pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-10-611

Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure
Cited by: 15
Author(s): Luciane V. Mello, Helen O’Meara, Daniel J. Rigden, Steve Paterson
Software Mentions: 3
Published: almost 18 years ago

10.1371/journal.pbio.1001669

An RNA-Binding Complex Involved in Ribosome Biogenesis Contains a Protein with Homology to tRNA CCA-Adding Enzyme
Cited by: 32
Author(s): Jinzhong Lin, Jing Lü, Yingang Feng, Mengyi Sun, Keqiong Ye
Software Mentions: 3
Published: about 13 years ago

10.3389/fgene.2021.620472

Case Report: Novel RPGRIP1L Gene Mutations Identified by Whole Exome Sequencing in a Patient With Multiple Primary Tumors
Cited by: 0
Author(s): Jianghong Guo, Yu Ye, Zhuqing Ji, Ming Yao, Xiaotian Xia, Xiaofeng Sha, Ming‐De Huang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pbio.3001057

The dominantly expressed class II molecule from a resistant MHC haplotype presents only a few Marek’s disease virus peptides by using an unprecedented binding motif
Cited by: 11
Author(s): Samer Halabi, Michael Ghosh, Stefan Stevanović, Hans‐Georg Rammensee, Luca D. Bertzbach, Benedikt B. Kaufer, Martin C. Moncrieffe, Bernd Kaspers, Sonja Härtle, Jim Kaufman
Software Mentions: 3
Published: over 5 years ago

10.1107/S1399004715005210

In meso in situ serial X-ray crystallography of soluble and membrane proteins
Cited by: 98
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Ezequiel Panepucci, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pbio.3000958

Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome
Cited by: 14
Author(s): Kai Ehrenbolger, Nathan Jespersen, Himanshu Sharma, Yuliya Y. Sokolova, Yuri S. Tokarev, Charles R. Vossbrinck, Jonas Barandun
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1008568

Rosetta design with co-evolutionary information retains protein function
Cited by: 10
Author(s): Samuel Schmitz, Moritz Ertelt, Rainer Merkl, Jens Meiler
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pbio.1001512

Conformational Change-Induced Repeat Domain Expansion Regulates Rap Phosphatase Quorum-Sensing Signal Receptors
Cited by: 56
Author(s): Vijay Parashar, Philip D. Jeffrey, Matthew B. Neiditch
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pbio.3000654

Cryo-EM structures of the human PA200 and PA200-20S complex reveal regulation of proteasome gate opening and two PA200 apertures
Cited by: 22
Author(s): Hongxin Guan, Youwang Wang, Ting Yu, Yini Huang, Mianhuan Li, Abdullah F. U. H. Saeed, Vanja Perčulija, Daliang Li, Jia Xiao, Dongmei Wang, Ping Zhu, Songying Ouyang
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pbio.1001994

Thermodynamic System Drift in Protein Evolution
Cited by: 74
Author(s): Kathryn M. Hart, Michael J. Harms, Bryan H. Schmidt, Carolyn Elya, Joseph W. Thornton, Susan Marqusee
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pbio.3001344

Structure of the human C9orf72-SMCR8 complex reveals a multivalent protein interaction architecture
Cited by: 6
Author(s): Julia Nörpel, Simone Cavadini, Andreas Schenk, Alexandra Graff-Meyer, Daniel Heß, Jan Seebacher, Jeffrey A. Chao, Varun Bhaskar
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-017-1541-z

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP
Cited by: 24
Author(s): Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
Software Mentions: 3
Published: over 9 years ago

10.1007/s11103-020-01052-5

Structural insights into Arabidopsis ethylene response factor 96 with an extended N-terminal binding to GCC box
Cited by: 12
Author(s): Chun‐Yen Chen, Pei‐Hsuan Lin, Kun-Hung Chen, Yi-Sheng Cheng
Software Mentions: 3
Published: about 6 years ago

10.1107/S1399004715004514

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
Cited by: 112
Author(s): Nicolas Coquelle, Aaron S. Brewster, U. Kapp, Anastasya Shilova, Britta Weinhausen, Manfred Burghammer, J.P. Colletier
Software Mentions: 3
Published: over 11 years ago

10.1093/gbe/evu235

Albuminoid Genes: Evolving at the Interface of Dispensability and Selection
Cited by: 12
Author(s): Alessandra Mozzi, Diego Forni, Rachele Cagliani, Jacopo Vertemara, Nereo Bresolin, Manuela Sironi
Software Mentions: 3
Published: about 12 years ago

