TCB Publications - Search
711. Skeletal dysplasia mutations effect on human filamins' structure and mechanosensing. Jonne Seppälä, Rafael C. Bernardi, Tatu J. K. Haataja, Maarit Hellman, Olli T. Pentikäinen, Klaus Schulten, Perttu Permi, Jari Ylänne, and Ulla Pentikäinen. Scientific Reports, 7:4218, 2017.
710. Angular measurements of the dynein ring reveal a stepping mechanism dependent on a flexible stalk. Lisa G. Lippert, Tali Dadosh, Jodi A. Hadden, Benjamin T. Diroll, Christopher B. Murray, Erika L.F. Holzbaur, Klaus Schulten, Samara L. Reck-Peterson, and Yale E. Goldman. Proceedings of the National Academy of Sciences, USA, 2017. In Press.
708. Detection and mapping of DNA methylation with 2D material nanopores. Hu Qiu, Aditya Sarathy, Klaus Schulten, and Jean-Pierre Leburton. npj 2D Materials and Applications, 1:3, 2017.
707. Quantitative characterization of domain motions in molecular machines. Suvrajit Maji, Rezvan Shahoei, Klaus Schulten, and Joachim Frank. Journal of Physical Chemistry B, 2017. In Press.
706. Structural insights into the functional cycle of the ATPase module of the 26S proteasome. Marc Wehmer, Till Rudack, Florian Beck, Antje Aufderheide, Günter Pfeifer, Jürgen M. Plitzko, Friedrich Förster, Klaus Schulten, Wolfgang Baumeister, and Eri Sakata. Proceedings of the National Academy of Sciences, USA, 114:1305-1310, 2017. (PMC: PMC5307450)
705. Computational de novo design of antibodies binding to a peptide with high affinity. Venkata Giridhar Poosarla, Tong Li, Boon Chong Goh, Klaus Schulten, Thomas K. Wood, and Costas D. Maranas. Biotechnology and Bioengineering, 114:1331-1342, 2017.
704. A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion. Mathieu Botte, Nathan Zaccai, Jelger Lycklama à Nijeholt, Remy Martin, Kèvin Knoops, Gabor Papai, Juan Zou, Aurélien Deniaud, Manikandan Karuppasamy, Qiyang Jiang, Abhishek Singha Roy, Klaus Schulten, Patrick Schultz, Juri Rappsilber, Giuseppe Zaccai, Imre Berger, Ian Collinson, and Christiane Schaffitzel. Scientific Reports, 6:38399, 2016. (PMC: PMC5141469)
703. Chemomechanical coupling in hexameric protein-protein interfaces harnesses energy within V-type ATPases. Abhishek Singharoy, Christophe Chipot, Mahmoud Moradi, and Klaus Schulten. Journal of the American Chemical Society, 139:293-310, 2016.
702. HIV-1 capsid function is regulated by dynamics: Quantitative atomic-resolution insights by integrating magic-angle-spinning NMR, QM/MM, and MD. Huilan Zhang, Guangjin Hou, Manman Lu, Jinwoo Ahn, In-Ja L. Byeon, Christopher J. Langmead, Juan R. Perilla, Ivan Hung, Peter L. Gor'kov, Zhehong Gan, William W. Brey, David A. Case, Klaus Schulten, Angela M. Gronenborn, and Tatyana Polenova. Journal of the American Chemical Society, 138:14066-14075, 2016.
701. Crystal structure and conformational change mechanism of a bacterial Nramp-family divalent metal transporter. Aaron T. Bozzi, Lukas B. Bane, Wilhelm A. Weihofen, Abhishek Singharoy, Eduardo R. Guillen, Hidde L. Ploegh, Klaus Schulten, and Rachelle Gaudet. Structure, 2016. In Press. (PMC: PMC5143219)
700. Mechanism of the primary charge transfer reaction in the cytochrome bc1 complex. Angela M. Barragan, Klaus Schulten, and Ilia A. Solov'yov. Journal of Physical Chemistry B, 120:11369-11380, 2016.
699. 3D implementation of the symbol nomenclature for graphical representation of glycans. David F. Thieker, Jodi A. Hadden, Klaus Schulten, and Robert J. Woods. Glycobiology, 26:786-787, 2016.
