pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.1007/s10858-019-00247-3

Characterization of H/D exchange in type 1 pili by proton-detected solid-state NMR and molecular dynamics simulations
Cited by: 4
Author(s): Songhwan Hwang, Carl Öster, Veniamin Chevelkov, Karin Giller, Adam Lange, Stefan Becker, Adam Lange
Software Mentions: 2
Published: over 6 years ago

10.1007/s10858-016-0029-x

Integrative NMR for biomolecular research
Cited by: 43
Author(s): Woonghee Lee, Gabriel Cornilescu, Hesam Dashti, Hamid R. Eghbalnia, Marco Tonelli, William M. Westler, Samuel E. Butcher, Katherine Henzler‐Wildman, John L. Markley
Software Mentions: 2
Published: over 9 years ago

10.1186/s13068-019-1457-0

The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases
Cited by: 77
Author(s): Leander Sützl, Gabriel Foley, Elizabeth M. J. Gillam, Mikael Bodén, Dietmar Haltrich
Software Mentions: 2
Published: over 6 years ago

10.1007/s10858-021-00365-x

A COVID moonshot: assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy
Cited by: 9
Author(s): A.L. Kantsadi, Emma Cattermole, Minos‐Timotheos Matsoukas, Georgios A. Spyroulias, Ioannis Vakonakis
Software Mentions: 2
Published: over 4 years ago

10.3390/cancers12061412

A H-REV107 Peptide Inhibits Tumor Growth and Interacts Directly with Oncogenic KRAS Mutants
Cited by: 10
Author(s): Chang Woo Han, Mi Suk Jeong, Soonhoi Ha, Se Bok Jang
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.51492

Structural basis of substrate recognition by a polypeptide processing and secretion transporter
Cited by: 23
Author(s): Virapat Kieuvongngam, Paul Dominic B. Olinares, Anthony Palillo, Michael L. Oldham, Brian T. Chait, Jue Chen
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.49439

Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity
Cited by: 33
Author(s): Zhijie Lin, Yang Zhou, Ruiling Xie, Zeyang Ji, Kun‐Liang Guan, Mingjie Zhang
Software Mentions: 2
Published: about 6 years ago

10.1155/2016/8683713

Structural Stability, Transitions, and Interactions within SoxYZCD-Thiosulphate from Sulfurimonas denitrificans: An In Silico Molecular Outlook for Maintaining Environmental Sulphur Cycle
Cited by: 1
Author(s): Sujay Ray, Arundhati Banerjee
Software Mentions: 2
Published: about 9 years ago

10.7554/eLife.71474

TMEM120A contains a specific coenzyme A-binding site and might not mediate poking- or stretch-induced channel activities in cells
Cited by: 18
Author(s): Yao Chai Rong, Jinghui Jiang, Yongfei Gao, Jing Guo, Danfeng Song, Wenhao Liu, Mingmin Zhang, Yan Zhao, Bailong Xiao, Zhongfan Liu
Software Mentions: 2
Published: about 4 years ago

10.3389/fimmu.2021.625808

Structural Basis of VSIG3: The Ligand for VISTA
Cited by: 11
Author(s): Xiaoxue Xie, Caiping Chen, Wenting Chen, Jingwei Jiang, Lanlan Wang, Tingting Li, Hongbin Sun, Jun Li
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2018.00489

Computational Insight Into the Structural Organization of Full-Length Toll-Like Receptor 4 Dimer in a Model Phospholipid Bilayer
Cited by: 17
Author(s): Mahesh Chandra Patra, Hyuk‐Kwon Kwon, Maria Batool, Sangdun Choi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0040066

The Crystal Structures of Dystrophin and Utrophin Spectrin Repeats: Implications for Domain Boundaries
Cited by: 27
Author(s): M. Muthu, Kylie A. Richardson, Andrew J. Sutherland-Smith
Software Mentions: 2
Published: over 13 years ago

10.7554/eLife.52774

Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate
Cited by: 94
Author(s): Fei X, Tristan A Bell, Simon Jenni, Benjamin M. Stinson, T.A. Baker, Stephen C. Harrison, Robert T. Sauer
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.56185

Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism
Cited by: 68
Author(s): Juraj Ahel, Anita Lehner, Antonia Vogel, Alexander Schleiffer, Anton Meinhart, David Haselbach, Tim Clausen
Software Mentions: 2
Published: over 5 years ago

10.34172/jcvtr.2020.02

Novel single nucleotide mutations in exon-10 of human coagulationFactor V gene in patients with pulmonary thromboembolism
Cited by: 1
Author(s): Latheef Kasala, D. Rajasekhar, V. Vanajakshamma
Software Mentions: 2
Published: almost 6 years ago

