Graduates of the MBTG

Graduates are listed by the year they were appointed to the training program

Trainees appointed in 2009

  • Sulyman Barkho

    Email: sb1899@gmail.com
    Linkedin: https://www.linkedin.com/in/sbarkho/
    Program: Chemistry & Biochemistry
    Advisor: Patricia Jennings

    Publications:

    Barkho S, Pierce LC, Li S, Adams JA, Jennings PA (2015) .Theoretical Insights Reveal Novel Motions in Csk's SH3 Domain That Control Kinase Activation.PLoS One. 10(6):e0127724.     PMC4507846

    Barkho S, Pierce LC, McGlone ML, Li S, Woods VL Jr, Walker RC, Adams JA, Jennings PA. (2013) Distal loop flexibility of a regulatory domain modulates dynamics and activity of C-terminal SRC kinase (csk). PLoS Comput Biol. 9(9):e1003188. PMC4452171

    Hailey KL, Capraro DT, Barkho S, Jennings PA (2013) Allosteric switching of agonist/antagonist activity by a single point mutation in the interluekin-1 receptor antagonist, IL-1Ra.. J Mol Biol. 2013 425(13):2382-92. PMC4059520

  • Jeffrey Brodin

    Email: jbrodin3@gmail.com
    Linkedin: https://www.linkedin.com/in/jeffrey-brodin-00703784/
    Program: Chemistry & Biochemistry
    Advisor: Akif Tezcan

    Publications:

    Salgado EN, Ambroggio XI, Brodin JD, Lewis RA, Kuhlman B, Tezcan FA. (2010) Metal templated design of protein interfaces.Proc Natl Acad Sci U S A. 107(5):1827-32. PMC2836610

    Brodin JD, Medina-Morales A, Ni T, Salgado EN, Ambroggio XI, Tezcan FA.(2010) Evolution of metal selectivity in templated protein interfaces. J Am Chem Soc. 132(25):8610-7. PMC2896502

    Salgado EN, Brodin JD, To MM, Tezcan FA. (2011) Templated construction of a Zn-selective protein dimerization motif. Inorg Chem. 2011 Jul 4;50(13):6323-9.

    Brodin JD, Ambroggio XI, Tang C, Parent KN, Baker TS, Tezcan FA. (2012) Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays. Nat Chem. 2012 4(5):375-82. PMC3335442

    Medina-Morales A, Perez A, Brodin JD, Tezcan FA. (2013) In vitro and cellular self-assembly of a Zn-binding protein cryptand via templated disulfide bonds. J Am Chem Soc. 135(32):12013-22. PMC4289141

    Brodin JD, Carr JR, Sontz PA, Tezcan FA. (2014) Exceptionally stable, redox-active supramolecular protein assemblies with emergent properties. Proc Natl Acad Sci U S A. 111(8):2897-902. PMC3939893

    Brodin JD, Smith SJ, Carr JR, Tezcan FA. (2015) Designed, Helical Protein Nanotubes with Variable Diameters from a Single Building Block. J Am Chem Soc. 137(33):10468-71.

    Churchfield LA, Medina-Morales A, Brodin JD, Perez A, Tezcan FA. (2016) De Novo Design of an Allosteric Metalloprotein Assembly with Strained Disulfide Bonds. J Am Chem Soc. 138(40):13163-13166. PMC5085265

  • Andrew Caldwell

    Email: abcaldwell@ucsd.edu
    Linkedin: https://www.linkedin.com/in/andrewbcaldwell/
    Program: Chemistry & Biochemistry
    Advisor: Alex Hoffman

    Publications: 

    Shih VF, Tsui R, Caldwell A, Hoffmann A. (2011) A single NFκB system for both canonical and non-canonical signaling. Cell Res. 21(1):86-102. PMC3193412

    Caldwell AB, Cheng Z, Vargas JD, Birnbaum HA, Hoffmann A. (2014) Network dynamics determine the autocrine and paracrine signaling functions of TNF. Genes Dev. 28(19):2120-33.     PMC4180974

  • Eileen Chen

    Email: me2youtw11@gmail.com
    Linkedin: https://www.linkedin.com/in/eileenchen111/
    Program: Chemistry & Biochemistry
    Advisor: Simpson Joseph

    Publications: 

    Chen E, Sharma MR, Shi X, Agrawal RK, Joseph S. (2014) Fragile X mental retardation protein regulates translation by binding directly to the ribosome. Mol Cell. 54(3):407-417. PMC4019695

    Chen E, Joseph S. (2015) Fragile X mental retardation protein: A paradigm for translational control by RNA-binding proteins. Biochimie. 114:147-54. PMC4458461

     

  • Natalie Shanks

    Email:
    Linkedin: https://www.linkedin.com/in/natalie-shanks-b7510171/
    Program: Chemistry & Biochemistry
    Advisor: Terunaga Nakagawa

    Publications:

    Shanks NF, Maruo T, Farina AN, Ellisman MH, Nakagawa T. (2010) Contribution of the global subunit structure and stargazin on the maturation of AMPA receptors. J Neurosci. 30(7):2728-40. PMC2842908

    Shanks NF, Savas JN, Maruo T, Cais O, Hirao A, Oe S, Ghosh A, Noda Y, Greger IH, Yates JR 3rd, Nakagawa T. (2012) Differences in AMPA and kainate receptor interactomes facilitate identification of AMPA receptor auxiliary subunit GSG1L. Cell Rep. 1(6):590-8. PMC3401968

