129f |
0.442 |
|
| 2006 |
Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. Molecular mechanics methods for predicting protein-ligand binding. Physical Chemistry Chemical Physics : Pccp. 8: 5166-77. PMID 17203140 DOI: 10.1039/B608269F |
0.65 |
|
| 2006 |
Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. Evolution of Structure and Function in the o-Succinylbenzoate Synthase/N-Acylamino Acid Racemase Family of the Enolase Superfamily Journal of Molecular Biology. 360: 228-250. PMID 16740275 DOI: 10.1016/J.Jmb.2006.04.055 |
0.324 |
|
| 2006 |
Groban ES, Narayanan A, Jacobson MP. Conformational changes in protein loops and helices induced by post-translational phosphorylation. Plos Computational Biology. 2: e32. PMID 16628247 DOI: 10.1371/Journal.Pcbi.0020032 |
0.348 |
|
| 2006 |
Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. Journal of Chemical Information and Modeling. 46: 243-53. PMID 16426060 DOI: 10.1021/Ci0502855 |
0.64 |
|
| 2006 |
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. Journal of Medicinal Chemistry. 49: 534-53. PMID 16420040 DOI: 10.1021/Jm050540C |
0.531 |
|
| 2006 |
Yu Z, Jacobson MP, Friesner RA. What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. Journal of Computational Chemistry. 27: 72-89. PMID 16261581 DOI: 10.1002/Jcc.20307 |
0.481 |
|
| 2005 |
Wong SE, Bernacki K, Jacobson M. Competition between intramolecular hydrogen bonds and solvation in phosphorylated peptides: simulations with explicit and implicit solvent. The Journal of Physical Chemistry. B. 109: 5249-58. PMID 16863191 DOI: 10.1021/Jp046333Q |
0.702 |
|
| 2005 |
Bernacki K, Kalyanaraman C, Jacobson MP. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods. Journal of Biomolecular Screening. 10: 675-81. PMID 16170049 DOI: 10.1177/1087057105281220 |
0.37 |
|
| 2005 |
Kalyanaraman C, Bernacki K, Jacobson MP. Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry. 44: 2059-71. PMID 15697231 DOI: 10.1021/Bi0481186 |
0.367 |
|
| 2004 |
Li X, Jacobson MP, Friesner RA. High-resolution prediction of protein helix positions and orientations. Proteins. 55: 368-82. PMID 15048828 DOI: 10.1002/Prot.20014 |
0.579 |
|
| 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 |
0.585 |
|
| 2004 |
Guallar V, Jacobson M, McDermott A, Friesner RA. Computational modeling of the catalytic reaction in triosephosphate isomerase. Journal of Molecular Biology. 337: 227-39. PMID 15001364 DOI: 10.1016/J.Jmb.2003.11.016 |
0.559 |
|
| 2004 |
Coutsias EA, Seok C, Jacobson MP, Dill KA. A kinematic view of loop closure. Journal of Computational Chemistry. 25: 510-28. PMID 14735570 DOI: 10.1002/Jcc.10416 |
0.356 |
|
| 2004 |
Yu Z, Jacobson MP, Josovitz J, Rapp CS, Friesner RA. First-shell solvation of ion pairs: Correction of systematic errors in implicit solvent models Journal of Physical Chemistry B. 108: 6643-6654. DOI: 10.1021/Jp037821L |
0.542 |
|
| 2004 |
Jacobson M, Sali A. Comparative Protein Structure Modeling and its Applications to Drug Discovery Annual Reports in Medicinal Chemistry. 39: 259-276. DOI: 10.1016/S0065-7743(04)39020-2 |
0.524 |
|
| 2002 |
Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. Journal of Structural and Functional Genomics. 2: 103-11. PMID 12836667 DOI: 10.1023/A:1020435630054 |
0.579 |
|
| 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 |
0.541 |
|
| 2002 |
Silva ML, Jacobson MP, Duan Z, Field RW. Unexpected simplicity in the S1-S0 dispersed fluorescence spectra of 13C2H2 Journal of Chemical Physics. 116: 7939-7947. DOI: 10.1063/1.1469018 |
0.433 |
|
| 2002 |
Jacobson MP, Kaminski GA, Friesner RA, Rapp CS. Force field validation using protein side chain prediction Journal of Physical Chemistry B. 106: 11673-11680. DOI: 10.1021/Jp021564N |
0.559 |
|
| 2001 |
Hoshina K, Iwasaki A, Yamanouchi K, Jacobson MP, Field RW. The infrared-ultraviolet dispersed fluorescence spectrum of acetylene: New classes of bright states Journal of Chemical Physics. 114: 7424-7442. DOI: 10.1063/1.1333006 |
0.436 |
|
| 2001 |