10.1083/jcb.201910059

Molecular basis of MKLP2-dependent Aurora B transport from chromatin to the anaphase central spindle
Cited by: 23
Author(s): Michela Serena, Ricardo Bastos, P.R. Elliott, Francis A. Barr
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.18972

Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments
Cited by: 76
Author(s): Didi He, Sam Hughes, Sally Vanden-Hehir, Atanas Georgiev, Kirsten Altenbach, Emma Tarrant, C. Logan Mackay, Kevin J. Waldron, David J. Clarke, Jon Marles‐Wright
Software Mentions: 2
Published: over 9 years ago

10.3390/cancers6031464

Phosphorylation of Large T Antigen Regulates Merkel Cell Polyomavirus Replication
Cited by: 19
Author(s): José Ángel Menéndez Díaz, Xin Wang, Sabrina H. Tsang, Jing Jiao, Jianxin You
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1002484

Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1
Cited by: 22
Author(s): Takehiro Nishimura, Guillaume Molinard, Tom J. Petty, Larissa Broger, Caroline Gabus, Thanos D. Halazonetis, Stéphane Thore, Jerzy Paszkowski
Software Mentions: 2
Published: almost 14 years ago

10.1007/s41048-018-0073-z

Significant expansion and red-shifting of fluorescent protein chromophore determined through computational design and genetic code expansion
Cited by: 6
Author(s): Li Wang, Xian Chen, Xuzhen Guo, Jiasong Li, Qi Liu, Fuying Kang, Xudong Wang, Cheng Hu, Haiping Li, Weimin Gong, Wei Zhuang, Liu Xiao-hong, Jiangyun Wang
Software Mentions: 2
Published: about 7 years ago

10.1016/j.bpj.2021.01.012

Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein
Cited by: 49
Author(s): Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham Dokainish, Suyong Re, Yuji Sugita
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.53322

Structure and activation mechanism of the BBSome membrane protein trafficking complex
Cited by: 57
Author(s): Sandeep Singh, Miao Gui, Fujiet Koh, M.C.J. Yip, Alan Brown
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.29150

Autoinhibition of ankyrin-B/G membrane target bindings by intrinsically disordered segments from the tail regions
Cited by: 26
Author(s): Keyu Chen, J. Li, Chao Wang, Zhiyi Wei, Mingjie Zhang
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.55607

Multi-state recognition pathway of the intrinsically disordered protein kinase inhibitor by protein kinase A
Cited by: 16
Author(s): Cristina Olivieri, Yingjie Wang, Geoffrey C. Li, V. S. Manu, Jonggul Kim, Benjamin R Stultz, Matthew Neibergall, Fernando Porcelli, Joseph M. Muretta, David D. Thomas, Jiali Gao, Donald K. Blumenthal, Susan S. Taylor, Gianluigi Veglia
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.03145

Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB
Cited by: 136
Author(s): Thomas Eicher, Markus A. Seeger, Claudio Anselmi, Wenchang Zhou, Lorenz Brandstätter, François Verrey, Kay Diederichs, José D. Faráldo-Gómez, Klaas M. Pos
Software Mentions: 2
Published: about 11 years ago

10.7554/eLife.55438

Mechanisms of nucleotide selection by telomerase
Cited by: 15
Author(s): Matthew A Schaich, Samantha L Sanford, Griffin A. Welfer, Samuel A. Johnson, Thu H Khoang, Patricia L. Opresko, Bret Freudenthal
Software Mentions: 2
Published: over 5 years ago

10.1111/jcmm.13547

Humanization of fibroblast growth factor 1 single‐chain antibody and validation for its antitumorigenic efficacy in breast cancer and glioma cells
Cited by: 11
Author(s): Xiaomin He, Shuyuan Du, Shiqian Gao, Jing‐Ying Chen, Ran‐Juan Cao, Zhenkai Xing, Alia Rizvi Syeda Kazim, Huali Yu, Qing‐Chuan Zheng, Xinen Zhu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0216427

Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain
Cited by: 22
Author(s): Md. Imran Khan, Deepu Dowarha, Revansiddha Katte, Ruey Hwang Chou, Anna Filipek, Chin Yu
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2014.00022

Immunoglobulin and T Cell Receptor Genes: IMGT® and the Birth and Rise of Immunoinformatics
Cited by: 168
Author(s): Marie‐Paule Lefranc
Software Mentions: 2
Published: almost 12 years ago

10.3389/fmed.2021.694668

Saudi Familial Hypercholesterolemia Patients With Rare LDLR Stop Gain Variant Showed Variable Clinical Phenotype and Resistance to Multiple Drug Regimen
Cited by: 6
Author(s): Zuhier Awan, Omran M. Rashidi, Bandar Ali Al-Shehri, Kaiser Jamil, Ramu Elango, Jumana Y. Al‐Aama, Robert A. Hegele, Noor Ahmad Shaik
Software Mentions: 2
Published: over 4 years ago