698. Binding site recognition and docking dynamics of a single electron transport protein: Cytochrome c2. Abhishek Singharoy, Angela M. Barragan, Sundarapandian Thangapandian, Emad Tajkhorshid, and Klaus Schulten. Journal of the American Chemical Society, 138:12077-12089, 2016.
697. Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters. Aaron T. Bozzi, Lukas B. Bane, Wilhelm Weihofen, Anne McCabe, Abhishek Singharoy, Chris Chipot, Klaus Schulten, and Rachelle Gaudet. Proceedings of the National Academy of Sciences, USA, 113:10310-10315, 2016. (PMC: PMC5027461)
696. Overall energy conversion efficiency of a photosynthetic vesicle. Melih Sener, Johan Strümpfer, Abhishek Singharoy, C. Neil Hunter, and Klaus Schulten. eLife, 10.7554/eLife.09541, 2016. (30 pages). (PMC: PMC5001839)
695. Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps. Abhishek Singharoy, Ivan Teo, Ryan McGreevy, John E. Stone, Jianhua Zhao, and Klaus Schulten. eLife, 10.7554/eLife.16105, 2016. (66 pages). (PMC: PMC4990421)
694. The structure of the human 26S proteasome at a resolution of 3.9 Å. Andreas Schweitzer, Antje Aufderheide, Till Rudack, Florian Beck, Gunter Pfeifer, Jurgen M. Plitzko, Eri Sakata, Klaus Schulten, Friedrich Forster, and Wolfgang Baumeister. Proceedings of the National Academy of Sciences, USA, 113:7816-7821, 2016. (PMC: PMC4948313)
693. Dynamic behavior of trigger factor on the ribosome. Julian Deeng, Kwok-Yan Chan, Eli O. van der Sluis, Lukas Bischoff, Otto Berninghausen, Wei Han, James Gumbart, Klaus Schulten, Birgitta Beatrix, and Roland Beckmann. Journal of Molecular Biology, 428:3588-3602, 2016.
692. A time-course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes. Kumud R Poudel, Yongming Dong, Hang Yu, Allen Su, Thuong Ho, Yan Liu, Klaus Schulten, and Jihong Bai. Molecular Biology of the Cell, 27:2119-2132, 2016. (PMC: PMC4927284)
691. Elucidation of lipid binding sites on lung surfactant protein A using X-ray crystallography, mutagenesis and molecular dynamics simulations. Boon Chong Goh, Huixing Wu, Michael J. Rynkiewicz, Klaus Schulten, Barbara A. Seaton, and Francis X. McCormack. Biochemistry, 55:3692-3701, 2016.
690. Early experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated OpenPOWER platforms. John E. Stone, Antti-Pekka Hynninen, James C. Phillips, and Klaus Schulten. International Workshop on OpenPOWER for HPC (IWOPH'16), pp. 188-206, 2016.
689. The water permeability and pore entrance structure of aquaporin-4 channels depend on lipid bilayer thickness. Jihong Tong, Zhe Wu, Margaret M. Briggs, Klaus Schulten, and Thomas J. Mclntosh. Biophysical Journal, 111:90-99, 2016. (PMC:  PMC4944661)
688. Adaptive multilevel splitting method for molecular dynamics calculation of benzamidine-trypsin dissociation time. Ivan Teo, Christopher G. Mayne, Klaus Schulten, and Tony Lelievre. Journal of Chemical Theory and Computation, 12:2983-2989, 2016.