    Shanks NF, Cais O, Maruo T, Savas JN, Zaika EI, Azumaya CM, Yates JR 3rd, Greger I, Nakagawa T. (2014) Molecular dissection of the interaction between the AMPA receptor and cornichon homolog-3. J Neurosci. 34(36):12104-20. PMC4152608

    Elegheert J, Kakegawa W, Clay JE, Shanks NF, Behiels E, Matsuda K, Kohda K, Miura E, Rossmann M, Mitakidis N, Motohashi J, Chang VT, Siebold C, Greger IH, Nakagawa T, Yuzaki M, Aricescu AR. Structural basis for integration of GluD receptors within synaptic organizer complexes. Science. 353(6296):295-9. PMC5291321

  • William Sinko

    Email: wsinko@gmail.com
    Linkedin: https://www.linkedin.com/in/williamsinko/
    Program: Chemistry & Biochemistry
    Advisor: J. Andrew McCammon

    Publications:

    Sierecki E, Sinko W, McCammon JA, Newton AC. (2010) Discovery of small molecule inhibitors of the PH domain leucine-rich repeat protein phosphatase (PHLPP) by chemical and virtual screening. J Med Chem. 53(19):6899-911. PMC2951065

    Sinko W, de Oliveira C, Williams S, Van Wynsberghe A, Durrant JD, Cao R, Oldfield E, McCammon JA. (2011) Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial target. Chem Biol Drug Des. 77(6):412-20. PMC3095679

    Sinko W, Sierecki E, de Oliveira CA, McCammon JA. (2012) Guide to virtual screening: application to the Akt phosphatase PHLPP. Methods Mol Biol. 819:561-73.

    Sinko W, de Oliveira CA, Pierce LC, McCammon JA. (2012) Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations. J Chem Theory Comput. 8(1):17-23. PMC3254191

    Zhu W, Zhang Y, Sinko W, Hensler ME, Olson J, Molohon KJ, Lindert S, Cao R, Li K, Wang K, Wang Y, Liu YL, Sankovsky A, de Oliveira CA, Mitchell DA, Nizet V, McCammon JA, Oldfield E. (2013) Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A. 110(1):123-8. PMC3538244

    Sinko W, Lindert S, McCammon JA. (2013) Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chem Biol Drug Des. 81(1):41-9. PMC3540989

    Arrar M, de Oliveira CA, Fajer M, Sinko W, McCammon JA. (2013) w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations. J Chem Theory Comput. 9(1):18-23. PMC3541756

    Sinko W, Miao Y, de Oliveira CA, McCammon JA. (2013) Population based reweighting of scaled molecular dynamics. J Phys Chem B. 117(42):12759-68. PMC3808002

    Feixas F, Lindert S, Sinko W, McCammon JA. (2014) Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem. 2014 Feb;186:31-45. PMC4459653

    Sinko W, Wang Y, Zhu W, Zhang Y, Feixas F, Cox CL, Mitchell DA, Oldfield E, McCammon JA. (2014) Undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads. J Med Chem. 57(13):5693-701. PMC4096218

    Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA. (2014) Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J Chem Theory Comput. 10(7):2677-2689. PMC4095935

    Kim MO, Feng X, Feixas F, Zhu W, Lindert S, Bogue S, Sinko W, de Oliveira C, Rao G, Oldfield E, McCammon JA. (2015) A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer-aided Drug Discovery. Chem Biol Drug Des. 85(6):756-69. PMC4412765

  • Jeramie Watrous

    Email: jeramie.watrous@gmail.com 
    Linkedin: https://www.linkedin.com/in/jeramie-watrous-6993b012/
    Program: Chemistry & Biochemistry
    Advisor: Pieter Dorrestein

    Publications: 

    Watrous J, Burns K, Liu WT, Patel A, Hook V, Bafna V, Barry CE 3rd, Bark S, Dorrestein PC. (2010) Expansion of the mycobacterial "PUPylome". Mol Biosyst. 6(2):376-85. PMC2846642

    Watrous J, Hendricks N, Meehan M, Dorrestein PC. (2010) Capturing bacterial metabolic exchange using thin film desorption electrospray ionization-imaging mass spectrometry. Anal Chem. 82(5):1598-600. PMC4112561

    Yang JY, Karr JR, Watrous JD, Dorrestein PC. (2011) Integrating '-omics' and natural product discovery platforms to investigate metabolic exchange in microbiomes. Curr Opin Chem Biol. 15(1):79-87. PMC3174688

    Watrous JD, Alexandrov T, Dorrestein PC. (2011) The evolving field of imaging mass spectrometry and its impact on future biological research. J Mass Spectrom. 46(2):209-22. PMC3303182

    Watrous JD, Dorrestein PC. (2011) Imaging mass spectrometry in microbiology. Nat Rev Microbiol. 9(9):683-94. PMC3710447

    Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC. (2012) Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci U S A. 109(26):E1743-52. PMC3387089

    Guthals A, Watrous JD, Dorrestein PC, Bandeira N. (2012) The spectral networks paradigm in high throughput mass spectrometry. Mol Biosyst.(10):2535-44. PMC3893064

    Yang JY, Phelan VV, Simkovsky R, Watrous JD, Trial RM, Fleming TC, Wenter R, Moore BS, Golden SS, Pogliano K, Dorrestein PC. (2012) Primer on agar-based microbial imaging mass spectrometry. J Bacteriol. 194(22):6023-8. PMC3486372

    Watrous JD, Phelan VV, Hsu CC, Moree WJ, Duggan BM, Alexandrov T, Dorrestein PC. (2013) Microbial metabolic exchange in 3D. ISME J.7(4):770-80. PMC3603389