10.1093/gbe/evv046

OASes and STING: Adaptive Evolution in Concert
Cited by: 38
Author(s): Alessandra Mozzi, Chiara Pontremoli, Diego Forni, Mario Clerici, Nereo Bresolin, Rachele Cagliani, Manuela Sironi
Software Mentions: 3
Published: over 11 years ago

10.1186/s40360-017-0128-7

Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects
Cited by: 42
Author(s): Matthieu Chartier, Louis–Philippe Morency, María Inés Zylber, Rafaël Najmanovich
Software Mentions: 3
Published: over 9 years ago

10.1186/s12860-020-00328-4

Identification of biomarkers for the accurate and sensitive diagnosis of three bacterial pneumonia pathogens using in silico approaches
Cited by: 7
Author(s): Olalekan Olanrewaju Bakare, Marshall Keyster, Ashley Pretorius
Software Mentions: 3
Published: almost 6 years ago

10.1111/tpj.12935

Hetero‐trans‐β‐glucanase, an enzyme unique to Equisetum plants, functionalizes cellulose
Cited by: 46
Author(s): Thomas J. Simmons, Kyle E. Mohler, Claire Holland, Florence Goubet, Lenka Franková, Douglas R. Houston, Andrew Hudson, Frank Meulewaeter, Stephen C. Fry
Software Mentions: 3
Published: about 11 years ago

10.3390/pharmaceutics13040554

Artocarpin Targets Focal Adhesion Kinase-Dependent Epithelial to Mesenchymal Transition and Suppresses Migratory-Associated Integrins in Lung Cancer Cells
Cited by: 10
Author(s): Nongyao Nonpanya, Kittipong Sanookpan, Nicharat Sriratanasak, Chanida Vinayanuwattikun, Duangdao Wichadakul, Boonchoo Sritularak, Pithi Chanvorachote
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-015-0478-5

New insights into the evolutionary history of plant sorbitol dehydrogenase
Cited by: 22
Author(s): Yuping Jia, D. Wong, Crystal Sweetman, John B. Bruning, Christopher M. Ford
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2105-11-446

Fast and accurate protein substructure searching with simulated annealing and GPUs
Cited by: 44
Author(s): Alex Stivala, Peter J. Stuckey, Anthony Wirth
Software Mentions: 3
Published: about 16 years ago

10.1074/jbc.RA119.010697

Structural basis of cell-surface signaling by a conserved sigma regulator in Gram-negative bacteria
Cited by: 3
Author(s): Jaime L. Jensen, Beau D. Jernberg, Sangita C. Sinha, Christopher L. Colbert
Software Mentions: 3
Published: over 6 years ago

10.1074/jbc.RA120.012788

Small molecule AX-024 reduces T cell proliferation independently of CD3ϵ/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain
Cited by: 10
Author(s): Kirsten Richter, Arne C. Rufer, Magali Muller, Dominique Burger, Fabio Casagrande, Tabea Grossenbacher, Sylwia Huber, Melanie N. Hug, Philipp Koldewey, Andrea D’Osualdo, Daniel Schlatter, Theodor Stoll, M.G. Rudolph
Software Mentions: 3
Published: over 6 years ago

10.1186/s13104-015-1760-1

Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation
Cited by: 6
Author(s): Noriko Inoguchi, Kittichai Chaiseeda, Mamoru Yamanishi, Moon Ki Kim, Yunho Jang, M. Bajaj, Catherine P. Chia, Donald F. Becker, Hideaki Moriyama
Software Mentions: 3
Published: almost 11 years ago

10.1016/j.jbc.2021.100927

Beyond PKA: Evolutionary and structural insights that define a docking and dimerization domain superfamily
Cited by: 3
Author(s): Heather R. Dahlin, Ning Zheng, John D. Scott
Software Mentions: 3
Published: about 5 years ago

10.1186/1756-0500-3-289

Dockomatic - automated ligand creation and docking
Cited by: 21
Author(s): Casey W. Bullock, Reed B. Jacob, Owen M. McDougal, Greg Hampikian, Tim Andersen
Software Mentions: 3
Published: almost 16 years ago

10.1186/s12859-019-3120-y

RNA 3D structure prediction guided by independent folding of homologous sequences
Cited by: 18
Author(s): Marcin Magnus, Kalli Kappel, Rhiju Das, Janusz M. Bujnicki
Software Mentions: 3
Published: about 7 years ago