10.3389/fmed.2021.724826

Novel MYO1D Missense Variant Identified Through Whole Exome Sequencing and Computational Biology Analysis Expands the Spectrum of Causal Genes of Laterality Defects
Cited by: 5
Author(s): Rabab Said Alsafwani, Khalidah Khalid Nasser, Thoraia Shinawi, Babajan Banaganapalli, Hanan Abdelhalim ElSokary, Zhaher F. Zaher, Noor Ahmad Shaik, Gaser Abdelmohsen, Jumana Y. Al‐Aama, Adam J. Shapiro, Osman O. Al‐Radi, Turki S Alahmadi
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.52628

Indirect sexual selection drives rapid sperm protein evolution in abalone
Cited by: 6
Author(s): Damien B. Wilburn, Lisa M. Tuttle, Rachel E. Klevit, Willie J. Swanson
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2020.00583

The Interaction of RecA With Both CheA and CheW Is Required for Chemotaxis
Cited by: 3
Author(s): Elisabet Frutos-Grilo, María Marsal, Oihane Irazoki, Jordi Barbé, Susana Campoy
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0075992

Ligand Pose and Orientational Sampling in Molecular Docking
Cited by: 123
Author(s): Ryan G. Coleman, Michael Carchia, Teague Sterling, John J. Irwin, Brian K. Shoichet
Software Mentions: 2
Published: about 12 years ago

10.7554/eLife.04601

Architecture of the ring formed by the tubulin homologue FtsZ in bacterial cell division
Cited by: 200
Author(s): Piotr Szwedziak, Qing Wang, Tanmay A. M. Bharat, M. Tsim, Jan Löwe
Software Mentions: 2
Published: almost 11 years ago

10.7554/eLife.03674

Molecular assembly of the period-cryptochrome circadian transcriptional repressor complex
Cited by: 87
Author(s): Shannon N. Nangle, Clark Rosensweig, Nobuya Koike, Hajime Tei, Joseph S. Takahashi, Carla B. Green, Ning Zheng
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.39720

Selective agonist of TRPML2 reveals direct role in chemokine release from innate immune cells
Cited by: 63
Author(s): Eva Plesch, Cheng‐Chang Chen, Elisabeth Butz, Anna Scotto Rosato, Einar Krogsaeter, Hua Yue, Karin Bartel, Marco Keller, Dina Robaa, Daniel Teupser, Lesca M. Holdt, Angelika M. Vollmar, Wolfgang Sippl, Rosa Puertollano, Diego L. Medina, Martin Biel, Christian Wahl‐Schott, Franz Bracher, Christian Grimm
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.04353

Structural basis of diverse membrane target recognitions by ankyrins
Cited by: 63
Author(s): Chao Wang, Zhiyi Wei, Keyu Chen, Fei Ye, Cong Yu, Vann Bennett, Mingjie Zhang
Software Mentions: 2
Published: about 11 years ago

10.3390/cancers12061523

New Anti-Cancer Strategy to Suppress Colorectal Cancer Growth Through Inhibition of ATG4B and Lysosome Function
Cited by: 13
Author(s): Yuanyuan Fu, Qianqian Gu, Li Luo, Jiangang Xu, Yuping Luo, Fan Xia, Fanghai Han, Hong Liu, Xiao Ming Yin, Zhiying Huang, Min Li
Software Mentions: 2
Published: over 5 years ago

10.1111/mpp.13055

Three LysM effectors of <i>Zymoseptoria tritici</i> collectively disarm chitin‐triggered plant immunity
Cited by: 24
Author(s): Hui Tian, Craig Mackenzie, Luis Rodríguez‐Moreno, Grardy C. M. van den Berg, Hongxin Chen, J. J. Rudd, J.R. Mesters, Bart P.H.J. Thomma
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2018.01750

Crystal Structures of R-Type Bacteriocin Sheath and Tube Proteins CD1363 and CD1364 From Clostridium difficile in the Pre-assembled State
Cited by: 12
Author(s): Nina Schwemmlein, Jan Pippel, E.M. Gazdag, Wulf Blankenfeldt
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0235133

Computational and structure-guided design of phosphoinositide substrate specificity into the tyrosine specific LMW-PTP enzyme
Cited by: 1
Author(s): Eyong Egbe, Colin Levy, Lydia Tabernero
Software Mentions: 2
Published: over 5 years ago

10.1242/jcs.226852

Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing
Cited by: 36
Author(s): Tiina Viita, Salla Kyheröinen, Bina Prajapati, Jori Virtanen, Mikko J. Frilander, Markku Varjosalo, Maria K. Vartiainen
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.43320

Cooperative cobinding of synthetic and natural ligands to the nuclear receptor PPARγ
Cited by: 51
Author(s): Jinsai Shang, Richard Brust, Sarah A. Mosure, Jared Bass, Paola Munoz-Tello, Hua Lin, Travis S. Hughes, Miru Tang, Qingfeng Ge, Theodore M. Kamenekca, D.J. Kojetin
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.09684

