Ecosyste.ms: Papers

10.1371/journal.pone.0240932

Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1
Cited by: 27
Author(s): Guillaume Gaullier, Genevieve Roberts, Uma M. Muthurajan, Samuel Bowerman, Johannes Rudolph, Jyothi Mahadevan, Asmita Jha, Purushka S. Rae, Karolin Luger
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-019-39276-1

Insights into the antigenic advancement of influenza A(H3N2) viruses, 2011–2018
Cited by: 45
Author(s): Patricia A. Jorquera, Vasiliy P. Mishin, Anton Chesnokov, Ha Nguyen, Brian R. Mann, Rebecca Garten, John Barnes, Erin Hodges, Juan de la Cruz, Xinhua Xu, Jackie Katz, David E. Wentworth, Larisa V. Gubareva
Software Mentions: 5
Published: over 5 years ago

10.1107/S2059798317000031

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode
Cited by: 18
Author(s): Kimberly A. Stanek, Jennifer Patterson-West, Peter S. Randolph, Cameron Mura
Software Mentions: 5
Published: over 7 years ago

10.1021/acs.jcim.1c00362

Data-Driven Ensemble Docking to Map Molecular Interactions of Steroid Analogs with Hepatic Organic Anion Transporting Polypeptides
Cited by: 5
Author(s): Alzbeta Tuerkova, Orsolya Ungvári, Réka Laczkó-Rigó, Erzsébet Mernyák, Gergely Szakács, Csilla Özvegy‐Laczka, Barbara Zdrazil
Software Mentions: 4
Published: over 3 years ago

10.1186/s13073-014-0081-7

Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach
Cited by: 31
Author(s): Huy Gia Vuong, Feixiong Cheng, Lin Chen, Zhongming Zhao
Software Mentions: 4
Published: about 10 years ago

10.1107/S0907444912046008

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement
Cited by: 8
Author(s): S.O. Dahms, Miriam Kuester, Carsten Streb, Christian Roth, Norbert Sträter, Manuel E. Than
Software Mentions: 4
Published: almost 12 years ago

10.4269/ajtmh.18-0980

Global Outbreaks and Origins of a Chikungunya Virus Variant Carrying Mutations Which May Increase Fitness for Aedes aegypti: Revelations from the 2016 Mandera, Kenya Outbreak
Cited by: 40
Author(s): Irina Maljkovic Berry, Fredrick Eyase, Simon Pollett, Samson L. Konongoi, Michael Joyce, Katherine Figueroa, Victor Ofula, Helen Koka, Edith Koskei, Albert Nyunja, James D. Mancuso, Richard G. Jarman, Rosemary Sang
Software Mentions: 4
Published: over 5 years ago

10.1007/s10822-017-0049-y

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
Cited by: 94
Author(s): Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikaël Trellet, João P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel‐Touris, Adrien Melquiond, Cunliang Geng, Jörg Schaarschmidt, Xue Li, Anna Vangone, Alexandre M. J. J. Bonvin
Software Mentions: 4
Published: over 7 years ago

10.1186/gb-2008-9-1-r11

CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships
Cited by: 36
Author(s): Wei-Cheng Lo, Ping Lyu
Software Mentions: 4
Published: almost 17 years ago

10.1007/s10822-020-00329-7

Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles
Cited by: 9
Author(s): Isaías Lans, Karen Palacio-Rodríguez, Claudio N. Cavasotto, Pilar Cossio
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-34855-0

Safranal induces DNA double-strand breakage and ER-stress-mediated cell death in hepatocellular carcinoma cells
Cited by: 75
Author(s): Ala’a Al-Hrout, Amphun Chaiboonchoe, Basel Khraiwesh, Chandraprabha Murali, Badriya Baig, Raafat El‐Awady, Hamadeh Tarazi, Amnah Alzahmi, David R. Nelson, Yaser E. Greish, Wafaa Ramadan, Kourosh Salehi‐Ashtiani, Amr Amin
Software Mentions: 4
Published: about 6 years ago