    Nguyen DD, Wu CH, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous JD, Phelan VV, van de Wiel C, Kersten RD, Mehnaz S, De Mot R, Shank EA, Charusanti P, Nagarajan H, Duggan BM, Moore BS, Bandeira N, Palsson BØ, Pogliano K, Gutiérrez M, Dorrestein PC. (2013) MS/MS networking guided analysis of molecule and gene cluster families. Proc Natl Acad Sci U S A.110(28):E2611-20. PMC3710860

    Traxler MF, Watrous JD, Alexandrov T, Dorrestein PC, Kolter R. (2014) Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome. MBio. 4(4). pii: e00459-13. PMC3747584

    Watrous J, Roach P, Heath B, Alexandrov T, Laskin J, Dorrestein PC. (2013) Metabolic profiling directly from the Petri dish using nanospray desorption electrospray ionization imaging mass spectrometry. Anal Chem. 85(21):10385-91. PMC3913783

    Winnikoff JR, Glukhov E, Watrous J, Dorrestein PC, Gerwick WH. (2014) Quantitative molecular networking to profile marine cyanobacterial metabolomes. J Antibiot (Tokyo). 67(1):105-12. PMC5105604

    Bleich R, Watrous JD, Dorrestein PC, Bowers AA, Shank EA. (2015) Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis. Proc Natl Acad Sci U S A. 112(10):3086-91. PMC4364203

    Michelsen CF, Watrous J, Glaring MA, Kersten R, Koyama N, Dorrestein PC, Stougaard P. (2015) Nonribosomal peptides, key biocontrol components for Pseudomonas fluorescens In5, isolated from a Greenlandic suppressive soil. MBio. 6(2):e00079. PMC4453515

    Oetjen J, Veselkov K, Watrous J, McKenzie JS, Becker M, Hauberg-Lotte L, Kobarg JH, Strittmatter N, Mróz AK, Hoffmann F, Trede D, Palmer A, Schiffler S, Steinhorst K, Aichler M, Goldin R, Guntinas-Lichius O, von Eggeling F, Thiele H, Maedler K, Walch A, Maass P, Dorrestein PC, Takats Z, Alexandrov T. Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry. Gigascience. 4:20. PMC4418095

    Van Der Voort M, Meijer HJ, Schmidt Y, Watrous J, Dekkers E, Mendes R, Dorrestein PC, Gross H, Raaijmakers JM. (2015) Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds. Front Microbiol. 6:693. PMC4493835

    Song C, Mazzola M, Cheng X, Oetjen J, Alexandrov T, Dorrestein P, Watrous J, van der Voort M, Raaijmakers JM. (2015) Molecular and chemical dialogues in bacteria-protozoa interactions. Sci Rep. 5:12837. PMC4542665

    de Bruijn I, Cheng X, de Jager V, Expósito RG, Watrous J, Patel N, Postma J, Dorrestein PC, Kobayashi D, Raaijmakers JM. (2015) Comparative genomics and metabolic profiling of the genus Lysobacter. BMC Genomics. 16:991. PMC4657364

    Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. (2016) Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 34(8):828-837. PMC5321674

Trainees appointed in 2010

  • Brandon Razooky

    Email: brandon.razooky@rockefeller.edu
    Linkedin: https://www.linkedin.com/in/brandon-razooky-46026557/
    Program: Chemistry & Biochemistry
    Advisor: Leor Weinberger

    Publications: 

    Singh A, Razooky B, Cox CD, Simpson ML, Weinberger LS. (2010) Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression. Biophys J. 98(8):L32-4. PMC2856162

    Razooky BS, Weinberger LS. (2011) Mapping the architecture of the HIV-1 Tat circuit: A decision-making circuit that lacks bistability and exploits stochastic noise. Methods. 53(1):68-77. PMC4096296

    Singh A, Razooky BS, Dar RD, Weinberger LS. (2012) Dynamics of protein noise can distinguish between alternate sources of gene-expression variability. Mol Syst Biol. 8:607. PMC3435505

    Razooky BS, Gutierrez E, Terry VH, Spina CA, Groisman A, Weinberger LS. (2012) Microwell devices with finger-like channels for long-term imaging of HIV-1 expression kinetics in primary human lymphocytes. Lab Chip. 12(21):4305-12. PMC3589574

    Dar RD, Razooky BS, Singh A, Trimeloni TV, McCollum JM, Cox CD, Simpson ML, Weinberger LS. (2012) Transcriptional burst frequency and burst size are equally modulated across the human genome. Proc Natl Acad Sci U S A. 109(43):17454-9. PMC3491463

    Rouzine IM, Razooky BS, Weinberger LS. (2014) Stochastic variability in HIV affects viral eradication. Proc Natl Acad Sci U S A. 111(37):13251-2. PMC4169906

    Dar RD, Razooky BS, Weinberger LS, Cox CD, Simpson ML. (2015) The Low Noise Limit in Gene Expression. PLoS One. 10(10):e0140969. PMC4619080

    Razooky BS, Pai A, Aull K, Rouzine IM, Weinberger LS. (2015) A hardwired HIV latency program. Cell. 160(5):990-1001. PMC4395878

    Dar RD, Shaffer SM, Singh A, Razooky BS, Simpson ML, Raj A, Weinberger LS. (2016) Transcriptional Bursting Explains the Noise-Versus-Mean Relationship in mRNA and Protein Levels. PLoS One. 11(7):e0158298. PMC4965078

    Razooky BS, Cao Y, Hansen MMK, Perelson AS, Simpson ML, Weinberger LS. (2017) Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean. PLoS Biol. 15(10):e2000841. PMC5646755

