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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

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  1. F. P. Panei & P. Gkeka & M. Bonomi, 2024. "Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  2. Janni Harju & Muriel C. F. Teeseling & Chase P. Broedersz, 2024. "Loop-extruders alter bacterial chromosome topology to direct entropic forces for segregation," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  3. Christian Hentrich & Mateusz Putyrski & Hanh Hanuschka & Waldemar Preis & Sarah-Jane Kellmann & Melissa Wich & Manuel Cavada & Sarah Hanselka & Victor S. Lelyveld & Francisco Ylera, 2024. "Engineered reversible inhibition of SpyCatcher reactivity enables rapid generation of bispecific antibodies," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  4. Hongjun Bai & Eric Lewitus & Yifan Li & Paul V. Thomas & Michelle Zemil & Mélanie Merbah & Caroline E. Peterson & Thujitha Thuraisamy & Phyllis A. Rees & Agnes Hajduczki & Vincent Dussupt & Bonnie Sli, 2024. "Contemporary HIV-1 consensus Env with AI-assisted redesigned hypervariable loops promote antibody binding," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  5. Yasmin Shamsudin & Alice R. Walker & Chey M. Jones & Todd J. Martínez & Steven G. Boxer, 2023. "Simulation-guided engineering of split GFPs with efficient β-strand photodissociation," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
  6. Zsolt Fazekas & Dóra K. Menyhárd & András Perczel, 2024. "LoCoHD: a metric for comparing local environments of proteins," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  7. Do Hoon Kwon & Feng Zhang & Brett A. McCray & Shasha Feng & Meha Kumar & Jeremy M. Sullivan & Wonpil Im & Charlotte J. Sumner & Seok-Yong Lee, 2023. "TRPV4-Rho GTPase complex structures reveal mechanisms of gating and disease," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  8. Jaewoon Jung & Cheng Tan & Yuji Sugita, 2024. "GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  9. Tom Dixon & Derek MacPherson & Barmak Mostofian & Taras Dauzhenka & Samuel Lotz & Dwight McGee & Sharon Shechter & Utsab R. Shrestha & Rafal Wiewiora & Zachary A. McDargh & Fen Pei & Rajat Pal & João , 2022. "Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry," Nature Communications, Nature, vol. 13(1), pages 1-24, December.
  10. Joseph G. Beton & Thomas Mulvaney & Tristan Cragnolini & Maya Topf, 2024. "Cryo-EM structure and B-factor refinement with ensemble representation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  11. Amy Rice & Sourav Haldar & Eric Wang & Paul S. Blank & Sergey A. Akimov & Timur R. Galimzyanov & Richard W. Pastor & Joshua Zimmerberg, 2022. "Planar aggregation of the influenza viral fusion peptide alters membrane structure and hydration, promoting poration," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  12. Ritaban Halder & Daniel A. Nissley & Ian Sitarik & Yang Jiang & Yiyun Rao & Quyen V. Vu & Mai Suan Li & Justin Pritchard & Edward P. O’Brien, 2023. "How soluble misfolded proteins bypass chaperones at the molecular level," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  13. Patrick Roth & Jean-Marc Jeckelmann & Inken Fender & Zöhre Ucurum & Thomas Lemmin & Dimitrios Fotiadis, 2024. "Structure and mechanism of a phosphotransferase system glucose transporter," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  14. Andreas Mardt & Tim Hempel & Cecilia Clementi & Frank Noé, 2022. "Deep learning to decompose macromolecules into independent Markovian domains," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  15. So-Hee Son & Gyuri Park & Junho Lim & Chang Yun Son & Seung Soo Oh & Ju Young Lee, 2022. "Chain flexibility of medicinal lipids determines their selective partitioning into lipid droplets," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  16. Cheng Shen & Yuqing Zhang & Wenwen Cui & Yimeng Zhao & Danqi Sheng & Xinyu Teng & Miaoqing Shao & Muneyoshi Ichikawa & Jin Wang & Motoyuki Hattori, 2023. "Structural insights into the allosteric inhibition of P2X4 receptors," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  17. Ryota Takaki & Atreya Dey & Guang Shi & D. Thirumalai, 2021. "Theory and simulations of condensin mediated loop extrusion in DNA," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
  18. Michael T. Robo & Ryan L. Hayes & Xinqiang Ding & Brian Pulawski & Jonah Z. Vilseck, 2023. "Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  19. Giacomo Janson & Gilberto Valdes-Garcia & Lim Heo & Michael Feig, 2023. "Direct generation of protein conformational ensembles via machine learning," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  20. Po-Yin Chen & Yung-Chih Chen & Po-Pang Chen & Kuan-Ting Lin & Karen Sargsyan & Chao-Ping Hsu & Wei-Le Wang & Kuo-Chiang Hsia & See-Yeun Ting, 2024. "A whole-cell platform for discovering synthetic cell adhesion molecules in bacteria," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  21. Re’em Moskovitz & Tossapol Pholcharee & Sophia M. DonVito & Bora Guloglu & Edward Lowe & Franziska Mohring & Robert W. Moon & Matthew K. Higgins, 2023. "Structural basis for DARC binding in reticulocyte invasion by Plasmodium vivax," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