687. QwikMD-integrative molecular dynamics toolkit for novices and experts. Joao V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, James C. Phillips, Peter L. Freddolino, and Klaus Schulten. Scientific Reports, 6:26536, 2016. (PMC: PMC4877583)
686. All-atom molecular dynamics of virus capsids as drug targets. Juan R. Perilla, Jodi A. Hadden, Boon Chong Goh, Christopher G. Mayne, and Klaus Schulten. Journal of Physical Chemistry Letters, 7:1836-1844, 2016. (PMC: PMC4876486)
685. Contributions of charged residues in structurally dynamic capsid surface loops to Rous sarcoma virus assembly. Katrina Heyrana, Boon Chong Goh, Juan Roberto Perilla, Tam-Linh N. Nguyen, Matthew R. England, Maria C. Bewley, Klaus Schulten, and Rebecca Craven. Journal of Virology, pp. (52 pages), 2016. In Press. (PMC: PMC4886791)
684. Flexibility coexists with shape persistence in cyanostar macrocycles. Yun Liu, Abhishek Singharoy, Christopher G. Mayne, Arkajyoti Sengupta, Krishnan Raghavachari, Klaus Schulten, and Amar H. Flood. Journal of the American Chemical Society, 138:4843-4851, 2016. (PMC: PMC4957974)
683. Recognition of poly-ubiquitins by the proteasome through protein re-folding guided by electrostatic and hydrophobic interactions. Yi Zhang, Lela Vukovic, Till Rudack, Wei Han, and Klaus Schulten. Journal of Physical Chemistry B, 120:8137-8146, 2016. (PMC: PMC5001906)
682. Disulfide bridges: bringing together frustrated structure in a bioactive peptide. Yi Zhang, Klaus Schulten, Martin Gruebele, Paramjit S. Bansal, David Wilson, and Norelle L. Daly. Biophysical Journal, 110:1744-1752, 2016. (PMC: PMC4850350)
681. Electrically tunable quenching of DNA fluctuations in biased solid-state nanopores. Hu Qiu, Anuj Girdhar, Klaus Schulten, and Jean-Pierre Leburton. ACS Nano, 10:4482-4488, 2016. (PMC: PMC4918906)
680. Evaluation of emerging energy-efficient heterogeneous computing platforms for biomolecular and cellular simulation workloads. John E. Stone, Michael J. Hallock, James C. Phillips, Joseph R. Peterson, Zaida Luthey-Schulten, and Klaus Schulten. 2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), pp. 89-100, 2016. (PMC: PMC4978513)
679. High performance molecular visualization: In-situ and parallel rendering with EGL. John E. Stone, Peter Messmer, Robert Sisneros, and Klaus Schulten. 2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), pp. 1014-1023, 2016. (PMC: PMC5061511)
678. Immersive molecular visualization with omnidirectional stereoscopic ray tracing and remote rendering. John E. Stone, William R. Sherman, and Klaus Schulten. 2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), pp. 1048-1057, 2016. (PMC: PMC5063251)
677. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations. David J. Hardy, Matthew A. Wolff, Jianlin Xia, Klaus Schulten, and Robert D. Skeel. Journal of Chemical Physics, 144:114112, 2016. (16 pages). (PMC: PMC4808071)
676. Cyclophilin A stabilizes HIV-1 capsid through a novel non-canonical binding site. Chuang Liu, Juan R. Perilla, Jiying Ning, Manman Lu, Guangjin Hou, Ruben Ramalho, Gregory Bedwell, In-Ja Byeon, Jinwoo Ahn, Jiong Shi, Angela Gronenborn, Peter Prevelige, Itay Rousso, Christopher Aiken, Tatyana Polenova, Klaus Schulten, and Peijun Zhang. Nature Communications, 7:10714:(10 pages), 2016. (PMC: PMC4785225)
675. Molecular mechanism of processive 3' to 5' RNA translocation in the active subunit of the RNA exosome complex. Lela Vukovic, Christophe Chipot, Debora L. Makino, Elena Conti, and Klaus Schulten. Journal of the American Chemical Society, 138:4069-4078, 2016. (PMC: PMC4988868)
674. Computational methodologies for real-space structural refinement of large macromolecular complexes. Boon Chong Goh, Jodi A. Hadden, Rafael C. Bernardi, Abhishek Singharoy, Ryan McGreevy, Till Rudack, C. Keith Cassidy, and Klaus Schulten. Annual Review of Biophysics, 45:253-278, 2016.
673. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. Ryan McGreevy, Ivan Teo, Abhishek Singharoy, and Klaus Schulten. Methods, 100:50-60, 2016. (PMC: PMC4848153)
672. Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. John E. Stone, Melih Sener, Kirby L. Vandivort, Angela Barragan, Abhishek Singharoy, Ivan Teo, Joao V. Ribeiro, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Craig MacGregor-Chatwin, Matthew P. Johnson, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten. Parallel Computing, 55:17-27, 2016. (PMC: PMC4890717)
671. Intrinsic stepwise translocation of stretched ssDNA in graphene nanopores. Hu Qiu, Aditya Sarathy, Jean-Pierre Leburton, and Klaus Schulten. Nano Letters, 15:8322-8330, 2015. (PMC: PMC4676420)
670. CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling. C. Keith Cassidy, Benjamin A. Himes, Frances J. Alvarez, Jun Ma, Gongpu Zhao, Juan R. Perilla, Klaus Schulten, and Peijun Zhang. eLife, 10.7554/eLife.08419, 2015. PMID: 26583751.
669. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation. Hang Yu, Wei Han, Wen Ma, and Klaus Schulten. Journal of Chemical Physics, 143:243142, 2015. (PMC: PMC4684271)
668. Nascent peptide assists the ribosome in recognizing chemically distinct small molecules. Pulkit Gupta, Bo Liu, Dorota Klepacki, Vrinda Gupta, Klaus Schulten, Alexander S. Mankin, and Nora Vazquez-Laslop. Nature Chemical Biology, pp. (6 pages), 2015. PMID: 26727240.
667. Dynamic allostery governs cyclophylin A-HIV capsid interplay. Manman Lu, Guangjin Hou, Huilan Zhang, Christopher L. Suiter, Jinwoo Ahn, In-Ja L. Byeon, Juan R. Perilla, Christopher J. Langmead, Ivan Hung, Peter L. Gor'kov, Zhehong Gan, William Brey, Christopher Aiken, Peijun Zhang, Klaus Schulten, Angela M. Gronenborn, and Tatyana Polenova. Proceedings of the National Academy of Sciences, USA, 112:14617-14622, 2015. (PMC: PMC4664340)
666. Chemical visualization of human pathogens: the Retroviral Capsids. Juan R. Perilla, Boon Chong Goh, John Stone, and Klaus Schulten. Proceedings of the 2015 ACM/IEEE Conference on Supercomputing, 2015. (4 pages).
665. Structural refinement of proteins by restrained molecular dynamics simulations with non-interacting molecular fragments. Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M. Islam, Klaus Schulten, and Benoit Roux. PLoS Computational Biology, 11:e1004368, 2015. (19 pages). (PMC: PMC4624691)
664. Tri-Modal therapy: Combining hyperthermia with repurposed bexarotene and ultrasound for treating liver cancer. Santosh K. Misra, Goutam Ghoshal, Manas R. Gartia, Zhe Wu, Mao Ye, Corinne R. Bromfield, Emery M. Williams, Krishnarao V. Tangella, Klaus Schulten, Partha S. Ray, Everette C. Burdette, and Dipanjan Pan. ACS Nano, 9:10695-10718, 2015. (PMC: PMC4820022)
663. Mapping mechanical force propagation through biomolecular complexes. Constantin Schoeler, Rafael C. Bernardi, Klara H. Malinowska, Ellis Durner, Wolfgang Ott, Edward A. Bayer, Klaus Schulten, Michael A. Nash, and Hermann E. Gaub. Nano Letters, 15:7370-7376, 2015. (PMC: PMC4721519)
662. Dynamic profiling of double-stranded RNA binding proteins. Xinlei Wang, Lela Vukovic, Hye Ran Koh, Klaus Schulten, and Sua Myong. Nucleic Acids Res., 43:7566-7576, 2015. (PMC: PMC4551942)
661. Macromolecular crystallography for synthetic abiological molecules: Combining xMDFF and PHENIX for structure determination of cyanostar macrocycles. Abhishek Singharoy, Balasubramanian Venkatakrishnan, Yun Liu, Christopher G. Mayne, Chun-Hsing Chen, Adam Zlotnick, Klaus Schulten, and Amar H. Flood. Journal of the American Chemical Society, 137:8810-8818, 2015. (PMC: PMC4504762)
660. Atomic modeling of an immature retroviral lattice using molecular dynamics and mutagenesis. Boon Chong Goh, Juan R. Perilla, Matthew R. England, Katrina J. Heyrana, Rebecca C. Craven, and Klaus Schulten. Structure, 23:1414-1425, 2015. (PMC: PMC4526393)
659. Comparing fast pressure jump and temperature jump protein folding experiments and simulations. Anna Jean Wirth, Yanxin Liu, Maxim B. Prigozhin, Klaus Schulten, and Martin Gruebele. Journal of the American Chemical Society, 137:7152-7159, 2015. (PMC: PMC4794261)
658. Comparative dynamics and sequence dependence of DNA and RNA binding to single walled carbon nanotubes. Markita P. Landry, Lela Vukovic, Sebastian Kruss, Gili Bisker, Alexandra M. Landry, Shahrin Islam, Rishabh Jain, Klaus Schulten, and Michael S. Strano. Journal of Physical Chemistry C, 119:10048-10058, 2015. (PMC: PMC4440682)