Jacobson MP, Child MS. Spectroscopic signatures of bond-breaking internal rotation. II. Rotation-vibration level structure and quantum monodromy in HCP Journal of Chemical Physics. 114: 262-275. DOI: 10.1063/1.1330746 |
0.554 |
|
| 2001 |
Jacobson MP, Child MS. Spectroscopic signatures of bond-breaking internal rotation. I. Saddle point induced polyad breakdown Journal of Chemical Physics. 114: 250-261. DOI: 10.1063/1.1330238 |
0.546 |
|
| 2001 |
Child MS, Jacobson MP, Cooper CD. Scaling laws for strongly anharmonic vibrational matrix elements Journal of Physical Chemistry A. 105: 10791-10799. DOI: 10.1021/Jp012582S |
0.434 |
|
| 2001 |
Jacobson MP, Child MS. Scaling rules for resonance dynamics near a saddle point: The pendulum as a zero-order model Journal of Physical Chemistry A. 105: 2834-2841. DOI: 10.1021/Jp0045080 |
0.539 |
|
| 2001 |
Ruckstuhl AF, Jacobson MP, Field RW, Dodd JA. Baseline subtraction using robust local regression estimation Journal of Quantitative Spectroscopy and Radiative Transfer. 68: 179-193. DOI: 10.1016/S0022-4073(00)00021-2 |
0.425 |
|
| 2001 |
Silva ML, Jacobson MP, Duan Z, Field RW. Anomalous simplicity of the à → X̃ dispersed fluorescence spectrum of 13c2h2 Journal of Molecular Structure. 565: 87-91. DOI: 10.1016/S0022-2860(00)00780-8 |
0.429 |
|
| 2000 |
Moss DB, Duan Z, Jacobson MP, O'Brien JP, Field RW. Observation of Coriolis Coupling between nu(2) + 4nu(4) and 7nu(4) in Acetylene &Xtilde;(1)Sigma(+)(g) by Stimulated Emission Pumping Spectroscopy. Journal of Molecular Spectroscopy. 199: 265-274. PMID 10637113 DOI: 10.1006/Jmsp.1999.7994 |
0.457 |
|
| 2000 |
Jacobson MP, Coy SL, Field RW, Lipson SJ, Lockwood RB, Vititoe DL, Blumberg WAM, Armstrong PS. Numerical Pattern Recognition Analysis of CO Atmospheric Simulation Experiments The Journal of Physical Chemistry A. 104: 249-257. DOI: 10.1021/Jp9924732 |
0.418 |
|
| 2000 |
Jacobson MP, Field RW. Acetylene at the Threshold of Isomerization The Journal of Physical Chemistry A. 104: 3073-3086. DOI: 10.1021/JP992428U |
0.315 |
|
| 2000 |
Jacobson MP, Field RW. Acetylene at the Threshold of Isomerization Journal of Physical Chemistry A. 104: x1-3086. DOI: 10.1021/Jp992428U |
0.468 |
|
| 2000 |
Jacobson MP, Field RW. Visualizing intramolecular vibrational redistribution: expectation values of resonance operators Chemical Physics Letters. 320: 553-560. DOI: 10.1016/S0009-2614(00)00306-7 |
0.43 |
|
| 1999 |
Jacobson MP, Jung C, Taylor HS, Field RW. State-by-state assignment of the bending spectrum of acetylene at 15000 cm-1: A case study of quantum-classical correspondence Journal of Chemical Physics. 111: 600-618. DOI: 10.1063/1.479341 |
0.446 |
|
| 1999 |
Jacobson MP, Silbey RJ, Field RW. Local mode behavior in the acetylene bending system The Journal of Chemical Physics. 110: 845-859. DOI: 10.1063/1.478052 |
0.564 |
|
| 1998 |
Jacobson MP, O’Brien JP, Field RW. Anomalously slow intramolecular vibrational redistribution in the acetylene X̃ 1Σg+ state above 10 000 cm−1 of internal energy The Journal of Chemical Physics. 109: 3831-3840. DOI: 10.1063/1.476983 |
0.441 |
|
| 1998 |
Jacobson MP, O'Brien JP, Silbey RJ, Field RW. Pure bending dynamics in the acetylene X̃1Σg + state up to 15000 cm-1 of internal energy Journal of Chemical Physics. 109: 121-133. DOI: 10.1063/1.476529 |
0.596 |
|
| 1998 |
O’Brien JP, Jacobson MP, Sokol JJ, Coy SL, Field RW. Numerical pattern recognition analysis of acetylene dispersed fluorescence spectra The Journal of Chemical Physics. 108: 7100-7113. DOI: 10.1063/1.476127 |
0.446 |
|
| 1997 |
Coy SL, Jacobson MP, Field RW. Identifying patterns in multicomponent signals by extended cross correlation The Journal of Chemical Physics. 107: 8357-8369. DOI: 10.1063/1.475036 |
0.425 |
|
| 1997 |
Jacobson MP, Coy SL, Field RW. Extended cross correlation: A technique for spectroscopic pattern recognition The Journal of Chemical Physics. 107: 8349-8356. DOI: 10.1063/1.475035 |
0.434 |
|
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