Mechanisms of ribosome stalling by SecM at multiple elongation steps
Cited by: 64
Author(s): Jun Zhang, Xiaoyi Pan, Kaige Yan, Shan Sun, Ning Gao, Sen-Fang Sui
Software Mentions: 2
Published: almost 10 years ago

10.1242/jcs.258399

Maintenance of complex I and its supercomplexes by NDUF-11 is essential for mitochondrial structure, function and health
Cited by: 13
Author(s): Amber Knapp-Wilson, Gonçalo C. Pereira, Emma Buzzard, Holly C Ford, A. Richardson, Robin A. Corey, Chris Neal, Paul Verkade, Andrew P. Halestrap, Vicki A. M. Gold, Patricia E. Kuwabara, Ian Collinson
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2018.01466

Insight Into the Interaction Between RNA Polymerase and VPg for Murine Norovirus Replication
Cited by: 10
Author(s): Jihye Lee, Beom Seok Park, Kang Rok Han, Scott B. Biering, Soo J Kim, Jayoung Choi, Jong Hyeon Seok, Intekhab Alam, Mi Sook Chung, Ho M. Kim, Seungmin Hwang, Kyung H. Kim
Software Mentions: 2
Published: over 7 years ago

10.1021/acs.jctc.0c01281

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties
Cited by: 29
Author(s): Kara K. Grotz, Sergio Cruz-León, Nadine Schwierz
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.09375

Mechanism of Na+-dependent citrate transport from the structure of an asymmetrical CitS dimer
Cited by: 53
Author(s): David Wöhlert, Maria J Grötzinger, Werner Kühlbrandt, Özkan Yıldız
Software Mentions: 2
Published: almost 10 years ago

10.3390/cancers12040813

Ensartinib (X-396) Effectively Modulates Pharmacokinetic Resistance Mediated by ABCB1 and ABCG2 Drug Efflux Transporters and CYP3A4 Biotransformation Enzyme
Cited by: 19
Author(s): Dimitrios Vagiannis, Eva Novotná, Adam Skarka, Sarah Kammerer, Jan-Heiner Küpper, Si Chen, Lei Guo, František Štaud, Jakub Hofman
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2021.669220

Interrogating the Role of the Two Distinct Fructose-Bisphosphate Aldolases of Bacillus methanolicus by Site-Directed Mutagenesis of Key Amino Acids and Gene Repression by CRISPR Interference
Cited by: 6
Author(s): Kerstin Schultenkämper, Desirée D. Gütle, Marina Gil López, Laura B. Keller, Lin Zhang, Oliver Einsle, Jean‐Pierre Jacquot, Volker F. Wendisch
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.06562

Cooperative base pair melting by helicase and polymerase positioned one nucleotide from each other
Cited by: 33
Author(s): Divya Nandakumar, Manjula Pandey, Smita S. Patel
Software Mentions: 2
Published: over 10 years ago

10.1186/1758-2946-4-17

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
Cited by: 5,518
Author(s): Marcus D. Hanwell, Donald Curtis, David Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey Hutchison
Software Mentions: 2
Published: over 13 years ago

10.7554/eLife.12856

Myosin III-mediated cross-linking and stimulation of actin bundling activity of Espin
Cited by: 21
Author(s): Haiyang Liu, Jianchao Li, Manmeet H. Raval, Ningning Yao, Xiǎoyīng Dèng, Qing Lü, Si Nie, Wei Feng, Jun Wan, Christopher M. Yengo, Weichen Liu, Mingjie Zhang
Software Mentions: 2
Published: almost 10 years ago

10.7554/eLife.07485

The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix
Cited by: 105
Author(s): David Barneda, Joan Planas-Iglesias, María L. Gaspar, Dariush Mohammadyani, Sunil Prasannan, Dirk Dormann, Gil‐Soo Han, Stephen A. Jesch, George M. Carman, Valerian E. Kagan, Malcolm G. Parker, Nicholas T. Ktistakis, Judith Klein‐Seetharaman, Ann M. Dixon, Susan A. Henry, Mark Christian
Software Mentions: 2
Published: almost 10 years ago

10.3389/fmicb.2021.659808

A MexR Mutation Which Confers Aztreonam Resistance to Pseudomonas aeruginosa
Cited by: 9
Author(s): Zhenzhen Ma, Congjuan Xu, Xinxin Zhang, Dan Wang, Xiaolei Pan, Huimin Liu, Guangbo Zhu, Fang Bai, Zhihui Cheng, Weihui Wu, Yongxin Jin
Software Mentions: 2
Published: over 4 years ago