10.1186/1472-6807-11-33

Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin/mitomycin C resistance in other bacteria
Cited by: 5
Author(s): Yu Song, A. Vit, Sean R. A. Devenish, H. K. Mahanty, Aymelt Itzen, Roger S. Goody, Wulf Blankenfeldt
Software Mentions: 3
Published: about 15 years ago

10.1371/journal.pcbi.1007747

ProteinVR: Web-based molecular visualization in virtual reality
Cited by: 40
Author(s): Kevin C. Cassidy, Jan Šefčík, Yogindra Raghav, Alexander Chang, Jacob D. Durrant
Software Mentions: 3
Published: over 6 years ago

10.1126/sciadv.aav8421

HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C
Cited by: 44
Author(s): M Collier, T. Reid Alderson, Carin Pamela de Villiers, D Nicholls, Heidi Y. Gastall, Timothy M. Allison, Matteo T. Degiacomi, Jiang He, Georg Mlynek, Dieter O. Fürst, Peter F.M. van der Ven, Kristina Djinović-Carugo, Andrew J. Baldwin, Hugh Watkins, Katja Gehmlich, Justin L. P. Benesch
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1009651

Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity
Cited by: 6
Author(s): Aaron D. Besterman, Thorsten Althoff, Peter Elfferich, Irma Gutierrez-Mejia, Joshua Sadik, Jonathan A. Bernstein, Yvette van Ierland, Anja A. Kattentidt-Mouravieva, Mark Nellist, Jeff Abramson, Julián A. Martínez-Agosto
Software Mentions: 3
Published: over 5 years ago

10.1155/2019/1205942

PIM1, CYP1B1, and HSPA2 Targeted by Quercetin Play Important Roles in Osteoarthritis Treatment by Achyranthes bidentata
Cited by: 7
Author(s): Dujun Ma, Yu Tian, Liping Peng, Lixin Wang, Zhouwei Liao, Wenming Xu
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2019.00293

Phylogenetic Distribution and Diversity of Bacterial Pseudo-Orthocaspases Underline Their Putative Role in Photosynthesis
Cited by: 17
Author(s): Marina Klemenčič, Johannes Asplund-Samuelsson, Marko Dolinar, Christiane Funk
Software Mentions: 3
Published: over 7 years ago

10.1093/jxb/ery353

Homology modeling andin vivofunctional characterization of the zinc permeation pathway in a heavy metal P-type ATPase
Cited by: 20
Author(s): Gilles Lekeux, Jean-Marc Crowet, Cécile Nouet, Marine Joris, Alice Jadoul, Bernard Bosman, Monique Carnol, Patrick Motté, Laurence Lins, Moreno Galleni, Marc Hanikenne
Software Mentions: 3
Published: almost 8 years ago

10.1111/cea.12230

Human <scp>I</scp> g <scp>E</scp> against the major allergen <scp>B</scp> et v 1 – defining an epitope with limited cross‐reactivity between different <scp>PR</scp> ‐10 family proteins
Cited by: 20
Author(s): Mattias Levin, Anna M. Davies, Maria Liljekvist, Fredrika Carlsson, Hannah J. Gould, Brian J. Sutton, Mats Ohlin
Software Mentions: 3
Published: almost 13 years ago

10.1007/s10822-016-9900-9

1001 Ways to run AutoDock Vina for virtual screening
Cited by: 122
Author(s): Mohammad Mahdi Jaghoori, Boris Bleijlevens, Sílvia D. Olabarriaga
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-017-01640-4

Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
Cited by: 7
Author(s): L. Xue, Qingping Wu, Ruimin Dong, Weiping Cai, Haoming Wu, Moutong Chen, Gang Chen, Juan Wang, Jumei Zhang
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-019-39984-8

Insights into the dynamic nature of the dsRNA-bound TLR3 complex
Cited by: 27
Author(s): Vijayakumar Gosu, Seung‐Woo Son, Donghyun Shin, Ki Duk Song
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.42426

TRIM28 promotes HIV-1 latency by SUMOylating CDK9 and inhibiting P-TEFb
Cited by: 61
Author(s): Xiancai Ma, Tao Yang, Yong Luo, Liyang Wu, Yawen Jiang, Sifa Zheng, Ting Pan, Bingfeng Liu, Guangyan Liu, Jun Li, Fei Yu, Zhangping He, Wanying Zhang, Jinyu Yang, Liting Liang, Yuanjun Guan, Xu Zhang, Linghua Li, Weiping Cai, Xiaoping Tang, Song Gao, Kai Deng, Hui Zhang
Software Mentions: 3
Published: almost 8 years ago

