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Items: 1 to 50 of 481

1.

In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States.

Yang W, Cassidy CK, Ames P, Diebolder CA, Schulten K, Luthey-Schulten Z, Parkinson JS, Briegel A.

MBio. 2019 Jul 2;10(4). pii: e00973-19. doi: 10.1128/mBio.00973-19.

2.

Pro-Nifuroxazide Self-Assembly Leads to Triggerable Nanomedicine for Anti-cancer Therapy.

Misra SK, Wu Z, Ostadhossein F, Ye M, Boateng K, Schulten K, Tajkhorshid E, Pan D.

ACS Appl Mater Interfaces. 2019 May 22;11(20):18074-18089. doi: 10.1021/acsami.9b01343. Epub 2019 May 13.

PMID:
31013055
3.

Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics.

Prigozhin MB, Zhang Y, Schulten K, Gruebele M, Pogorelov TV.

Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5356-5361. doi: 10.1073/pnas.1814927116. Epub 2019 Mar 5.

4.

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B.

J Chem Theory Comput. 2018 Dec 11;14(12):6748-6749. doi: 10.1021/acs.jctc.8b01075. Epub 2018 Nov 27. No abstract available.

PMID:
30480445
5.

Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein.

Lawson MR, Ma W, Bellecourt MJ, Artsimovitch I, Martin A, Landick R, Schulten K, Berger JM.

Mol Cell. 2018 Sep 20;71(6):911-922.e4. doi: 10.1016/j.molcel.2018.07.014. Epub 2018 Aug 16.

6.

All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits.

Hadden JA, Perilla JR, Schlicksup CJ, Venkatakrishnan B, Zlotnick A, Schulten K.

Elife. 2018 Apr 27;7. pii: e32478. doi: 10.7554/eLife.32478.

7.

Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase.

Ma W, Whitley KD, Chemla YR, Luthey-Schulten Z, Schulten K.

Elife. 2018 Apr 17;7. pii: e34186. doi: 10.7554/eLife.34186.

8.

Molecular mechanism of extreme mechanostability in a pathogen adhesin.

Milles LF, Schulten K, Gaub HE, Bernardi RC.

Science. 2018 Mar 30;359(6383):1527-1533. doi: 10.1126/science.aar2094.

9.

NAMD goes quantum: an integrative suite for hybrid simulations.

Melo MCR, Bernardi RC, Rudack T, Scheurer M, Riplinger C, Phillips JC, Maia JDC, Rocha GB, Ribeiro JV, Stone JE, Neese F, Schulten K, Luthey-Schulten Z.

Nat Methods. 2018 May;15(5):351-354. doi: 10.1038/nmeth.4638. Epub 2018 Mar 26.

10.

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.

Scheurer M, Rodenkirch P, Siggel M, Bernardi RC, Schulten K, Tajkhorshid E, Rudack T.

Biophys J. 2018 Feb 6;114(3):577-583. doi: 10.1016/j.bpj.2017.12.003.

11.

Detection and Mapping of DNA Methylation with 2D Material Nanopores.

Qiu H, Sarathy A, Schulten K, Leburton JP.

NPJ 2D Mater Appl. 2017;1. pii: 3. doi: 10.1038/s41699-017-0005-7. Epub 2017 Apr 11.

12.

Quenching protein dynamics interferes with HIV capsid maturation.

Wang M, Quinn CM, Perilla JR, Zhang H, Shirra R Jr, Hou G, Byeon IJ, Suiter CL, Ablan S, Urano E, Nitz TJ, Aiken C, Freed EO, Zhang P, Schulten K, Gronenborn AM, Polenova T.

Nat Commun. 2017 Nov 24;8(1):1779. doi: 10.1038/s41467-017-01856-y.

13.

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B.

J Chem Theory Comput. 2017 Dec 12;13(12):5933-5944. doi: 10.1021/acs.jctc.7b00875. Epub 2017 Nov 22. Erratum in: J Chem Theory Comput. 2018 Dec 11;14(12):6748-6749.

14.

CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction.

Alvarez FJD, He S, Perilla JR, Jang S, Schulten K, Engelman AN, Scheres SHW, Zhang P.

Sci Adv. 2017 Sep 15;3(9):e1701264. doi: 10.1126/sciadv.1701264. eCollection 2017 Sep.

15.

Detection of methylation on dsDNA using nanopores in a MoS2 membrane.

Shim J, Banerjee S, Qiu H, Smithe KKH, Estrada D, Bello J, Pop E, Schulten K, Bashir R.

Nanoscale. 2017 Oct 12;9(39):14836-14845. doi: 10.1039/c7nr03092d.

16.

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations.

Perilla JR, Schulten K.

Nat Commun. 2017 Jul 19;8:15959. doi: 10.1038/ncomms15959.

17.

Skeletal Dysplasia Mutations Effect on Human Filamins' Structure and Mechanosensing.

Seppälä J, Bernardi RC, Haataja TJK, Hellman M, Pentikäinen OT, Schulten K, Permi P, Ylänne J, Pentikäinen U.