10.3390/cancers12020456

An Epitope on EGFR Loading Catastrophic Internalization Serve as a Novel Oncotarget for Hepatocellular Carcinoma Therapy
Cited by: 0
Author(s): Dianshuai Huang, Qingjie Fan, Zhiyi Liu, Shuqin Zhang, Wei Huang, Hongrui Li, Chaozhao Liang, Fenyong Sun
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0134084

Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes
Cited by: 12
Author(s): Radhika Ganu, Yasuko Ishida, Markos Koutmos, Sergios‐Orestis Kolokotronis, Alfred L. Roca, Timothy A. Garrow, Lawrence B. Schook
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.53853

Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump
Cited by: 10
Author(s): Xin Xu, Huigang Shi, Xiaohua Gong, Pu Chen, Ying Gao, Xinzheng Zhang, Song Xiang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0242686

Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ
Cited by: 12
Author(s): William C. Scott, Brian Lowrance, Alexander C Anderson, Joel T. Weadge
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.cell.2020.01.010

Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody
Cited by: 89
Author(s): Philipp Schommers, Henning Gruell, Morgan E. Abernathy, My-Kim Tran, Adam S. Dingens, Harry B. Gristick, Christopher O. Barnes, Till Schoofs, Maike Schlotz, Kanika Vanshylla, Christoph Kreer, Daniela Weiland, Udo Holtick, Christof Scheid, Markus M. Valter, Marit J. van Gils, Rogier W. Sanders, Jörg Janne Vehreschild, Oliver A. Cornely, Clara Lehmann, Gerd Fätkenheuer, Michael S. Seaman, Jesse D Bloom, Pamela J. Björkman, Florian Klein
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.62163

Transport mechanism of P4 ATPase phosphatidylcholine flippases
Cited by: 37
Author(s): Lin Bai, Qinglong You, Bhawik Kumar Jain, Huiyuan Duan, Amanda Kovach, Todd R. Graham, Huilin Li
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.54449

Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement
Cited by: 63
Author(s): Asmita V. Patel, Camille M. Moore, B.J. Greber, Jie Luo, Stefan A Zukin, Jeff Ranish, Eva Nogales
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13321-019-0390-3

Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening
Cited by: 5
Author(s): Anna Lovrics, Veronika F.S. Pape, Dániel Szisz, Adrián Kalászi, Petra Heffeter, Csaba Magyar, Gergely Szakács
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.67336

Contingency and chance erase necessity in the experimental evolution of ancestral proteins
Cited by: 24
Author(s): Victoria Cochran Xie, Jinyue Pu, Brian P. H. Metzger, Joseph W. Thornton, Bryan C. Dickinson
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.64395

Complex structures of Rsu1 and PINCH1 reveal a regulatory mechanism of the ILK/PINCH/Parvin complex for F-actin dynamics
Cited by: 8
Author(s): Haibin Yang, Leishu Lin, Kang Sun, Ting Zhang, Wan Chen, Lianghui Li, Yuchen Xie, Chuanyue Wu, Zhiyi Wei, Cong Yu
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.00327

The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat
Cited by: 65
Author(s): Ursula Schulze‐Gahmen, Heather Upton, Andrew Birnberg, Katherine Bao, Seemay Chou, Nevan J. Krogan, Qiang Zhou, Tom Alber
Software Mentions: 2
Published: over 12 years ago

10.7554/eLife.55853

Cryo-EM structures and functional properties of CALHM channels of the human placenta
Cited by: 24
Author(s): Katarzyna Drożdżyk, Marta Sawicka, Maria-Isabel Bahamonde-Santos, Jonas Zaugg, Dawid Deneka, Christiane Albrecht, Raimund Dutzler
Software Mentions: 2
Published: over 5 years ago

10.1186/s13321-020-00460-5

Molecular representations in AI-driven drug discovery: a review and practical guide
Cited by: 176
Author(s): Laurianne David, Amol Thakkar, Rocío Mercado, Ola Engkvist
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.07646

Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets
Cited by: 73
Author(s): N.T. Schirle, Jessica Sheu‐Gruttadauria, Stanley D. Chandradoss, Chirlmin Joo, Ian J. MacRae
Software Mentions: 2
Published: about 10 years ago

10.7554/eLife.01739

FRET-based reporters for the direct visualization of abscisic acid concentration changes and distribution in Arabidopsis
Cited by: 198
Author(s): Rainer Waadt, Katsundo Hitomi, Noriyuki Nishimura, Chiharu Hitomi, Stephen Adams, Elizabeth D. Getzoff, Julian I. Schroeder
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.23644

CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin
Cited by: 112
Author(s): Katharina van Pee, Alexander Neuhaus, Edoardo D’Imprima, Deryck J. Mills, Werner Kühlbrandt, Özkan Yıldız
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2018.03329