10.1038/s42003-020-01123-9

Structure and function of a malaria transmission blocking vaccine targeting Pfs230 and Pfs230-Pfs48/45 proteins
Cited by: 34
Author(s): Kavita Singh, Martin Burkhardt, Sofia Nakuchima, Raúl Herrera, Olga Muratova, Apostolos G. Gittis, Emily Kelnhofer, Karine Reiter, Margery Smelkinson, Daniel Veltri, Bruce J. Swihart, Richard L. Shimp, Vu Nguyen, Baoshan Zhang, Nicholas J. MacDonald, Patrick E. Duffy, David N. Garboczi, David L. Narum
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-40323-0

Molecular cloning, GTP recognition mechanism and tissue-specific expression profiling of myxovirus resistance (Mx) protein in Labeo rohita (Hamilton) after Poly I:C induction
Cited by: 14
Author(s): Basanta Kumar Das, Pragyan Roy, Ajaya Kumar Rout, Deepak Ranjan Sahoo, Soumya Prasad Panda, Sushmita Pattanaik, Budheswar Dehury, Bijay Kumar Behera, Sudhansu Sekhar Mishra
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms20225734

A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity
Cited by: 23
Author(s): Ryan Hunt, Gaya Hettiarachchi, Upendra Katneni, Nancy Hernandez, David D. Holcomb, Jacob Kames, Redab Alnifaidy, Brian C. Lin, Nobuko Hamasaki-Katagiri, Aaron Wesley, Tal Kafri, Christina Morris, Laura Bouché, Maria Panico, Tal Schiller, Juan C. Ibla, Haim Bar, Amra Ismail, Howard R. Morris, Anton A. Komar
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms20225574

Establishing Computational Approaches Towards Identifying Malarial Allosteric Modulators: A Case Study of Plasmodium falciparum Hsp70s
Cited by: 10
Author(s): Arnold Amusengeri, Lindy Astl, Kevin A. Lobb, Gennady M. Verkhivker, Özlem Tastan Bishop
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.46754

The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs
Cited by: 33
Author(s): Axelle Marchant, Angel F. Cisneros, Alexandre K. Dubé, Isabelle Gagnon‐Arsenault, Diana Ascencio, Honey A. Jain, Simon Aubé, Chris Eberlein, Daniel Evans-Yamamoto, Nozomu Yachie, Christian R. Landry
Software Mentions: 3
Published: about 7 years ago

10.3389/fpls.2019.00070

Mechanism Underlying Heat Stability of the Rice Endosperm Cytosolic ADP-Glucose Pyrophosphorylase
Cited by: 6
Author(s): Seon‐Kap Hwang, S. S. Singh, Jitendra Maharana, S. N. Kalita, Aytuğ Tuncel, Tanmayee Rath, Debashis Panda, Mahendra Kumar Modi, Thomas W. Okita
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2017.00048

Porphyromonas gingivalis Uses Specific Domain Rearrangements and Allelic Exchange to Generate Diversity in Surface Virulence Factors
Cited by: 37
Author(s): Stuart G. Dashper, Helen Mitchell, Christine A. Seers, Simon Gladman, Torsten Seemann, Dieter Bulach, P. Scott Chandry, Keith J. Cross, Steven M. Cleal, Eric C. Reynolds
Software Mentions: 3
Published: almost 10 years ago

10.1128/mBio.02858-18

Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket
Cited by: 13
Author(s): Pierrick Craveur, A.T. Gres, Karen A. Kirby, Dandan Liu, John A. Hammond, Yisong Deng, Stefano Forli, David S. Goodsell, James R. Williamson, Stefan G. Sarafianos, Arthur J. Olson
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-40892-0

Steered molecular dynamic simulations of conformational lock of Cu, Zn-superoxide dismutase
Cited by: 11
Author(s): Bao-Lin Xiao, Yan-Na Ning, Nan-Nan Niu, Di Li, Ali Akbar Moosavi-Movahedi, Nader Sheibani, Jun Hong
Software Mentions: 3
Published: over 7 years ago

10.1016/j.csbj.2018.10.008

Quantitative comparison of ABC membrane protein type I exporter structures in a standardized way
Cited by: 4
Author(s): Georgina Csizmadia, Bianka Farkas, Zoltán Spagina, Hedvig Tordai, Tamás Hegedüs
Software Mentions: 3
Published: almost 9 years ago