Sci Rep. 2017 Jun 26;7(1):4218. doi: 10.1038/s41598-017-04441-x.

18.

Angular measurements of the dynein ring reveal a stepping mechanism dependent on a flexible stalk.

Lippert LG, Dadosh T, Hadden JA, Karnawat V, Diroll BT, Murray CB, Holzbaur ELF, Schulten K, Reck-Peterson SL, Goldman YE.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4564-E4573. doi: 10.1073/pnas.1620149114. Epub 2017 May 22.

19.

Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles.

Comer J, Schulten K, Chipot C.

J Chem Theory Comput. 2017 Jun 13;13(6):2523-2532. doi: 10.1021/acs.jctc.7b00264. Epub 2017 May 12.

PMID:
28475319
20.

Selected Publications of Klaus Schulten.

Schulten K.

J Phys Chem B. 2017 Apr 20;121(15):3210-3227. doi: 10.1021/acs.jpcb.7b02902. No abstract available.

PMID:
28423906
21.

Abbreviated Curriculum Vitae of Klaus Schulten.

Schulten K.

J Phys Chem B. 2017 Apr 20;121(15):3209. doi: 10.1021/acs.jpcb.7b02901. No abstract available.

PMID:
28423905
22.

Colleagues of Klaus Schulten.

Schulten K.

J Phys Chem B. 2017 Apr 20;121(15):3207-3208. doi: 10.1021/acs.jpcb.7b02900. No abstract available.

PMID:
28423904
23.

Lateral Segregation of Photosystem I in Cyanobacterial Thylakoids.

MacGregor-Chatwin C, Sener M, Barnett SFH, Hitchcock A, Barnhart-Dailey MC, Maghlaoui K, Barber J, Timlin JA, Schulten K, Hunter CN.

Plant Cell. 2017 May;29(5):1119-1136. doi: 10.1105/tpc.17.00071. Epub 2017 Mar 31. Erratum in: Plant Cell. 2017 Jul;29(7):1794.

24.

Quantitative Characterization of Domain Motions in Molecular Machines.

Maji S, Shahoei R, Schulten K, Frank J.

J Phys Chem B. 2017 Apr 20;121(15):3747-3756. doi: 10.1021/acs.jpcb.6b10732. Epub 2017 Mar 2.

25.

Structural insights into the functional cycle of the ATPase module of the 26S proteasome.

Wehmer M, Rudack T, Beck F, Aufderheide A, Pfeifer G, Plitzko JM, Förster F, Schulten K, Baumeister W, Sakata E.

Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):1305-1310. doi: 10.1073/pnas.1621129114. Epub 2017 Jan 23.

26.

Computational de novo design of antibodies binding to a peptide with high affinity.

Poosarla VG, Li T, Goh BC, Schulten K, Wood TK, Maranas CD.

Biotechnol Bioeng. 2017 Jun;114(6):1331-1342. doi: 10.1002/bit.26244. Epub 2017 Feb 2.

27.

CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments.

Qi Y, Lee J, Singharoy A, McGreevy R, Schulten K, Im W.

J Phys Chem B. 2017 Apr 20;121(15):3718-3723. doi: 10.1021/acs.jpcb.6b10568. Epub 2016 Dec 23.

28.

Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.

Singharoy A, Chipot C, Moradi M, Schulten K.

J Am Chem Soc. 2017 Jan 11;139(1):293-310. doi: 10.1021/jacs.6b10744. Epub 2016 Dec 23.

29.

A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion.

Botte M, Zaccai NR, Nijeholt JL, Martin R, Knoops K, Papai G, Zou J, Deniaud A, Karuppasamy M, Jiang Q, Roy AS, Schulten K, Schultz P, Rappsilber J, Zaccai G, Berger I, Collinson I, Schaffitzel C.

Sci Rep. 2016 Dec 7;6:38399. doi: 10.1038/srep38399.

30.

Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter.

Bozzi AT, Bane LB, Weihofen WA, Singharoy A, Guillen ER, Ploegh HL, Schulten K, Gaudet R.

Structure. 2016 Dec 6;24(12):2102-2114. doi: 10.1016/j.str.2016.09.017. Epub 2016 Nov 10.

31.

Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering.

Stone JE, Sherman WR, Schulten K.

IEEE Int Symp Parallel Distrib Process Workshops Phd Forum. 2016 May;2016:1048-1057. Epub 2016 Aug 4.

32.

High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL.

Stone JE, Messmer P, Sisneros R, Schulten K.

IEEE Int Symp Parallel Distrib Process Workshops Phd Forum. 2016 May;2016:1014-1023. Epub 2016 Aug 4.

33.

HIV-1 Capsid Function Is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD.

Zhang H, Hou G, Lu M, Ahn J, Byeon IL, Langmead CJ, Perilla JR, Hung I, Gor'kov PL, Gan Z, Brey WW, Case DA, Schulten K, Gronenborn AM, Polenova T.

J Am Chem Soc. 2016 Oct 26;138(42):14066-14075. doi: 10.1021/jacs.6b08744. Epub 2016 Oct 18.