    Hansen MMK, Wen WY, Ingerman E, Razooky BS, Thompson CE, Dar RD, Chin CW, Simpson ML, Weinberger LS. (2018) A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization. Cell. 173(7):1609-1621.e15. PMC6044448

  • Nicholas Schafer

    Email: 
    Linkedin: https://www.linkedin.com/in/npschafer/
    Program: Chemistry & Biochemistry
    Advisor: 

    Publications: 

    Davtyan A, Schafer NP, Zheng W, Clementi C, Wolynes PG, Papoian GA.(2012) AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. J Phys Chem B. 116(29):8494-503. PMC3406225

    Zheng W, Schafer NP, Davtyan A, Papoian GA, Wolynes PG. (2012) Predictive energy landscapes for protein-protein association. Proc Natl Acad Sci U S A.109(47):19244-9. PMC3511104

    Schafer NP, Hoffman RM, Burger A, Craig PO, Komives EA, Wolynes PG. (2012) Discrete kinetic models from funneled energy landscape simulations. PLoS One. 7(12):e50635. PMC3520928

    Zheng W, Schafer NP, Wolynes PG. (2013) Frustration in the energy landscapes of multidomain protein misfolding. Proc Natl Acad Sci U S A. 110(5):1680-5. PMC3562767

    Truong HH, Kim BL, Schafer NP, Wolynes PG. (2013) Funneling and frustration in the energy landscapes of some designed and simplified proteins. J Chem Phys. 139(12):121908. PMC3732306

    Zheng W, Schafer NP, Wolynes PG. (2013) Free energy landscapes for initiation and branching of protein aggregation. Proc Natl Acad Sci U S A. 110(51):20515-20. PMC3870682

    Kim BL, Schafer NP, Wolynes PG. (2014) Predictive energy landscapes for folding α-helical transmembrane proteins. Proc Natl Acad Sci U S A. 111(30):11031-6. PMC4121805

    Morcos F, Schafer NP, Cheng RR, Onuchic JN, Wolynes PG. (2014) Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection. Proc Natl Acad Sci U S A. 111(34):12408-13. PMC4151759

    Schafer NP, Kim BL, Zheng W, Wolynes PG. (2014) Learning To Fold Proteins Using Energy Landscape Theory. Isr J Chem. 54(8-9):1311-1337. PMC4189132

  • Sarah Smith

    Email: sarah.smith115@gmail.com
    Linkedin: https://www.linkedin.com/in/sarah-smith-88a692a5/
    Program: 
    Advisor: Akif Tezcan

    Publications:

    Smith SJ, Du K, Radford RJ, Tezcan FA. (2013) Functional, metal-based crosslinkers for α-helix induction in short peptides. Chem Sci. 4(9):3740-3747. PMC3800689

    Brodin JD, Smith SJ, Carr JR, Tezcan FA. (2015) Designed, Helical Protein Nanotubes with Variable Diameters from a Single Building Block. J Am Chem Soc. 137(33):10468-71.

    Smith SJ, Radford RJ, Subramanian RH, Barnett BR, Figueroa JS, Tezcan FA. (2016) Tunable Helicity, Stability and DNA-Binding Properties of Short Peptides with Hybrid Metal Coordination Motifs. Chem Sci. 2016 7(8):5453-5461. PMC5085262

    Subramanian RH, Smith SJ, Alberstein RG, Bailey JB, Zhang L, Cardone G, Suominen L, Chami M, Stahlberg H, Baker TS, Tezcan FA. (2018) Self-Assembly of a Designed Nucleoprotein Architecture through Multimodal Interactions. ACS Cent Sci. 4(11):1578-1586. PMC6276041

     

Trainees appointed in 2011

  • Zachary Berndsen

    Email: zacharyberndsen@gmail.com 
    Linkedin: https://www.linkedin.com/in/zachary-t-berndsen-0ba988b1/
    Program: Chem/Biochem
    Advisor: Douglas Smith

    Publications:

    Berndsen ZT, Keller N, Grimes S, Jardine PJ, Smith DE. (2014) Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging. Proc Natl Acad Sci U S A. 111(23):8345-50.     PMC4060647

    Berndsen ZT, Keller N, Smith DE. (2015) Continuous allosteric regulation of a viral packaging motor by a sensor that detects the density and conformation of packaged DNA. Biophys J. 108(2):315-24. PMC4302192

    Keller N, Berndsen ZT, Jardine PJ, Smith DE. (2017) Experimental comparison of forces resisting viral DNA packaging and driving DNA ejection. Phys Rev E. 95(5-1):052408.

  • Patrick Blachly

    Email: pblachly@gmail.com 
    Linkedin: https://www.linkedin.com/in/pblachly/
    Program: Chem/Biochem
    Advisor: J. Andrew McCammon

    Publications:

    Williams SL, Blachly PG, McCammon JA. (2011) Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study. Proteins. 79(12):3381-8. PMC3227005

    Blachly PG, de Oliveira CA, Williams SL, McCammon JA. (2013) Utilizing a dynamical description of IspH to aid in the development of novel antimicrobial drugs. PLoS Comput Biol. 9(12):e1003395. PMC3868525

    Martin DP, Blachly PG, Marts AR, Woodruff TM, de Oliveira CA, McCammon JA, Tierney DL, Cohen SM. (2014) Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site. J Am Chem Soc. 136(14):5400-6. PMC4104174

    Martin DP, Blachly PG, McCammon JA, Cohen SM. (2014) Exploring the influence of the protein environment on metal-binding pharmacophores. J Med Chem. 57(16):7126-35. PMC4148168