10.3390/ijms20040884

Identification and Evaluation of Inhibitors of Lipase from Malassezia restricta using Virtual High-Throughput Screening and Molecular Dynamics Studies
Cited by: 67
Author(s): Shahid Ali, Faez Iqbal Khan, Taj Mohammad, Dongming Lan, Md. Imtaiyaz Hassan, Yonghua Wang
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-08842-w

Exploring Leishmania secretory proteins to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach
Cited by: 226
Author(s): Nazia Khatoon, Rajan Kumar Pandey, Vijay Kumar Prajapati
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-018-37699-w

The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail
Cited by: 15
Author(s): Tyler Weaver, Jiachen Liu, Katelyn E. Connelly, Chris Coble, Katayoun Varzavand, Emily C. Dykhuizen, Catherine A. Musselman
Software Mentions: 3
Published: over 7 years ago

10.1083/jcb.202005130

SUMOylation stabilizes sister kinetochore biorientation to allow timely anaphase
Cited by: 4
Author(s): Shaowu Xue, Menglu Wang, Claudia Schaffner, Olga O. Nerusheva, Dean Clift, Christos Spanos, David A. Kelly, Michael H. Tatham, Andreas U. Wallek, Yehui Wu, Juri Rappsilber, A. Arockia Jeyaprakash, Zuzana Storchová, Ronald T. Hay, Adèle L. Marston
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2018.02086

The Diversity of Mammalian Hemoproteins and Microbial Heme Scavengers Is Shaped by an Arms Race for Iron Piracy
Cited by: 6
Author(s): Alessandra Mozzi, Diego Forni, Mario Clerici, Rachele Cagliani, Manuela Sironi
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.46497

Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade
Cited by: 80
Author(s): Tom O. Delmont, Evan Kiefl, Ozsel Kilinc, Özcan C. Esen, Ismail Uysal, Michael S. Rappé, Steven Giovannoni, A. Murat Eren
Software Mentions: 3
Published: about 7 years ago

10.3389/fpls.2019.00466

Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling
Cited by: 34
Author(s): Marius L. Theune, Ulrich Bloss, Luise H. Brand, Friederike Ladwig, Dierk Wanke
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-40564-z

Decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the United States
Cited by: 38
Author(s): Fangzhou Chen, Todd P. Knutson, Stephanie Rossow, Linda J. Saif, Douglas Marthaler
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0116688

Identification of STAT1 and STAT3 Specific Inhibitors Using Comparative Virtual Screening and Docking Validation
Cited by: 29
Author(s): Małgorzata Szeląg, Anna Czerwoniec, Joanna Wesoły, Hans A.R. Bluyssen
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-018-37506-6

Mechanism of action of the moonlighting protein EfTu as a Substance P sensor in Bacillus cereus
Cited by: 9
Author(s): Awa Ndiaye, Valérie Borrel, Pierre‐Jean Racine, Thomas Clamens, Ségolène Depayras, Olivier Maillot, Béatrice Schaack, Sylvie Chevalier, Olivier Lesouhaitier, Marc Feuilloley
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms19030916

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations
Cited by: 2
Author(s): Long‐Can Mei, Yanping Zhou, Lizhe Zhu, Changlin Liu, Zhuo Wu, Fangkui Wang, Ge‐Fei Hao, Di Yu, Hong Yuan, Yanfang Cui
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.22086

Molecular architecture of the 90S small subunit pre-ribosome
Cited by: 116
Author(s): Qiaoyan Sun, Xing Zhu, Qiong Jia, Wenling An, Pengfei Lan, Dan Tan, Rongchang Chen, Bing Wang, Sanduo Zheng, Cheng Zhang, Xining Chen, Wei Zhang, Jing Chen, Meng‐Qiu Dong, Keqiong Ye
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2016.00266

Identification and Characterization of the Sucrose Synthase 2 Gene (Sus2) in Durum Wheat
Cited by: 14
Author(s): Mariateresa Volpicella, Immacolata Fanizza, Claudia Leoni, Ágata Gadaleta, Domenica Nigro, B. Gattulli, Giacomo Mangini, Antonio Blanco, Luigi R. Ceci
Software Mentions: 3
Published: over 10 years ago