Structural and Physiological Exploration of Salmonella Typhi YfdX Uncovers Its Dual Function in Bacterial Antibiotic Stress and Virulence
Cited by: 6
Author(s): Hye Seon Lee, Mi Kyung Lee, Jun‐Seob Kim, Hae-Ran Lee, Hang‐Sik Shin, Moo‐Seung Lee, Kyeong Sik Jin, Cheol-Hee Kim, Bonsu Ku, Choong-Min Ryu, Seung Jun Kim
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.cell.2021.06.020

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum
Cited by: 571
Author(s): C Liu, H. Ginn, Wanwisa Dejnirattisai, Piyada Supasa, Beibei Wang, Aekkachai Tuekprakhon, Rungtiwa Nutalai, Daming Zhou, Alexander J. Mentzer, Yuguang Zhao, Duyvesteyn Hme., César López-Camacho, J Slon-Campos, T S Walter, Donal Skelly, Síle A. Johnson, Thomas G. Ritter, Chris Mason, Sue Ann Costa Clemens, Felipe Gomes Naveca, Valdinete Alves do Nascimento, Fernanda Nascimento, Cristiano Fernandes da Costa, Paola Cristina Resende, Alex Pauvolid‐Corrêa, Marilda Mendonça Siqueira, Christina Dold, Nigel Temperton, Tao Dong, Andrew J. Pollard, Julian C. Knight, Derrick W. Crook, Teresa Lambe, Elizabeth A. Clutterbuck, Sagida Bibi, Amy Flaxman, Mustapha Bittaye, Sandra Belij‐Rammerstorfer, Sarah C. Gilbert, Tariq Malik, Miles W. Carroll, Paul Klenerman, Eleanor Barnes, Susanna Dunachie, Vicky L. Baillie, Natali Serafin, Zanele Ditse, K Da Silva, Neil G. Paterson, Mark A. Williams, David R. Hall, Shabir A. Madhi, Marta C Nunes, Philip Goulder, Elizabeth E. Fry, Juthathip Mongkolsapaya, Jingshan Ren, D.I. Stuart, Gavin Screaton
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.58242

Molecular rationale for antibody-mediated targeting of the hantavirus fusion glycoprotein
Cited by: 17
Author(s): Ilona Rissanen, Robert Stass, Stefanie A. Krumm, Jeffrey Seow, Ruben J.G. Hulswit, Guido C. Paesen, Jussi Hepojoki, Olli Vapalahti, Åke Lundkvist, Olivier Reynard, Viktor E. Volchkov, Katie J. Doores, J.T. Huiskonen, Thomas A. Bowden
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.34202

Local and global influences on protein turnover in neurons and glia
Cited by: 154
Author(s): Aline Ricarda Dörrbaum, Lisa Kochen, Julian D. Langer, Erin M. Schuman
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2021.632095

Integrated Proteomic and Transcriptomic Analyses Reveal the Roles of Brucella Homolog of BAX Inhibitor 1 in Cell Division and Membrane Homeostasis of Brucella suis S2
Cited by: 2
Author(s): Guangdong Zhang, Fangli Zhong, Lei Chen, Peipei Qin, Junmei Li, Feijie Zhi, Lulu Tian, Dong Zhou, Peng Lin, Huatao Chen, Kai-Fu Tang, Wei Liu, Yaping Jin, Aihua Wang
Software Mentions: 2
Published: almost 5 years ago

10.1172/JCI142823

An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection
Cited by: 16
Author(s): Cory A. Brennick, Mariam M. George, Marmar Moussa, Adam T. Hagymasi, Sahar Al Seesi, Tatiana Shcheglova, Ryan P Englander, Grant L.J. Keller, Jeremy L. Balsbaugh, Brian M. Baker, Andrea Schietinger, Ion Măndoiu, Pramod K. Srivastava
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.cell.2021.03.055

Antibody evasion by the P.1 strain of SARS-CoV-2
Cited by: 480
Author(s): Wanwisa Dejnirattisai, Daming Zhou, Piyada Supasa, C Liu, Alexander J. Mentzer, H. Ginn, Yuguang Zhao, Duyvesteyn Hme., Aekkachai Tuekprakhon, Rungtiwa Nutalai, Beibei Wang, César López-Camacho, J Slon-Campos, Thomas S. Walter, Donal Skelly, Sue Ann Costa Clemens, Felipe Gomes Naveca, Valdinete Alves do Nascimento, Felipe Franco Nascimento, Cristiano Fernandes da Costa, Paola Cristina Resende, Alex Pauvolid‐Corrêa, Marilda Mendonça Siqueira, Christina Dold, Robert H. Levin, Tao Dong, Andrew J. Pollard, Julian C. Knight, Derrick W. Crook, Teresa Lambe, Elizabeth A. Clutterbuck, Sagida Bibi, Amy Flaxman, Mustapha Bittaye, Sandra Belij‐Rammerstorfer, Sarah C. Gilbert, Miles W. Carroll, Paul Klenerman, Eleanor Barnes, Susanna Dunachie, Neil G. Paterson, Mark A. Williams, ' Hall, Ruben J.G. Hulswit, Thomas A. Bowden, Elizabeth E. Fry, Juthathip Mongkolsapaya, Jingshan Ren, D.I. Stuart, Gavin Screaton
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.09832