10.3390/biom11040549

Conformational Plasticity-Rigidity Axis of the Coagulation Factor VII Zymogen Elucidated by Atomistic Simulations of the N-Terminally Truncated Factor VIIa Protease Domain
Cited by: 6
Author(s): Jesper J. Madsen, Ole H. Olsen
Software Mentions: 4
Published: over 3 years ago

10.1016/j.celrep.2020.107928

Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family
Cited by: 17
Author(s): Adam S. B. Jalal, Ngat T. Tran, Clare E. M. Stevenson, Elliot W. Chan, Rebecca Lo, Xiao Tan, Agnes Noy, David M. Lawson, Tung B. K. Le
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0208641

Use of a sequential high throughput screening assay to identify novel inhibitors of the eukaryotic SRP-Sec61 targeting/translocation pathway
Cited by: 5
Author(s): W. Klein, Claudia Rutz, Jamina Eckhard, Becky Provinciael, Edgar Specker, Martin Neuenschwander, Gunnar Kleinau, Patrick Scheerer, Jens-Peter von Kries, Marc Nazaré, Kurt Vermeire, Ralf Schülein
Software Mentions: 4
Published: almost 6 years ago

10.1107/S2059798318001353

<i>Gyre</i>and<i>gimble</i>: a maximum-likelihood replacement for Patterson correlation refinement
Cited by: 13
Author(s): Airlie J. McCoy, Robert D. Oeffner, Claudia Millán, Massimo Sammito, Isabel Usón, Randy J. Read
Software Mentions: 4
Published: over 6 years ago

10.1107/S2059798316001224

Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry
Cited by: 5
Author(s): Blaine H. M. Mooers
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0178931

In silico discovery of substituted pyrido[2,3-d]pyrimidines and pentamidine-like compounds with biological activity in myotonic dystrophy models
Cited by: 10
Author(s): Àlex L. González, Piotr Konieczny, Beatriz Llamusí, Estefanía Delgado‐Pinar, José I. Borrell, Jordi Teixidó, Enrique García‐España, Manuel Pérez-Alonso, Roger Estrada‐Tejedor, Rubén Artero
Software Mentions: 4
Published: over 7 years ago

10.1107/S1399004713032549

Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D
Cited by: 29
Author(s): Federico Forneris, B. Tom Burnley, Piet Gros
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pcbi.1007219

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
Cited by: 11
Author(s): Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini, Alessandro Paiardini
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0021931

Real-Time PyMOL Visualization for Rosetta and PyRosetta
Cited by: 51
Author(s): Evan H. Baugh, Sergey Lyskov, Brian D. Weitzner, Jeffrey J. Gray
Software Mentions: 4
Published: over 13 years ago

10.3389/fmolb.2020.00027

Conformational Changes Induced by S34Y and R98C Variants in the Death Domain of Myd88
Cited by: 2
Author(s): Vijayakumar Gosu, Kyeong-Hye Won, Jae-Don Oh, Donghyun Shin
Software Mentions: 4
Published: over 4 years ago

10.3389/fmolb.2021.715972

Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks
Cited by: 5
Author(s): Noelia Ferruz, Florian Michel, Francisco Lobos, Steffen Schmidt, Birte Höcker
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2018.01144

Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters of Pseudomonas aeruginosa
Cited by: 32
Author(s): Venkata Krishnan Ramaswamy, Attilio Vittorio Vargiu, Giuliano Malloci, Jürg Dreier, Paolo Ruggerone
Software Mentions: 4
Published: over 6 years ago

10.1093/bib/bbv037

Building a virtual ligand screening pipeline using free software: a survey
Cited by: 68
Author(s): Enrico Glaab
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms18010228

Molecular Basis for the Neutralization of Tumor Necrosis Factor α by Certolizumab Pegol in the Treatment of Inflammatory Autoimmune Diseases
Cited by: 32
Author(s): Jee Un Lee, Woo‐Ri Shin, Ji Young Son, Kyung Yeon Yoo, Yong‐Seok Heo
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13018-021-02552-w