10.1002/ctm2.296

Ursodesoxycholic acid alleviates liver fibrosis via proregeneration by activation of the ID1‐WNT2/HGF signaling pathway
Cited by: 8
Author(s): Dong Xi, Yun Luo, Shan Lu, Han Ma, Wenchao Zhang, Yue Zhu, Guibo Sun, Xiaobo Sun
Software Mentions: 3
Published: almost 6 years ago

10.3389/frobt.2018.00133

Authenticity, Interactivity, and Collaboration in VR Learning Games
Cited by: 9
Author(s): Meredith Thompson, Annie Wang, Dan Roy, Eric Klopfer
Software Mentions: 3
Published: almost 8 years ago

10.1016/j.dib.2016.01.016

Molecular determinants and interaction data of cyclic peptide inhibitor with the extracellular domain of TrkB receptor
Cited by: 5
Author(s): Nitin Chitranshi, Vivek Kumar Gupta, Yogita Dheer, Veer Bala Gupta, Roshana Vander Wall, Stuart L. Graham
Software Mentions: 3
Published: over 10 years ago

10.1016/j.str.2021.04.004

Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein
Cited by: 8
Author(s): Patryk Ludzia, E.D. Lowe, Gabriele Marcianò, Shabaz Mohammed, Christina Redfield, Bungo Akiyoshi
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-46094-y

Human Corneal Expression of SLC4A11, a Gene Mutated in Endothelial Corneal Dystrophies
Cited by: 23
Author(s): Deepti Malhotra, Sampath K. Loganathan, Anthony M. Chiu, Chris M. Lukowski, Joseph R. Casey
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-33193-5

Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas
Cited by: 10
Author(s): Hong‐Hsiang Guan, Yin-Cheng Hsieh, Po‐Chun Lin, Yen‐Chieh Huang, Masato Yoshimura, Liying Chen, Shao-Kang Chen, Phimonphan Chuankhayan, Chien-Chih Lin, Nai-Chi Chen, Atsushi Nakagawa, Sunney I. Chan, Chun‐Jung Chen
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-29865-x

EPO does not promote interaction between the erythropoietin and beta-common receptors
Cited by: 18
Author(s): Karen S. Cheung Tung Shing, Sophie E. Broughton, Tracy L. Nero, Kevin R. Gillinder, Melissa Ilsley, Hayley S. Ramshaw, Angel F. Lopez, Michael D. W. Griffin, Michael W. Parker, Andrew C. Perkins, Urmi Dhagat
Software Mentions: 3
Published: about 8 years ago

10.1093/jxb/eru266

Experimental and bioinformatic characterization of a recombinant polygalacturonase-inhibitor protein from pearl millet and its interaction with fungal polygalacturonases
Cited by: 8
Author(s): S. Prabhu, Ratna Singh, Stephan Kolkenbrock, Neerakkal Sujeeth, Nour Eddine El Gueddari, Bruno M. Moerschbacher, K. Ramachandra Kini, Martin Wagenknecht
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0232959

Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability
Cited by: 7
Author(s): Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-020-01401-6

Structure-based dynamic analysis of the glycine cleavage system suggests key residues for control of a key reaction step
Cited by: 13
Author(s): Han Zhang, Yuchen Li, Jinglei Nie, Jie Ren, An‐Ping Zeng
Software Mentions: 3
Published: almost 6 years ago

10.1038/s42003-021-02518-y

14-3-3 proteins inactivate DAPK2 by promoting its dimerization and protecting key regulatory phosphosites
Cited by: 18
Author(s): Matej Horvath, Olívia Petrvalská, Petr Heřman, Veronika Obšilová, Tomáš Obšil
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-017-08747-8

Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters
Cited by: 56
Author(s): Venkata Krishnan Ramaswamy, Attilio Vittorio Vargiu, Giuliano Malloci, Jürg Dreier, Paolo Ruggerone
Software Mentions: 3
Published: about 9 years ago

10.1007/s10822-018-0148-4

Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3
Cited by: 19
Author(s): Panagiotis I. Koukos, Xue Li, Alexandre M. J. J. Bonvin
Software Mentions: 3
Published: about 8 years ago

10.1186/s13321-016-0157-z

Ligand-based virtual screening interface between PyMOL and LiSiCA
Cited by: 9
Author(s): Athira Athira, Samo Lešnik, Tanja Štular, Dušanka Janežič, Janez Konc
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-018-29058-6