  22. Julia Skokowa & Birte Hernandez Alvarez & Murray Coles & Malte Ritter & Masoud Nasri & Jérémy Haaf & Narges Aghaallaei & Yun Xu & Perihan Mir & Ann-Christin Krahl & Katherine W. Rogers & Kateryna Maks, 2022. "A topological refactoring design strategy yields highly stable granulopoietic proteins," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  23. Nathan R. Kern & Jumin Lee & Yeol Kyo Choi & Wonpil Im, 2024. "CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  24. Kalyan S. Chakrabarti & Simon Olsson & Supriya Pratihar & Karin Giller & Kerstin Overkamp & Ko On Lee & Vytautas Gapsys & Kyoung-Seok Ryu & Bert L. Groot & Frank Noé & Stefan Becker & Donghan Lee & Th, 2022. "A litmus test for classifying recognition mechanisms of transiently binding proteins," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  25. Dawei Sun & Yonglian Sun & Eric Janezic & Tricia Zhou & Matthew Johnson & Caleigh Azumaya & Sigrid Noreng & Cecilia Chiu & Akiko Seki & Teresita L. Arenzana & John M. Nicoludis & Yongchang Shi & Baome, 2023. "Structural basis of antibody inhibition and chemokine activation of the human CC chemokine receptor 8," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  26. Shana Bergman & Rosemary J. Cater & Ambrose Plante & Filippo Mancia & George Khelashvili, 2023. "Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  27. David P. McDonogh & Julian D. Gale & Paolo Raiteri & Denis Gebauer, 2024. "Redefined ion association constants have consequences for calcium phosphate nucleation and biomineralization," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  28. Jongdae Won & Jinsung Kim & Hyeongseop Jeong & Jinhyeong Kim & Shasha Feng & Byeongseok Jeong & Misun Kwak & Juyeon Ko & Wonpil Im & Insuk So & Hyung Ho Lee, 2023. "Molecular architecture of the Gαi-bound TRPC5 ion channel," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  29. Yang Li & Chengxin Zhang & Chenjie Feng & Robin Pearce & P. Lydia Freddolino & Yang Zhang, 2023. "Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  30. Kuang-Ting Ko & Frank Lennartz & David Mekhaiel & Bora Guloglu & Arianna Marini & Danielle J. Deuker & Carole A. Long & Matthijs M. Jore & Kazutoyo Miura & Sumi Biswas & Matthew K. Higgins, 2022. "Structure of the malaria vaccine candidate Pfs48/45 and its recognition by transmission blocking antibodies," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  31. S. M. Ayala Mariscal & M. L. Pigazzini & Y. Richter & M. Özel & I. L. Grothaus & J. Protze & K. Ziege & M. Kulke & M. ElBediwi & J. V. Vermaas & L. Colombi Ciacchi & S. Köppen & F. Liu & J. Kirstein, 2022. "Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT," Nature Communications, Nature, vol. 13(1), pages 1-25, December.
  32. Jeffrey A. Ruffolo & Lee-Shin Chu & Sai Pooja Mahajan & Jeffrey J. Gray, 2023. "Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  33. Fengwei Li & Junjie Liu & Chao Liu & Ziyan Liu & Xiangda Peng & Yinyue Huang & Xiaoyu Chen & Xiangnan Sun & Sen Wang & Wei Chen & Dan Xiong & Xiaotong Diao & Sheng Wang & Jingjing Zhuang & Chuanliu Wu, 2024. "Cyclic peptides discriminate BCL-2 and its clinical mutants from BCL-XL by engaging a single-residue discrepancy," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  34. Jin H. Yang & Hugo B. Brandão & Anders S. Hansen, 2023. "DNA double-strand break end synapsis by DNA loop extrusion," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  35. Chulwon Choi & Jungnam Bae & Seonghan Kim & Seho Lee & Hyunook Kang & Jinuk Kim & Injin Bang & Kiheon Kim & Won-Ki Huh & Chaok Seok & Hahnbeom Park & Wonpil Im & Hee-Jung Choi, 2023. "Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  36. Rodrigo G. Fernandez Lahore & Niccolò P. Pampaloni & Enrico Schiewer & M.-Marcel Heim & Linda Tillert & Johannes Vierock & Johannes Oppermann & Jakob Walther & Dietmar Schmitz & David Owald & Andrew J, 2022. "Calcium-permeable channelrhodopsins for the photocontrol of calcium signalling," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  37. Nicolas Papadopoulos & Audrey Nédélec & Allison Derenne & Teodor Asvadur Şulea & Christian Pecquet & Ilyas Chachoua & Gaëlle Vertenoeil & Thomas Tilmant & Andrei-Jose Petrescu & Gabriel Mazzucchelli &, 2023. "Oncogenic CALR mutant C-terminus mediates dual binding to the thrombopoietin receptor triggering complex dimerization and activation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  38. Yi-Tzu Kuo & Amanda Souza Câmara & Veit Schubert & Pavel Neumann & Jiří Macas & Michael Melzer & Jianyong Chen & Jörg Fuchs & Simone Abel & Evelyn Klocke & Bruno Huettel & Axel Himmelbach & Dmitri Dem, 2023. "Holocentromeres can consist of merely a few megabase-sized satellite arrays," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
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