Study on the potential active components and molecular mechanism of Xiao Huoluo Pills in the treatment of cartilage degeneration of knee osteoarthritis based on bioinformatics analysis and molecular docking technology
Cited by: 13
Author(s): Weijian Chen, Tianye Lin, Qi He, Peng Yang, Gangyu Zhang, Fayi Huang, Zihao Wang, Hao Peng, Baolin Li, Liqing Du, Haibin Wang
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.02304

An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases
Cited by: 71
Author(s): Jeffrey I. Boucher, Joseph Jacobowitz, Brian C Beckett, Scott Classen, Douglas L. Theobald
Software Mentions: 4
Published: over 10 years ago

10.1107/S2059798317017582

<i>ARCIMBOLDO</i>on coiled coils
Cited by: 39
Author(s): Iracema Caballero, Massimo Sammito, Claudia Millán, А. А. Лебедев, Nicolas Soler, Isabel Usón
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.00231

Structural and Biochemical Characterization of BdsA from Bacillus subtilis WU-S2B, a Key Enzyme in the “4S” Desulfurization Pathway
Cited by: 14
Author(s): Tianning Su, Jing Su, Shiheng Liu, Conggang Zhang, Jing He, Yan Huang, Sujuan Xu, Lichuan Gu
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.38888

Structural principles of SNARE complex recognition by the AAA+ protein NSF
Cited by: 68
Author(s): K. Ian White, Minglei Zhao, Ucheor B. Choi, Richard A. Pfuetzner, Axel T. Brunger
Software Mentions: 4
Published: about 6 years ago

10.1107/S139900471400087X

Anomalies in the refinement of isoleucine
Cited by: 3
Author(s): Karen R. M. Berntsen, Gert Vriend
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0219823

Structures of TOG1 and TOG2 from the human microtubule dynamics regulator CLASP1
Cited by: 11
Author(s): Jonathan B. Leano, Kevin C. Slep
Software Mentions: 4
Published: over 5 years ago

10.1111/pbi.12520

Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Cited by: 89
Author(s): Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Dadakhalandar Doddamani, Lekha T. Pazhamala, Aamir W. Khan, Mahendar Thudi, Suk-Ha Lee, Rajeev K. Varshney
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.63429

Structural basis for human TRPC5 channel inhibition by two distinct inhibitors
Cited by: 33
Author(s): Kangcheng Song, Mengping Wei, Wenjun Guo, Quan Li, Yimin Kang, Jing-Xiang Wu
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.29880

Inferring joint sequence-structural determinants of protein functional specificity
Cited by: 13
Author(s): Andrew F. Neuwald, L. Aravind, Stephen F. Altschul
Software Mentions: 4
Published: almost 7 years ago

10.1186/1471-2164-14-523

Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains
Cited by: 38
Author(s): Yuanyuan Li, Xiao Chang, Wen-Bang Yu, Hao Li, Zhiqiang Ye, Hui Yu, Baohong Liu, Yan Zhang, Siliang Zhang, Bang‐Ce Ye, Yixue Li
Software Mentions: 4
Published: almost 12 years ago

10.7554/eLife.16761

Origin of a folded repeat protein from an intrinsically disordered ancestor
Cited by: 40
Author(s): Hongbo Zhu, Edgardo Sepúlveda, M.D. Hartmann, Manjunatha Kogenaru, Astrid Ursinus, Eva Sulz, R. Albrecht, Murray Coles, Jörg Martin, Andrei N. Lupas
Software Mentions: 4
Published: about 8 years ago

10.1007/s13205-014-0231-z

Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae
Cited by: 15
Author(s): Mohd Shahbaaz, Faizan Ahmad, Md. Imtaiyaz Hassan
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pbio.3000123

Structural basis of DSF recognition by its receptor RpfR and its regulatory interaction with the DSF synthase RpfF
Cited by: 22
Author(s): E.J. Waldron, Donald R. Snyder, Nicolas L. Fernandez, Emily Sileo, Daigo Inoyama, Joel S. Freundlich, Christopher M. Waters, Vaughn S. Cooper, Matthew B. Neiditch
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.str.2011.03.023