657. The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center. Michael T. Englander, Joshua L. Avins, Rachel C. Fleisher, Bo Liu, Philip R. Effraim, Jiangning Wang, Klaus Schulten, Thomas S. Leyh, Ruben L. Gonzalez Jr., and Virginia W. Cornish. Proceedings of the National Academy of Sciences, USA, 112:6038-6043, 2015. (PMC: PMC4434717)
656. Molecular dynamics simulations of large macromolecular complexes. Juan R. Perilla, Boon Chong Goh, C. Keith Cassidy, Bo Liu, Rafael C. Bernardi, Till Rudack, Hang Yu, Zhe Wu, and Klaus Schulten. Current Opinion in Structural Biology, 31:64-74, 2015. (PMC: PMC4476923)
655. Tunable graphene quantum point contact transistor for DNA detection and characterization. Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton. Nanotechnology, 26:134005, 2015. (10 pages). (PMC: PMC4400256)
654. Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution. Wen Ma and Klaus Schulten. Journal of the American Chemical Society, 137:3031-3040, 2015. (PMC: PMC4393844)
653. Enhanced sampling techniques in molecular dynamics simulations of biological systems. Rafael C. Bernardi, Marcelo C. R. Melo, and Klaus Schulten. Biochimica et Biophysica Acta, 1850:872-877, 2015. (PMC: PMC4339458)
652. Multilevel summation method for electrostatic force evaluation. David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten. Journal of Chemical Theory and Computation, 11:766-779, 2015. (PMC: PMC4325600)
651. Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex. Angela M. Barragan, Antony R. Crofts, Klaus Schulten, and Ilia A. Solov'yov. Journal of Physical Chemistry B, 119:433-447, 2015. (PMC: PMC4297238)
650. CheY's acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli. Milana Fraiberg, Oshri Afanzar, C. Keith Cassidy, Alexandra Gabashvili, Klaus Schulten, Yishai Levin, and Michael Eisenbach. Molecular Microbiology, 95:231-244, 2015. (PMC: PMC4426874)
649. Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules. Jeffrey Comer, James Phillips, Klaus Schulten, and Christophe Chipot. Journal of Chemical Theory and Computation, 10:5276-5285, 2014. (DNA P41).
648. Die Geheimnisse des Lebens berechnen. Till Rudack, Juan Perilla, and Klaus Schulten. Spektrum der Wissenschaft, 11:86-95, November 2014. (DNA P41).
647. Ultrastable cellulosome-adhesion complex tightens under load. Constantin Schoeler, Klara H. Malinowska, Rafael C. Bernardi, Lukas F. Milles, Markus A. Jobst, Ellis Durner, Wolfgang Ott, Daniel B. Fried, Edward A. Bayer, Klaus Schulten, Hermann E. Gaub, and Michael A. Nash. Nature Communications, 5:5635, 2014. (PMC: PMC4266597)
646. Petascale Tcl with NAMD, VMD, and Swift/T. James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Klaus Schulten. In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14, pp. 6-17. IEEE Press, 2014.
645. Visualization of energy conversion processes in a light harvesting organelle at atomic detail. Melih Sener, John E. Stone, Angela Barragan, Abhishek Singharoy, Ivan Teo, Kirby L. Vandivort, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SC '14. IEEE Press, 2014. (4 pages).
644. Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores. Chaitanya Sathe, Anuj Girdhar, Jean-Pierre Leburton, and Klaus Schulten. Nanotechnology, 25:445105, 2014. (9 pages). (PMC: PMC4244269)
643. A highly tilted membrane configuration for the pre-fusion state of synaptobrevin. Andrew E. Blanchard, Mark J. Arcario, Klaus Schulten, and Emad Tajkhorshid. Biophysical Journal, 107:2112-2121, 2014. (PMC: PMC4223215)
642. On the different types of vibrations interacting with electronic excitations in the PE545 and FMO antenna systems. Mortaza Aghtar, Johann Strümpfer, Carsten Olbrich, Klaus Schulten, and Ulrich Kleinekathoefer. Journal of Physical Chemistry Letters, 5:3131-3137, 2014. (DNA P41).