34.

Correction to "Recognition of Poly-Ubiquitins by the Proteasome through Protein Refolding Guided by Electrostatic and Hydrophobic Interactions".

Zhang Y, Vuković L, Rudack T, Han W, Schulten K.

J Phys Chem B. 2016 Oct 13;120(40):10614. Epub 2016 Sep 28. No abstract available.

PMID:
27681365
35.

Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc1 Complex.

Barragan AM, Schulten K, Solov'yov IA.

J Phys Chem B. 2016 Nov 10;120(44):11369-11380. Epub 2016 Oct 12.

36.

Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters.

Bozzi AT, Bane LB, Weihofen WA, McCabe AL, Singharoy A, Chipot CJ, Schulten K, Gaudet R.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10310-5. doi: 10.1073/pnas.1607734113. Epub 2016 Aug 29.

37.

Overall energy conversion efficiency of a photosynthetic vesicle.

Sener M, Strumpfer J, Singharoy A, Hunter CN, Schulten K.

Elife. 2016 Aug 26;5. pii: e09541. doi: 10.7554/eLife.09541.

38.

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads.

Stone JE, Hallock MJ, Phillips JC, Peterson JR, Luthey-Schulten Z, Schulten K.

IEEE Int Symp Parallel Distrib Process Workshops Phd Forum. 2016 May;2016:89-100.

39.

3D implementation of the symbol nomenclature for graphical representation of glycans.

Thieker DF, Hadden JA, Schulten K, Woods RJ.

Glycobiology. 2016 Aug;26(8):786-7. doi: 10.1093/glycob/cww076. Epub 2016 Aug 11. No abstract available.

40.

Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2.

Singharoy A, Barragan AM, Thangapandian S, Tajkhorshid E, Schulten K.

J Am Chem Soc. 2016 Sep 21;138(37):12077-89. doi: 10.1021/jacs.6b01193. Epub 2016 Sep 7.

41.

The Water Permeability and Pore Entrance Structure of Aquaporin-4 Depend on Lipid Bilayer Thickness.

Tong J, Wu Z, Briggs MM, Schulten K, McIntosh TJ.

Biophys J. 2016 Jul 12;111(1):90-9. doi: 10.1016/j.bpj.2016.05.039.

42.

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.

Singharoy A, Teo I, McGreevy R, Stone JE, Zhao J, Schulten K.

Elife. 2016 Jul 7;5. pii: e16105. doi: 10.7554/eLife.16105.

43.

Structure of the human 26S proteasome at a resolution of 3.9 Å.

Schweitzer A, Aufderheide A, Rudack T, Beck F, Pfeifer G, Plitzko JM, Sakata E, Schulten K, Förster F, Baumeister W.

Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):7816-21. doi: 10.1073/pnas.1608050113. Epub 2016 Jun 24.

44.

Elucidation of Lipid Binding Sites on Lung Surfactant Protein A Using X-ray Crystallography, Mutagenesis, and Molecular Dynamics Simulations.

Goh BC, Wu H, Rynkiewicz MJ, Schulten K, Seaton BA, McCormack FX.

Biochemistry. 2016 Jul 5;55(26):3692-701. doi: 10.1021/acs.biochem.6b00048. Epub 2016 Jun 21.

45.

Dynamic Behavior of Trigger Factor on the Ribosome.

Deeng J, Chan KY, van der Sluis EO, Berninghausen O, Han W, Gumbart J, Schulten K, Beatrix B, Beckmann R.

J Mol Biol. 2016 Sep 11;428(18):3588-602. doi: 10.1016/j.jmb.2016.06.007. Epub 2016 Jun 16.

PMID:
27320387
46.

Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing.

Stone JE, Sener M, Vandivort KL, Barragan A, Singharoy A, Teo I, Ribeiro JV, Isralewitz B, Liu B, Goh BC, Phillips JC, MacGregor-Chatwin C, Johnson MP, Kourkoutis LF, Hunter CN, Schulten K.

Parallel Comput. 2016 Jul;55:17-27.

47.

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms.

Stone JE, Hynninen AP, Phillips JC, Schulten K.

High Perform Comput (2016). 2016 Jun;9945:188-206. doi: 10.1007/978-3-319-46079-6_14. Epub 2016 Oct 6.

48.

QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.

Ribeiro JV, Bernardi RC, Rudack T, Stone JE, Phillips JC, Freddolino PL, Schulten K.

Sci Rep. 2016 May 24;6:26536. doi: 10.1038/srep26536.

49.

A time course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes.

Poudel KR, Dong Y, Yu H, Su A, Ho T, Liu Y, Schulten K, Bai J.

Mol Biol Cell. 2016 Jul 1;27(13):2119-32. doi: 10.1091/mbc.E16-04-0264. Epub 2016 May 11.

50.

Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time.

Teo I, Mayne CG, Schulten K, Lelièvre T.

J Chem Theory Comput. 2016 Jun 14;12(6):2983-9. doi: 10.1021/acs.jctc.6b00277. Epub 2016 May 18.

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