Insights into the Evolution of a Complex Virus from the Crystal Structure of Vaccinia Virus D13
Cited by: 79
Author(s): Mohammad W. Bahar, Stephen C. Graham, David I. Stuart, Jonathan M. Grimes
Software Mentions: 4
Published: over 13 years ago

10.7554/eLife.53789

Insights into herpesvirus assembly from the structure of the pUL7:pUL51 complex
Cited by: 23
Author(s): Benjamin G Butt, Danielle Owen, Cy M. Jeffries, Lyudmila Ivanova, C.P. Hill, Jennifer D. Houghton, Firoz Ahmed, Robin Antrobus, Dmitri I. Svergun, John J. Welch, Colin M. Crump, Stephen C. Graham
Software Mentions: 4
Published: over 4 years ago

10.3389/fmolb.2021.715215

Decoding Partner Specificity of Opioid Receptor Family
Cited by: 3
Author(s): Carlos Barreto, Salete J. Baptista, António Preto, Daniel Silvério, Rita Melo, Irina S. Moreira
Software Mentions: 4
Published: about 3 years ago

10.1107/S2059798318009324

New tools for the analysis and validation of cryo-EM maps and atomic models
Cited by: 536
Author(s): Pavel V. Afonine, Bruno P. Klaholz, Nigel W. Moriarty, Billy K. Poon, Oleg V. Sobolev, Thomas C. Terwilliger, Paul D. Adams, Alexandre Urzhumtsev
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2018.02581

Structural and Functional Characterization of PA14/Flo5-Like Adhesins From Komagataella pastoris
Cited by: 6
Author(s): Michael D. Kock, Stefan Brückner, Nina Wozniak, M. Maestre-Reyna, M. Veelders, Julia Schlereth, Hans‐Ulrich Mösch, Lars‐Oliver Essen
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.266

Analyzing machupo virus-receptor binding by molecular dynamics simulations
Cited by: 9
Author(s): Austin G. Meyer, Sara L. Sawyer, Andrew D. Ellington, Claus O. Wilke
Software Mentions: 4
Published: over 10 years ago

10.3762/bjoc.16.199

Computational tools for drawing, building and displaying carbohydrates: a visual guide
Cited by: 12
Author(s): Kanhaya Lal, Rafael Bermeo, Serge Pérez
Software Mentions: 4
Published: about 4 years ago

10.15252/embj.2019102926

Structural basis of semaphorin‐plexin <i>cis</i> interaction
Cited by: 15
Author(s): Daniel Rozbeský, Marieke G. Verhagen, Dimple Karia, Gergely Nagy, Luis Álvarez, R.A. Robinson, K. Harlos, Sergi Padilla‐Parra, R. Jeroen Pasterkamp, Emma Jones
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0108852

Expression, Purification, and Structural Insights for the Human Uric Acid Transporter, GLUT9, Using the Xenopus laevis Oocytes System
Cited by: 34
Author(s): Benjamin Clémençon, Benjamin P. Lüscher, Michael Fine, Marc Baumann, Daniel Surbek, Olivier Bonny, Matthias A. Hediger
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.ppat.1009824

pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spread
Cited by: 12
Author(s): Tomasz H. Benedyk, Julia Muenzner, Viv Connor, Yue Han, Katherine A. Brown, Kaveesha J. Wijesinghe, Yunhui Zhuang, Susanna Colaco, Guido A. Stoll, Owen S. Tutt, Stanislava Svobodova, Dmitri I. Svergun, Neil Bryant, Janet E. Deane, Andrew E. Firth, Cy M. Jeffries, Colin M. Crump, Stephen C. Graham
Software Mentions: 4
Published: over 3 years ago