641. Fibril elongation by Aβ17-42: Kinetic network analysis of hybrid-resolution molecular dynamics simulations. Wei Han and Klaus Schulten. Journal of the American Chemical Society, 136:12450-12460, 2014. (PMC: PMC4156860)
640. Stable small quantum dots for synaptic receptor tracking on live neurons. En Cai, Pinghua Ge, Sang Hak Lee, Okunola Jeyifous, Yong Wang, Yanxin Liu, Katie Wilson, Sung Jun Lim, Michelle Baird, John Stone, Kwan Young Lee, Michael Davidson, Hee Jung Chung, Klaus Schulten, Andrew Smith, William Green, and Paul R. Selvin. Angewandte Chemie - International Edition in English, 126:12692-12696, 2014. (PMC: PMC4240739)
639. Synaptotagmin's role in neurotransmitter release likely involves Ca2+-induced conformational transition. Zhe Wu and Klaus Schulten. Biophysical Journal, 107:1156-1166, 2014. (PMC: PMC4156666)
638. A structural model of the active ribosome-bound membrane protein insertase YidC. Stephan Wickles, Abhishek Singharoy, Jessica Andreani, Stefan Seemayer, Lukas Bischoff, Otto Berninghausen, Johannes Soeding, Klaus Schulten, Eli van der Sluis, and Roland Beckmann. eLife, 3:e03035, 2014. (17 pages). (PMC: PMC4124156)
637. Gate-modulated graphene quantum point contact device for DNA sensing. Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton. Journal of Computational Electronics, 13:839-846, 2014. (PMC: PMC4224323)
636. xMDFF: Molecular dynamics flexible fitting of low-resolution X-Ray structures. Ryan McGreevy, Abhishek Singharoy, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo Perozo, and Klaus Schulten. Acta Crystallographica D, 70:2344-2355, 2014. (PMC: PMC4157446)
635. Macrolide antibiotics allosterically predispose the ribosome for translation arrest. Shanmugapriya Sothiselvam, Bo Liu, Wei Han, Dorota Klepacki, Gemma C. Atkinson, Age Brauer, Maido Remm, Tanel Tenson, Klaus Schulten, Nora Vázquez-Laslop, and Alexander S. Mankin. Proceedings of the National Academy of Sciences, USA, 111:9804-9809, 2014. (PMC: PMC4103360)
634. Molecular dynamics study of enhanced Man5B enzymatic activity. Rafael C. Bernardi, Isaac Cann, and Klaus Schulten. Biotechnology for Biofuels, 7:1-8, 2014. (PMC: PMC4074406)
633. Diffusive models of membrane permeation with explicit orientational freedom. Jeffrey Comer, Klaus Schulten, and Christophe Chipot. Journal of Chemical Theory and Computation, 10:2710-2718, 2014. (DNA P41).
632. Substrate recognition and specificity of double-stranded RNA binding proteins. Lela Vukovic, Hye Ran Koh, Sua Myong, and Klaus Schulten. Biochemistry, 53:3457-3466, 2014. (PMC: PMC4051425)
631. Light harvesting by lamellar chromatophores in Rhodospirillum photometricum. Danielle Chandler, Johan Strümpfer, Melih Sener, Simon Scheuring, and Klaus Schulten. Biophysical Journal, 106:2503-2510, 2014. (PMC: PMC4052275)
630. GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting. John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten. Faraday Discussion, 169:265-283, 2014. (PMC: PMC4208074)
629. CHARMM-GUI PACE CG builder for solution, micelle, and bilayer coarse-grained simulations. Yifei Qi, Xi Cheng, Wei Han, Sunhwan Jo, Klaus Schulten, and Wonpil Im. Journal of Chemical Information and Modeling, 54:1003-1009, 2014.