Structural determinants of specificity and regulation of activity in the allosteric loop network of human KLK8/neuropsin
Cited by: 7
Author(s): Mekdes Debela, Viktor Magdolen, Wolfgang Skala, Brigitta Elsässer, Eric L. Schneider, Charles S. Craik, Martin L. Biniossek, Oliver Schilling, Wolfram Bode, Hans Brandstetter, Peter Goettig
Software Mentions: 3
Published: over 8 years ago

10.1093/database/bau102

PolyprOnline: polyproline helix II and secondary structure assignment database
Cited by: 35
Author(s): Romain Chebrek, Sylvain Léonard, Alexandre G. de Brevern, Jean‐Christophe Gelly
Software Mentions: 3
Published: almost 12 years ago

10.3390/genes12010034

Biological Regulatory Network (BRN) Analysis and Molecular Docking Simulations to Probe the Modulation of IP3R Mediated Ca2+ Signaling in Cancer
Cited by: 2
Author(s): Humaira Ismatullah, Ishrat Jabeen, Muhammad Saeed
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13321-019-0354-7

Bayesian optimization for conformer generation
Cited by: 34
Author(s): Lucian Chan, Geoffrey Hutchison, Garrett M. Morris
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-36267-6

The reduced activity of PP-1α under redox stress condition is a consequence of GSH-mediated transient disulfide formation
Cited by: 7
Author(s): Simranjit Singh, Simon Lämmle, Heiko Giese, Susanne Kämmerer, Stefanie Meyer-Roxlau, Ezzaldin Ahmed Alfar, Hassan Dihazi, Kaomei Guan, Ali El‐Armouche, Florian Richter
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.56889

An ER translocon for multi-pass membrane protein biogenesis
Cited by: 68
Author(s): Philip T. McGilvray, S. Anghel, Arunkumar Sundaram, Frank Zhong, Michael J. Trnka, James R. Fuller, Hong Yu Hu, Alma L. Burlingame, Robert J. Keenan
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-34508-2

“Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations
Cited by: 16
Author(s): Yasaman Karami, Tristan Bitard‐Feildel, Élodie Laine, Alessandra Carbone
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-32040-x

The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8+ T lymphocyte response
Cited by: 20
Author(s): Manas Ranjan Dikhit, Sushmita Das, Vijaya Mahantesh, Akhilesh Kumar, Ashish Kumar Singh, Budheswar Dehury, Ajaya Kumar Rout, Vahab Ali, Ganesh Chandra Sahoo, Roshan Kamal Topno, Krishna Pandey, Vidya Nand Rabi Das, Sanjiva Bimal, Pradeep Das
Software Mentions: 3
Published: about 8 years ago

10.1038/s42003-021-02532-0

Modulation of Toll-like receptor 1 intracellular domain structure and activity by Zn2+ ions
Cited by: 7
Author(s): Владислав А. Лушпа, Marina V. Goncharuk, Cong Lin, Arthur O. Zalevsky, Irina A. Talyzina, Aleksandra Luginina, Daniil Vakhrameev, M.B. Shevtsov, Sergey A. Goncharuk, Alexander S. Arseniev, Valentin Borshchevskiy, Xiaohui Wang, K.S. Mineev
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms20081996

Two Sides of the Coin: Ezrin/Radixin/Moesin and Merlin Control Membrane Structure and Contact Inhibition
Cited by: 45
Author(s): Katharine A. Michie, Adam Bermeister, Neil O. Robertson, Sophia C. Goodchild, Paul M. G. Curmi
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms221910493

Discovery and Validation of Lmj_04_BRCT Domain, a Novel Therapeutic Target: Identification of Candidate Drugs for Leishmaniasis
Cited by: 6
Author(s): José Peña-Guerrero, Celia Fernández-Rubio, Aroia Burguete-Mikeo, Rima El-Dirany, Alfonso T. García-Sosa, Paul A. Nguewa
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0257206

Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease
Cited by: 4
Author(s): R. V. Sriram Uday, Rajdip Misra, Annaram Harika, Sandip Dolui, Achintya Saha, Samir Kumar Pal, V. Ravichandiran, Nakul C. Maiti
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-40432-w

Reactive centre loop dynamics and serpin specificity
Cited by: 28
Author(s): Emilia M. Marijanovic, James Fodor, Blake T. Riley, Benjamin T. Porebski, Maurício G. S. Costa, Itamar Kass, David E. Hoke, Sheena McGowan, Ashley M. Buckle
Software Mentions: 3
Published: over 7 years ago