    Kim MO, Blachly PG, Kaus JW, McCammon JA. (2015) Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies. J Phys Chem B. 119(3):861-72. PMC4306499

    Blachly PG, Sandala GM, Giammona DA, Liu T, Bashford D, McCammon JA, Noodleman L. (2014) Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition. J Chem Theory Comput. 10(9):3871-3884. PMC4159220

    Blachly PG, Sandala GM, Giammona DA, Bashford D, McCammon JA, Noodleman L. (2015) Broken-Symmetry DFT Computations for the Reaction Pathway of IspH, an Iron-Sulfur Enzyme in Pathogenic Bacteria. Inorg Chem. 54(13):6439-61. PMC4568833

    Kim MO, Blachly PG, McCammon JA. (2015) Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PLoS Comput Biol. 11(10):e1004341. PMC4623973

  • Lindsay Dawson

    Email: lindsay.dawson1@gmail.com 
    Linkedin: https://www.linkedin.com/in/lindsayadawson/
    Program: Chem/Biochem
    Advisor: Stanley Opella

    Publications: 

    Cook GA, Dawson LA, Tian Y, Opella SJ. (2013) Three-dimensional structure and interaction studies of hepatitis C virus p7 in 1,2-dihexanoyl-sn-glycero-3-phosphocholine by solution nuclear magnetic resonance. Biochemistry. 52(31):5295-303. PMC3855088

  • Lindsey Handley

    Email: lindseyhandley@gmail.com 
    Linkedin: https://www.linkedin.com/in/lindseydhandley/
    Program: Chem/Biochem
    Advisor: Elizabeth Komives

    Publications:

    Cervantes CF, Handley LD, Sue SC, Dyson HJ, Komives EA. (2013) Long-range effects and functional consequences of stabilizing mutations in the ankyrin repeat domain of IκBα. J Mol Biol. 425(5):902-13. PMC3744861

    Handley LD, Treuheit NA, Venkatesh VJ, Komives EA. (2015) Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin. Biochemistry. 54(43):6650-8. PMC4697735

    Handley LD, Fuglestad B, Stearns K, Tonelli M, Fenwick RB, Markwick PR, Komives EA.(2017) NMR reveals a dynamic allosteric pathway in thrombin. Sci Rep. 7:39575. PMC5216386

  • Benjamin Madej

    Email: bdmadej@gmail.com 
    Linkedin: https://www.linkedin.com/in/benjamin-madej-12b3b314/
    Program: Chem/Biochem
    Advisor: Ross Walker

    Publications:

    Skjevik ÅA, Madej BD, Walker RC, Teigen K. (2012) LIPID11: a modular framework for lipid simulations using amber. J Phys Chem B. 116(36):11124-36. PMC3771533

    Dickson CJ, Madej BD, Skjevik AA, Betz RM, Teigen K, Gould IR, Walker RC. (2014) Lipid14: The Amber Lipid Force Field. J Chem Theory Comput. 10(2):865-879. PMC3985482

    Skjevik ÅA, Madej BD, Dickson CJ, Teigen K, Walker RC, Gould IR. (2015) All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields. Chem Commun (Camb). 51(21):4402-5. PMC5084445

    Madej BD, Gould IR, Walker RC. (2015) A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field. J Phys Chem B. 119(38):12424-35. PMC5079186

    Skjevik ÅA, Madej BD, Dickson CJ, Lin C, Teigen K, Walker RC, Gould IR. (2016) Simulation of lipid bilayer self-assembly using all-atom lipid force fields. Phys Chem Chem Phys. 18(15):10573-84. PMC5091658

  • Christopher Pierse

    Email:
    Linkedin: https://www.linkedin.com/in/christopher-pierse/
    Program: Physics
    Advisor: Olga Dudko

    Publications:

    Pierse CA, Dudko OK. (2013) Kinetics and energetics of biomolecular folding and binding. Biophys J. 105(9):L19-22.  PMC3824551

    Pierse CA, Dudko OK. (2017) Distinguishing Signatures of Multipathway Conformational Transitions. Phys Rev Lett.118(8):088101.

  • Chelsea Stewart

    Email:
    Program: BMS
    Advisor: Partho Ghosh

    Publications:

    Stewart CM, Buffalo CZ, Valderrama JA, Henningham A, Cole JN, Nizet V, Ghosh P. (20160 Coiled-coil destabilizing residues in the group A Streptococcus M1 protein are required for functional interaction. Proc Natl Acad Sci U S A. 113(34):9515-20. PMC5003295

    Döhrmann S, LaRock CN, Anderson EL, Cole JN, Ryali B, Stewart C, Nonejuie P, Pogliano J, Corriden R, Ghosh P, Nizet V. (2017) Group A Streptococcal M1 Protein Provides Resistance against the Antimicrobial Activity of Histones. sSci Rep. 7:43039. PMC5318940

  • Zhaleh Amini

    Email: zhalehnamini@gmail.com
    Linkedin: https://www.linkedin.com/in/zhalehamini/
    Program: Chem/Biochem
    Advisor: Ulrich Muller 

    Publications:

    Amini ZN, Müller UF. (2013) Low selection pressure aids the evolution of cooperative ribozyme mutations in cells. J Biol Chem. 288(46):33096-106. PMC3829158

    Amini ZN, Olson KE, Müller UF. (2014) Spliceozymes: ribozymes that remove introns from pre-mRNAs in trans. PLoS One. 9(7):e101932. PMC4094466