10.1128/JVI.01127-19

Evolutionary Dynamics of Oropouche Virus in South America
Cited by: 14
Author(s): Bernardo Gutierrez, Emma L. Wise, Steven T. Pullan, Christopher Logue, Thomas A. Bowden, Marina Escalera-Zamudio, Gabriel Trueba, Márcio Roberto Teixeira Nunes, Nuno Rodrigues Faria, Oliver G. Pybus
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSphere.00298-16

Human Norovirus Aptamer Exhibits High Degree of Target Conformation-Dependent Binding Similar to That of Receptors and Discriminates Particle Functionality
Cited by: 18
Author(s): Matthew D. Moore, Benjamin G. Bobay, Brittany S. Mertens, Lee‐Ann Jaykus
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0092257

Esterase LpEst1 from Lactobacillus plantarum: A Novel and Atypical Member of the αβ Hydrolase Superfamily of Enzymes
Cited by: 23
Author(s): Y. Álvarez, María Esteban-Torres, Álvaro Cortés-Cabrera, Federico Gago, I. Acebrón, R. Benavente, Karin Mardo, Blanca de las Rivas, Rosario Múñoz, José M. Mancheño
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-021-87061-w

Vitamin D and lumisterol derivatives can act on liver X receptors (LXRs)
Cited by: 47
Author(s): Andrzej Słomiński, Tae Kang Kim, Shariq Qayyum, Yuwei Song, Zorica Janjetovic, Allen S.W. Oak, Radomir M. Slominski, Chander Raman, Joanna Stefan, Carlos A. Mier‐Aguilar, Venkatram R. Atigadda, David K. Crossman, Andriy G. Golub, Yaroslav V. Bilokin, Edith K.Y. Tang, Jake Y. Chen, Robert C. Tuckey, Anton M. Jetten
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-68693-w

Inhibition of indole production increases the activity of quinolone antibiotics against E. coli persisters
Cited by: 13
Author(s): Ashraf Zarkan, Marta Matuszewska, Stephen Trigg, Meng Zhang, Daaniyah Belgami, Cameron Croft, Junyan Liu, Sawssen El-Ouisi, Jack Greenhalgh, James S. Duboff, Taufiq Rahman, David Summers
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0080371

Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus
Cited by: 33
Author(s): C. Leyrat, Max Renner, K. Harlos, Jonathan M. Grimes
Software Mentions: 4
Published: about 11 years ago

10.1016/j.mcpro.2021.100065

Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits
Cited by: 5
Author(s): F. Schober, Ilian Atanassov, David Moore, Javier Calvo‐Garrido, Marco F. Moedas, Anna Wedell, Christoph Freyer, Anna Wredenberg
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-74648-y

Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches
Cited by: 20
Author(s): Stephanie Portelli, Yoochan Myung, Nicholas Furnham, Sundeep Chaitanya Vedithi, Douglas E V Pires, David B. Ascher
Software Mentions: 4
Published: about 4 years ago

10.3390/molecules24142529

High Impact: The Role of Promiscuous Binding Sites in Polypharmacology
Cited by: 8
Author(s): Natacha Cerisier, Michel Petitjean, Leslie Regad, Quentin Bayard, Manon Réau, Anne Badel, Anne-Claude Camproux
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.10234

Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function
Cited by: 48
Author(s): Alejandro Berrío, Valerie Gartner, Gregory A. Wray
Software Mentions: 4
Published: about 4 years ago

10.1186/s13072-017-0142-4

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure
Cited by: 18
Author(s): Sergey V. Ulianov, Aleksandra A. Galitsyna, Ilya M. Flyamer, Arkadiy K. Golov, Ekaterina E. Khrameeva, Maxim Imakaev, Nezar Abdennur, Mikhail S. Gelfand, А. В. Гаврилов, Sergey V. Razin
Software Mentions: 4
Published: over 7 years ago

10.1099/mgen.0.000541

Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins
Cited by: 5
Author(s): Thomas Hollin, Lukasz Jaroszewski, Jason E. Stajich, Adam Godzik, Karine G. Le Roch
Software Mentions: 4
Published: over 3 years ago