628. Molecular insights into the membrane-associated phosphatidylinositol 4-kinase IIα. Qiangjun Zhou, Jiangmei Li, Hang Yu, Yujia Zhai, Zhen Gao, Yanxin Liu, Xiaoyun Pang, Lunfeng Zhang, Klaus Schulten, Fei Sun, and Chang Chen. Nature Communications, 5:3552, 2014. (10 pages). (PMC: PMC3974213)
627. Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides. Michaël L. Cartron, John D. Olsen, Melih Sener, Philip J. Jackson, Amanda A. Brindley, Pu Qian, Mark J. Dickman, Graham J. Leggett, Klaus Schulten, and C. Neil Hunter. Biochimica et Biophysica Acta - Bioenergetics, 1837:1769-1780, 2014. (PMC: PMC4143486)
626. Calculation of lipid-bilayer permeabilities using an average force. Jeffrey Comer, Klaus Schulten, and Christophe Chipot. Journal of Chemical Theory and Computation, 10:554-564, 2014. (DNA P41).
625. Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment. Yanxin Liu, Maxim B. Prigozhin, Klaus Schulten, and Martin Gruebele. Journal of the American Chemical Society, 136:4265-4272, 2014.
624. Single molecule FRET reveals pore size and opening mechanism of MscL. Yong Wang, Yanxin Liu, Hannah A. DeBerg, Takeshi Nomura, Melinda Tonks Hoffman, Paul R. Rohde, Klaus Schulten, Boris Martinac, and Paul R. Selvin. eLife, 3:e01834, 2014. (21 pages).
623. Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating. Ramya Gamini, Wei Han, John E. Stone, and Klaus Schulten. PLoS Computational Biology, 10:e1003488, 2014. (14 pages). (PMC: PMC3952814)
622. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Qufei Li, Sherry Wanderling, Marcin Paduch, David Medovoy, Abhishek Singharoy, Ryan McGreevy, Carlos Villalba-Galea, Raymond E. Hulse, Benoit Roux, Klaus Schulten, Anthony Kossiakoff, and Eduardo Perozo. Nature Structural & Molecular Biology, 21:244-252, 2014. (PMC: 4116111)
621. Quantum biology of retinal. Shigehiko Hayashi and Klaus Schulten. In Masoud Mohseni, Yasser Omar, Greg Engel, and Martin B. Plenio, editors, Quantum Effects in Biology, pp. 237-263. Cambridge University Press, 2014.
620. A chemical compass for bird navigation. Ilia A. Solov'yov, P. J. Hore, Thorsten Ritz, and Klaus Schulten. In Masoud Mohseni, Yasser Omar, Greg Engel, and Martin B. Plenio, editors, Quantum Effects in Biology, chapter 10, pp. 218-236. Cambridge University Press, 2014.
619. Structure, function, and quantum dynamics of pigment-protein complexes. Ioan Kosztin and Klaus Schulten. In Masoud Mohseni, Yasser Omar, Greg Engel, and Martin B. Plenio, editors, Quantum Effects in Biology, pp. 123-143. Cambridge University Press, 2014.
618. Separation of photo-induced radical pair in cryptochrome to a functionally critical distance. Ilia Solov'yov, Tatiana Domratcheva, and Klaus Schulten. Scientific Reports, 4:3845, 2014. (8 pages). (PMC:  PMC4894384)
617. Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Wei Jiang, James Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James Gumbart, Yun Luo, Klaus Schulten, and Benoit Roux. Computer Physics Communications, 185:908-916, 2014. (PMC: PMC4059768)
616. Graphene quantum point contact transistor for DNA sensing. Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton. Proceedings of the National Academy of Sciences, USA, 110:16748-16753, 2013. (PMC: 3801026)
615. A computational kinetic model of diffusion for molecular systems. Ivan Teo and Klaus Schulten. Journal of Chemical Physics, 139:121929, 2013. (15 pages). (PMC: 3795746)
614. Characterization of folding mechanisms of Trp-cage and WW-domain by network analysis of simulations with a hybrid-resolution model. Wei Han and Klaus Schulten. Journal of Physical Chemistry B, 117:13367-13377, 2013. (PMC: 3811923)
613. Rapid parameterization of small molecules using the Force Field Toolkit. Christopher G. Mayne, Jan Saam, Klaus Schulten, Emad Tajkhorshid, and James C. Gumbart. Journal of Computational Chemistry, 34:2757-2770, 2013. (PMC: 3874408)
612. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten, Christopher Aiken, and Peijun Zhang. Nature, 497:643-646, 2013. (PMC:  3729984)
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