10.1101/2021.02.21.432184

High-Throughput, Single-Copy Sequencing Reveals SARS-CoV-2 Spike Variants Coincident with Mounting Humoral Immunity during Acute COVID-19
Cited by: 4
Author(s): Sung Hee Ko, Elham Bayat Mokhtari, Prakriti Mudvari, Sydney Stein, Christopher D. Stringham, Danielle A. Wagner, Sabrina Ramelli, Marcos J. Ramos‐Benitez, Jeffrey R Strich, Richard T. Davey, Tongqing Zhou, John Misasi, Peter D. Kwong, Daniel S. Chertow, Nancy J. Sullivan, Eli Boritz
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-39588-2

The IKK-binding domain of NEMO is an irregular coiled coil with a dynamic binding interface
Cited by: 18
Author(s): Adam H. Barczewski, Michael J. Ragusa, Dale F. Mierke, Maria Pellegrini
Software Mentions: 3
Published: over 7 years ago

10.1128/mBio.00373-17

Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus
Cited by: 243
Author(s): Simon J. Anthony, Kirsten Gilardi, Vineet D. Menachery, Tracey Goldstein, Benard Ssebide, R. Mbabazi, Isamara Navarrete-Macias, Eliza Liang, Heather L. Wells, Alan C. Hicks, Alexandra Petrosov, Denis K. Byarugaba, Kari Debbink, Kenneth H. Dinnon, Trevor Scobey, Scott H. Randell, Boyd Yount, Michael R. Cranfield, Christine K. Johnson, Ralph S. Baric, W. Ian Lipkin, Jonna A. K. Mazet
Software Mentions: 3
Published: over 9 years ago

10.1128/mBio.03066-19

How Bacterial Chemoreceptors Evolve Novel Ligand Specificities
Cited by: 45
Author(s): José A. Gavira, Vadim M. Gumerov, Míriam Rico-Jiménez, Marharyta Petukh, Amit A. Upadhyay, Álvaro Ortega, Miguel A. Matilla, Igor B. Zhulin, Tino Krell
Software Mentions: 3
Published: over 6 years ago

10.1155/2014/697532

In SilicoAntitubercular Activity Analysis of Benzofuran and Naphthofuran Derivatives
Cited by: 5
Author(s): Prashantha Karunakar, C. R. Girija, Venkatappa Krishnamurthy, V. Krishna, K. V. Shivakumar
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-019-39641-0

Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H
Cited by: 13
Author(s): Chang Woo Lee, Sun Ha Park, Chang-Sung Jeong, Sun Mi Shin, Hyun Park, Jun Hyuck Lee
Software Mentions: 3
Published: over 7 years ago

10.1080/14756366.2021.1931862

Structure-based virtual screening of highly potent inhibitors of the nematode chitinase CeCht1
Cited by: 7
Author(s): Wei Chen, Qi Chen, Ashutosh Kumar, Xi Jiang, Kam Y. J. Zhang, Qing Yang
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.27829

Structure-based analysis of CysZ-mediated cellular uptake of sulfate
Cited by: 9
Author(s): Zahra Assur Sanghai, Qun Liu, Oliver B Clarke, Meagan Belcher Dufrisne, Pattama Wiriyasermkul, Maria Giese, Edgar Leal-Pinto, Brian Kloss, Shantelle Tabuso, J. Love, Marco Punta, Surajit Banerjee, Kanagalaghatta R. Rajashankar, Burkhard Rost, Diomedes E. Logothetis, Matthias Quick, Wayne A. Hendrickson, Filippo Mancia
Software Mentions: 3
Published: over 8 years ago

10.1534/g3.119.400224

Contraction of the ROS Scavenging Enzyme GlutathioneS-Transferase Gene Family in Cetaceans
Cited by: 11
Author(s): Ran Tian, Inge Seim, Wenhua Ren, Shixia Xu
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.57861

Profiling of myristoylation in Toxoplasma gondii reveals an N-myristoylated protein important for host cell penetration
Cited by: 19
Author(s): Malgorzata Broncel, Caia Dominicus, Luis Vigetti, Stephanie D. Nofal, Edward Bartlett, Bastien Touquet, Alex Hunt, Bethan A. Wallbank, Stefania Federico, Stephen Matthews, J. M. Young, Edward W. Tate, Isabelle Tardieux, Moritz Treeck
Software Mentions: 3
Published: over 6 years ago

Projects: pypi: PyMOL

Science Score: 90/100

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Papers Mentioning PyMOL 8,266