Dna2 nuclease-helicase structure, mechanism and regulation by Rpa
Cited by: 89
Author(s): Chun Zhou, Sergei Pourmal, Nikola P. Pavletich
Software Mentions: 2
Published: about 10 years ago

10.7554/eLife.21829

Structure of the transporter associated with antigen processing trapped by herpes simplex virus
Cited by: 80
Author(s): Michael L. Oldham, Nikolaus Grigorieff, Jue Chen
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2021.679246

Genetic Characteristics of Human Parainfluenza Virus Types 1–4 From Patients With Clinical Respiratory Tract Infection in China
Cited by: 8
Author(s): Nan Shao, Bo Liu, Yan Xiao, Xinming Wang, Lili Ren, Jie Dong, Lu Sun, Yafang Zhu, Ting Zhang, Fan Yang
Software Mentions: 2
Published: over 4 years ago

10.1016/j.cell.2018.10.037

Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design
Cited by: 52
Author(s): Yin Dong, Hua Wang, A.C.W. Pike, Stephen A. Cochrane, Sadra Hamedzadeh, Filip J. Wyszyński, S.R. Bushell, Sylvain Royer, David A. Widdick, Andaleeb Sajid, Helena I. Boshoff, Yumi Park, Ricardo Dantas de Lucas, Weimin Liu, Seung Seo Lee, Takuya Machida, Leanne Minall, Shahid Mehmood, Katsiaryna Belaya, Weiwei Liu, Amy Chu, L. Shrestha, Shubhashish M.M. Mukhopadhyay, Claire Strain-Damerell, R. Chalk, N. Burgess-Brown, Mervyn J. Bibb, Clifton E. Barry, Carol V. Robinson, David Beeson, Benjamin G. Davis, E.P. Carpenter
Software Mentions: 2
Published: about 7 years ago

10.1007/s10822-020-00277-2

Conformational analysis of macrocycles: comparing general and specialized methods
Cited by: 16
Author(s): Gustav Olanders, Hiba Alogheli, Peter Brandt, Anders Karlén
Software Mentions: 2
Published: almost 6 years ago

10.1007/s10822-020-00301-5

A Taxicab geometry quantification system to evaluate the performance of in silico methods: a case study on adenosine receptors ligands
Cited by: 0
Author(s): Kamil Kuder, Ilona Michalik, Katarzyna Kieć‐Kononowicz, Peter Kolb
Software Mentions: 2
Published: over 5 years ago

10.1007/s10822-015-9839-2

Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding
Cited by: 8
Author(s): Barbara Kalinowska, Piotr Fabian, Katarzyna Stąpor, Irena Roterman
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.50722

A polyomavirus peptide binds to the capsid VP1 pore and has potent antiviral activity against BK and JC polyomaviruses
Cited by: 4
Author(s): Jason M. Kane, Susan Fong, Jacob Shaul, Alexandra Frommlet, Andreas Frank, Mark Knapp, Dirksen E. Bussiere, Peter Kim, Elizabeth Ornelas, Carlos Cuellar, Anastasia Hyrina, Johanna R. Abend, Charles Wartchow
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.41848

An unexpected INAD PDZ tandem-mediated plcβ binding in Drosophila photo receptors
Cited by: 9
Author(s): Fei Ye, Yuguang Huang, J. Li, Yinfa Ma, Chensu Xie, Zexu Liu, Xiǎoyīng Dèng, Jun Wan, Tian Xue, Wei Liu, Mingjie Zhang
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.15537

A bend, flip and trap mechanism for transposon integration
Cited by: 22
Author(s): Elizabeth R. Morris, Heather Grey, Grant McKenzie, Anita C. Jones, Julia M. Richardson
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2020.605705

Discovery of an Antibiotic-Related Small Protein of Biocontrol Strain Pseudomonas sp. Os17 by a Genome-Mining Strategy
Cited by: 1
Author(s): Kasumi Takeuchi, Wataru Tsuchiya, Zui Fujimoto, Kosumi Yamada, Nobutaka Someya, Toshimasa Yamazaki
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.10034

Structural determinants of nuclear export signal orientation in binding to exportin CRM1
Cited by: 68
Author(s): Ho Yee Joyce Fung, Szu Chin Fu, Chad A. Brautigam, Yuh Min Chook
Software Mentions: 2
Published: about 10 years ago

10.1002/jcc.26559

<scp> <i>MonteCarbo</i> </scp> : A software to generate and dock multifunctionalized ring molecules
Cited by: 0
Author(s): Santiago Alonso-Gil
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21114146