    Amini ZN, Müller UF. (2015) Increased efficiency of evolved group I intron spliceozymes by decreased side product formation. RNA. 21(8):1480-9. PMC4509937

  • Donald Johnson

    Email:
    Linkedin: https://www.linkedin.com/in/donald-johnson-phd/
    Program: Chem/Biochem
    Advisor: Mark Ellisman, Susan Taylor

    Publications:

    Bushong EA, Johnson DD Jr, Kim KY, Terada M, Hatori M, Peltier ST, Panda S, Merkle A, Ellisman MH. (2015) X-ray microscopy as an approach to increasing accuracy and efficiency of serial block-face imaging for correlated light and electron microscopy of biological specimens. Microsc Microanal. 21(1):231-8.  PMC4415271

  • Ignacio Lopez

    Email:
    Linkedin: 
    Program: Chem/Biochem
    Advisor: Judy Kim

    Publications:

    Kang G, López-Peña I, Oklejas V, Gary CS, Cao W, Kim JE. (2012) Förster resonance energy transfer as a probe of membrane protein folding. Biochim Biophys Acta. 1818(2):154-61. PMC3253952

    López-Peña I, Leigh BS, Schlamadinger DE, Kim JE. (2015) Insights into Protein Structure and Dynamics by Ultraviolet and Visible Resonance Raman Spectroscopy. Biochemistry. 54(31):4770-83.     PMC5092233

  • Hoang Thien Nguyen

    Email: 
    Linkedin: 
    Program: Chem/Biochem
    Advisor: Hector Viadiu

    Publications:

    Ethayathulla AS, Nguyen HT, Viadiu H. (2013) Crystal structures of the DNA-binding domain tetramer of the p53 tumor suppressor family member p73 bound to different full-site response elements. J Biol Chem. 288(7):4744-54. PMC3576079

    Ciribilli Y, Monti P, Bisio A, Nguyen HT, Ethayathulla AS, Ramos A, Foggetti G, Menichini P, Menendez D, Resnick MA, Viadiu H, Fronza G, Inga A. (2013) Transactivation specificity is conserved among p53 family proteins and depends on a response element sequence code. Nucleic Acids Res. 41(18):8637-53. PMC3794606

    Mulero MC, Huang DB, Nguyen HT, Wang VY, Li Y, Biswas T, Ghosh G. (2017) DNA-binding affinity and transcriptional activity of the RelA homodimer of nuclear factor κB are not correlated. J Biol Chem. 292(46):18821-18830. PMC5704467

Trainees appointed in 2012

  • Joseph Kaus

    Email: joekaus@gmail.com
    Linkedin: https://www.linkedin.com/in/joe-kaus-56323a97/
    Program: Chem/Biochem
    Advisor: J. Andrew McCammon

    Publications:

    Kaus JW, Arrar M, McCammon JA. (2014) Accelerated adaptive integration method. J Phys Chem B. 118(19):5109-18. PMC4025579

    Kim MO, Blachly PG, Kaus JW, McCammon JA. (2015) Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies. J Phys Chem B. 119(3):861-72. PMC4306499

    Kaus JW, McCammon JA. (2015) Enhanced ligand sampling for relative protein-ligand binding free energy calculations. J Phys Chem B. 119(20):6190-7. PMC4442669

    Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L. (2015) How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations. J Chem Theory Comput. 11(6):2670-9. PMC4462751

  • Jessica Peters

    Email: jessica.peters@ucsf.edu 
    Linkedin: https://www.linkedin.com/in/jessica-peters-biochemist/
    Program: Chem/Biochem
    Advisor: Navtej Toor

    Publications:

    Robart AR, Chan RT, Peters JK, Rajashankar KR, Toor N. (2014) Crystal structure of a eukaryotic group II intron lariat. Nature. 514(7521):193-7. PMC4197185

    Peters JK, Toor N. (2015) Group II intron lariat: Structural insights into the spliceosome. RNA Biol. 12(9):913-7. PMC4615233

    Chan RT, Peters JK, Robart AR, Wiryaman T, Rajashankar KR, Toor N. (2018) Structural basis for the second step of group II intron splicing. Nat Commun. 9(1):4676. PMC6224600

  • Alan West

    Email:
    Linkedin: https://www.linkedin.com/in/alan-west-66594a80/
    Program: BMS
    Advisor: Kevin Corbett

    Publications:

    West AMV, Komives EA, Corbett KD. (2018) Conformational dynamics of the Hop1 HORMA domain reveal a common mechanism with the spindle checkpoint protein Mad2. Nucleic Acids Res. 46(1):279-292. PMC5758881

    West AM, Rosenberg SC, Ur SN, Lehmer MK, Ye Q, Hagemann G, Caballero I, Usón I, MacQueen AJ, Herzog F, Corbett KD. (2019) A conserved filamentous assembly underlies the structure of the meiotic chromosome axis. Elife. 8. pii: e40372. PMC6349405

  • Clifford Woodford

    Email: crwoodford4@gmail.com 
    Linkedin: https://www.linkedin.com/in/clifford-woodford-5183567b/
    Program: Chem/Biochem
    Advisor: Roger Tsien

    Publications:

    Woodford CR, Frady EP, Smith RS, Morey B, Canzi G, Palida SF, Araneda RC, Kristan WB Jr, Kubiak CP, Miller EW, Tsien RY. (2015) Improved PeT molecules for optically sensing voltage in neurons. J Am Chem Soc.137(5):1817-24. PMC4513930