Linking Biochemical and Structural States of SERCA: Achievements, Challenges, and New Opportunities
Cited by: 32
Author(s): Rodrigo Aguayo‐Ortiz, L. Michel Espinoza-Fonseca
Software Mentions: 2
Published: over 5 years ago

10.1016/j.cell.2017.06.025

Development of a Novel Lead that Targets M. tuberculosis Polyketide Synthase 13
Cited by: 115
Author(s): Anup Aggarwal, Maloy Kumar Parai, N.D. Shetty, Deeann Wallis, Lisa K. Woolhiser, Courtney Hastings, Noton K. Dutta, Stacy Galaviz, Ramesh Dhakal, Rupesh Shrestha, Shoko Wakabayashi, Chris Walpole, David J. Matthews, David M. Floyd, Paul Scullion, Jennifer Riley, Ola Epemolu, Suzanne Norval, Thomas Snavely, Gregory T. Robertson, Eric J. Rubín, Thomas R. Ioerger, F A Sirgel, Ruben van der Merwe, Paul D. van Helden, Peter M. Keller, Erik C. Böttger, Petros C. Karakousis, Anne J. Lenaerts, James C. Sacchettini
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2015.01380

A Zinc-Dependent Protease AMZ-tk from a Thermophilic Archaeon is a New Member of the Archaemetzincin Protein Family
Cited by: 9
Author(s): Baolei Jia, Zhengqun Li, Jinliang Liu, Ying Sun, Xiaomeng Jia, Yuan Xuan, Jiayan Zhang, Che Ok Jeon
Software Mentions: 2
Published: almost 10 years ago

10.1210/js.2019-00260

Using Structural Analysis In Silico to Assess the Impact of Missense Variants in MEN1
Cited by: 14
Author(s): Richard Caswell, Martina Owens, Adam C. Gunning, Sian Ellard, Caroline F. Wright
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2017.00541

Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin
Cited by: 21
Author(s): Javier Querol-García, Francisco Fernández, Ana V. Marín, Sara Gómez, Daniel Fullà, Cecilia Melchor-Tafur, V. Franco-Hidalgo, Sebastián Albertí, Judith Juanhuix, Santiago Rodrı́guez de Córdoba, José R. Regueiro, M. Cristina Vega
Software Mentions: 2
Published: over 8 years ago

10.14202/vetworld.2018.480-487

Molecular characterization of canine parvovirus variants (CPV-2a, CPV-2b, and CPV-2c) based on the VP2 gene in affected domestic dogs in Ecuador
Cited by: 25
Author(s): David De la Torre, Eulalia Mafla, Byron Puga, Linda Erazo, Claudete S. Astolfi-Ferreira, A. A. Ferreira
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.01925

Characterization of ML-005, a Novel Metaproteomics-Derived Esterase
Cited by: 6
Author(s): Premankur Sukul, Natalie Lupilov, Lars I. Leichert
Software Mentions: 2
Published: about 7 years ago

10.1016/j.cell.2021.01.037

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
Cited by: 508
Author(s): Emma C. Thomson, Laura E. Rosen, James G. Shepherd, Roberto Spreafico, Ana da Silva Filipe, Jason A. Wojcechowskyj, Chris Davis, Luca Piccoli, David Pascall, Josh R Dillen, Spyros Lytras, Nadine Czudnochowski, Rajiv Shah, Marcel Meury, Natasha Jesudason, Anna De Marco, Kathy Li, Jessica Bassi, Áine O’Toole, Dora Pinto, Rachel Colquhoun, Katja Culap, Ben Jackson, Fabrizia Zatta, Andrew Rambaut, Stefano Jaconi, Vattipally B Sreenu, Jay C. Nix, Ivy Zhang, Ruth F. Jarrett, William G. Glass, Martina Beltramello, Kyriaki Nomikou, Matteo Samuele Pizzuto, L. Tong, Elisabetta Cameroni, Tristan I. Croll, Natasha Johnson, Julia di Iulio, Arthur Wickenhagen, Alessandro Ceschi, Aoife M Harbison, Daniel Mair, Paolo Ferrari, Katherine Smollett, Federica Sallusto, Stephen Carmichael, Christian Garzoni, Jenna Nichols, Massimo Galli, Joseph Hughes, Agostino Riva, Antonia Ho, Marco Schiuma, Malcolm G Semple, Peter Openshaw, Elisa Fadda, J Kenneth Baillie, John D. Chodera, Suzannah J. Rihn, Samantha Lycett, Herbert W. Virgin, Amalio Telenti, Davide Corti, David L. Robertson, Gyorgy Snell
Software Mentions: 2
Published: over 4 years ago

Projects: pypi: PyMOL

Science Score: 90/100

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Papers Mentioning PyMOL 8,266