Trainees appointed in 2013

  • Lewis Churchfield

    Email: lewis.churchfield@gmail.com
    Linkedin: https://www.linkedin.com/in/lewis-churchfield/
    Program: Chem/Biochem
    Advisor: Akif Tezcan

    Publications:

    Bailey JB, Subramanian RH, Churchfield LA, Tezcan FA. (2016) Metal-Directed Design of Supramolecular Protein Assemblies. Methods Enzymol. 580:223-50. PMC5131729

    Churchfield LA, Medina-Morales A, Brodin JD, Perez A, Tezcan FA. (2016) De Novo Design of an Allosteric Metalloprotein Assembly with Strained Disulfide Bonds. J Am Chem Soc. 138(40):13163-13166. PMC5085265

    Churchfield LA, Alberstein RG, Williamson LM, Tezcan FA. (2018) Determining the Structural and Energetic Basis of Allostery in a De Novo Designed Metalloprotein Assembly. J Am Chem Soc. 140(31):10043-10053. PMC6085756

  • Jamie Schiffer

    Email: schiff.jamie@gmail.com
    Linkedin: https://www.linkedin.com/in/jamie-schiffer-52044b86/
    Program: Chem/Biochem
    Advisor: Elizabeth Komives

    Publications:

    Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro RE, Komives EA. (2015) How the ankyrin and SOCS box protein, ASB9, binds to creatine kinase. Biochemistry. 54(8):1673-80. PMC4348336

    Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives EA. (2016) Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. Structure. 24(8):1248-1256. PMC4972691

    Schiffer JM, Feher VA, Malmstrom RD, Sida R, Amaro RE. (2016) Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A. Biophys J. 111(8):1631-1640. PMC5071553

    Mulero MC, Shahabi S, Ko MS, Schiffer JM, Huang DB, Wang VY, Amaro RE, Huxford T, Ghosh G. (2018) Protein Cofactors Are Essential for High-Affinity DNA Binding by the Nuclear Factor κB RelA Subunit. Biochemistry. 57(20):2943-2957. PMC5993198

    Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE. (2019) Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophys J. 116(2):205-214. PMC6349996

  • Bryan Stephens

    Email: bsstephens3@gmail.com
    Linkedin: 
    Program: BMS
    Advisor: Tracy Handel

    Publications:

    Stephens B, Handel TM. (2013) Chemokine receptor oligomerization and allostery. Prog Mol Biol Transl Sci. 115:375-420. PMC4072031

    Kufareva I, Stephens B, Gilliland CT, Wu B, Fenalti G, Hamel D, Stevens RC, Abagyan R, Handel TM. (2013) A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer. Methods Mol Biol. 1013:93-127. PMC4091634

    Ziarek JJ, Getschman AE, Butler SJ, Taleski D, Stephens B, Kufareva I, Handel TM, Payne RJ, Volkman BF. (2013) Sulfopeptide probes of the CXCR4/CXCL12 interface reveal oligomer-specific contacts and chemokine allostery. ACS Chem Biol. 8(9):1955-63. PMC3783652

    Kawamura T, Stephens B, Qin L, Yin X, Dores MR, Smith TH, Grimsey N, Abagyan R, Trejo J, Kufareva I, Fuster MM, Salanga CL, Handel TM. (2014) A general method for site specific fluorescent labeling of recombinant chemokines. PLoS One. 9(1):e81454. PMC3904831

    Kufareva I, Stephens BS, Holden LG, Qin L, Zhao C, Kawamura T, Abagyan R, Handel TM. (2014) Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: molecular modeling and experimental validation. Proc Natl Acad Sci U S A. 111(50):E5363-72. PMC4273337

    Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM. (2017) Structural basis of ligand interaction with atypical chemokine receptor 3. Nat Commun. 8:14135. PMC5253664

    Kufareva I, Gustavsson M, Zheng Y, Stephens BS, Handel TM. (2017) What Do Structures Tell Us About Chemokine Receptor Function and Antagonism? Annu Rev Biophys.46:175-198. PMC5764094

    Grimsey NJ, Narala R, Rada CC, Mehta S, Stephens BS, Kufareva I, Lapek J, Gonzalez DJ, Handel TM, Zhang J, Trejo J. (2018) A Tyrosine Switch on NEDD4-2 E3 Ligase Transmits GPCR Inflammatory Signaling. Cell Rep. 24(12):3312-3323.e5. PMC6226018

  • Nicholas Tiee

    Email: n.tiee90@gmail.com
    Linkedin: https://www.linkedin.com/in/nicholas-tiee-83a897ba/
    Program: Chem/Biochem
    Advisor: Patricia A. Jennings

    Publications:

    Cheng RR, Haglund E, Tiee NS, Morcos F, Levine H, Adams JA, Jennings PA, Onuchic JN. (2018) Designing bacterial signaling interactions with coevolutionary landscapes. PLoS One. 13(8):e0201734. PMC6101370

  • Bryan Arias

    Email:
    Linkedin: https://www.linkedin.com/in/bryan-arias-40b22327/
    Program: Biology
    Advisor: Simpson Joseph

    Publications:

    Arias-Mireles BH, de Rozieres CM, Ly K, Joseph S. (2018) BRNA Modulates the Interaction between Influenza A Virus NS1 and Human PABP1 Biochemistry 57(26) 3590-3598. PMC6205234

Trainees appointed in 2014

  • Chris Fisher

    Email: fishercjf@gmail.com

    Linkedin: https://www.linkedin.com/in/christopher-james-fisher/

    Program: Chem/Biochem

    Advisor: Kamil Godula

    Publications:

    Huang ML, Cohen M, Fisher CJ, Schooley RT, Gagneux P, Godula K. (2015) Determination of receptor specificities for whole influenza viruses using multivalent glycan arrays. Chem Commun (Camb). 51(25):5326-9. PMC4359031

    Cohen M, Fisher CJ, Huang ML, Lindsay LL, Plancarte M, Boyce WM, Godula K, Gagneux P. (2016) Capture and characterization of influenza A virus from primary samples using glycan bead arrays. Virology. 493:128-35. PMC4860064

    Huang ML, Fisher CJ, Godula K. (2016) Glycomaterials for probing host-pathogen interactions and the immune response. Exp Biol Med (Maywood). 241(10):1042-53. PMC4950362

    Cohen M, Senaati HP, Fisher CJ, Huang ML, Gagneux P, Godula K. (2016) Synthetic Mucus Nanobarriers for Identification of Glycan-Dependent Primary Influenza A Infection Inhibitors. ACS Cent Sci. 2(10):710-714. PMC5084083

    Huang ML, Michalak AL, Fisher CJ, Christy M, Smith RAA, Godula K. (2018) Small Molecule Antagonist of Cell Surface Glycosaminoglycans Restricts Mouse Embryonic Stem Cells in a Pluripotent State. Stem Cells. 36(1):45-54. PMC6237099

  • Chris Lee

    Email: chrislee4123@gmail.com 
    Linkedin: 
    Program: Chem/Biochem
    Advisor: J. Andrew McCammon

    Publications:

    Malmstrom RD, Lee CT, Van Wart A, Amaro RE. (2014) On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins. J Chem Theory Comput.  10(7):2648-2657. PMC4248791

    Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. (2016) Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model. 56(4):721-33. PMC5280572

    Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. (2016) Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev. 116(11):6370-90. PMC4901368

    Votapka LW, Lee CT, Amaro RE. (2016) Two Relations to Estimate Membrane Permeability Using Milestoning. J Phys Chem B. 120(33):8606-16. PMC5002937

    Jagger BR, Lee CT, Amaro RE. (2018) Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J Phys Chem Lett. 9(17):4941-4948. PMC6443090

    Lee CT, Amaro RE. (2018) Exascale Computing: A New Dawn for Computational Biology. Comput Sci Eng. 2018 Sep-Oct;20(5):18-25. PMC6458592

    Taylor BC, Lee CT, Amaro RE. (2019) Structural basis for ligand modulation of the CCR2 conformational landscape. Proc Natl Acad Sci U S A. 116(17):8131-8136. PMC6486717

    Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ. (20190 The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. ACM Trans Math Softw. 45(3). pii: 28. PMC6716611

  • Kristen Ramsey

    Email: kmramseyphd@gmail.com
    Linkedin: https://www.linkedin.com/in/kristen-ramsey-824284a1/
    Program: Chem/Biochem
    Advisor: Elizabeth Komives, Gourisankar Ghosh

    Publications:

    Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives EA. (2016) Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα. Biophys J.110(4):887-95. PMC4776026

    Ramsey KM, Dembinski HE, Chen W, Ricci CG, Komives EA. (2017) DNA and IκBα Both Induce Long-Range Conformational Changes in NFκB. J Mol Biol. 429(7):999-1008. PMC5389416

    Ramsey KM, Narang D, Komives EA. (2018) Prediction of the presence of a seventh ankyrin repeat in IκBε from homology modeling combined with hydrogen-deuterium exchange mass spectrometry (HDX-MS). Protein Sci.  27(9):1624-1635. PMC6194264

    Ramsey KM, Chen W, Marion JD, Bergqvist S, Komives EA. (2019) Exclusivity and Compensation in NFκB Dimer Distributions and IκB Inhibition. Biochemistry. 58(21):2555-2563. PMC6642826

  • Jeff Wagner

    Email: jwagnerjpl@gmail.com
    Linkedin: https://www.linkedin.com/in/jeffrey-r-wagner/
    Program: Chem/Biochem
    Advisor: Rommie Amaro

    Publications:

    Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. (2016) Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev. 116(11):6370-90. PMC4901368

    Wagner JR, Sørensen J, Hensley N, Wong C, Zhu C, Perison T, Amaro RE. POVME 3.0: Software for Mapping Binding Pocket Flexibility. J Chem Theory Comput. 13(9):4584-4592. PMC5751414

    Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H. (2017) Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Sci Rep. 7(1):17415. PMC5727031

    Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. (2019) Determinants of Oligonucleotide Selectivity of APOBEC3B. J Chem Inf Model. 59(5):2264-2273. PMC6644697

    Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE. (2019) Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. Structure. 27(8):1326-1335.e4. PMC6685748

Trainees appointed in 2015

  • Charles Lin

    Email: midnight2103@gmail.com
    Linkedin: https://www.linkedin.com/in/charles-l-a9646bb9/
    Program: Chem/Biochem
    Advisor: Ross Walker

    Publications:

    Skjevik ÅA, Madej BD, Dickson CJ, Lin C, Teigen K, Walker RC, Gould IR. (2016) Simulation of lipid bilayer self-assembly using all-atom lipid force fields. Phys Chem Chem Phys. 18(15):10573-84. PMC5091658

    Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC. (2018) Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J Comput Chem. 39(19):1354-1358.

    Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg A, Case DA, Walker RC, York DM. (2018) GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. J Chem Inf Model. 58(10):2043-2050. PMC6226240

    Ben-Shalom IY, Lin C, Kurtzman T, Walker RC, Gilson MK. (2019) Simulating Water Exchange to Buried Binding Sites. J Chem Theory Comput. 15(4):2684-2691. PMC6456390