10.1002/mbo3.320

Altered acetylation and succinylation profiles in <i>Corynebacterium glutamicum</i> in response to conditions inducing glutamate overproduction
Cited by: 49
Author(s): Yuta Mizuno, Megumi Nagano‐Shoji, Shosei Kubo, Y. Kawamura, Ayako Yoshida, Hisashi Kawasaki, Makoto Nishiyama, Minoru Yoshida, Saori Kosono
Software Mentions: 4
Published: almost 9 years ago

10.1107/S2052252517008557

Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
Cited by: 22
Author(s): Keitaro Yamashita, N. Kuwabara, Takanori Nakane, Taichi Murai, Eiichi Mizohata, Michihiro Sugahara, Dongqing Pan, Tetsuya Masuda, Mamoru Suzuki, Tomomi Satō, Atsushi Kodan, Tomohiro Yamaguchi, Eriko Nango, Tomoyuki Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Hiroshi Manya, Tamao Endo, Ryuichi Kato, Toshiya Senda, Hiroaki Katô, So Iwata, Hideo Ago, Masaki Yamamoto, Fumiaki Yumoto, Toru Nakatsu
Software Mentions: 4
Published: over 7 years ago

10.1074/jbc.RA118.004767

Two distinct conformations of factor H regulate discrete complement-binding functions in the fluid phase and at cell surfaces
Cited by: 9
Author(s): Amy J. Osborne, Ruodan Nan, Arthur I. Miller, Jayesh S. Bhatt, Jayesh Gor, Stephen J. Perkins
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms19092483

IDP–CRF: Intrinsically Disordered Protein/Region Identification Based on Conditional Random Fields
Cited by: 18
Author(s): Yumeng Liu, Xiaolong Wang, Bin Liu
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.0030058

Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
Cited by: 84
Author(s): Oliver Sander, Tobias Sing, Iris E. Sommer, Andrew Low, Peter K. Cheung, P. Richard Harrigan, Thomas Lengauer, Francisco S. Domingues
Software Mentions: 4
Published: over 17 years ago

10.1371/journal.pcbi.1008936

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?
Cited by: 15
Author(s): Jon Kapla, Ismael Rodríguez‐Espigares, Flavio Ballante, Jana Selent, Jens Carlsson
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pcbi.1003750

A Real-Time All-Atom Structural Search Engine for Proteins
Cited by: 10
Author(s): Gabriel González, Brett T. Hannigan, William F. DeGrado
Software Mentions: 4
Published: over 10 years ago

10.1007/s10295-019-02189-z

Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases
Cited by: 6
Author(s): Jesus F. Barajas, R.P. McAndrew, Mitchell G. Thompson, Tyler W. H. Backman, Bo Pang, Tristan de Rond, J.H. Pereira, Veronica T. Benites, Héctor García Martín, Edward E. K. Baidoo, Nathan J. Hillson, Paul D. Adams, Jay D. Keasling
Software Mentions: 4
Published: over 5 years ago

10.1101/2021.03.17.435863

Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies
Cited by: 31
Author(s): Allison J Greaney, Tyler N Starr, Christopher O. Barnes, Yiska Weisblum, Fabian Schmidt, Marina Caskey, Christian Gaebler, Alice Cho, Marianna Agudelo, Shlomo Finkin, Zijun Wang, Daniel Poston, Frauke Muecksch, Théodora Hatziioannou, Paul D. Bieniasz, Davide F. Robbiani, Michel C. Nussenzweig, Pamela J. Björkman, Jesse D. Bloom
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pcbi.1008061

Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds
Cited by: 16
Author(s): Brian Coventry, David Baker
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-52537-3

Structural characterization of the RH1-LZI tandem of JIP3/4 highlights RH1 domains as a cytoskeletal motor-binding motif
Cited by: 19
Author(s): Fernando Vilela, Christophe Velours, Mélanie Chenon, Magali Aumont-Niçaise, Valérie Campanacci, Aurélien Thureau, Olena Pylypenko, Jessica Andréani, P. Llinas, J. Menetrey
Software Mentions: 4
Published: about 5 years ago

10.1186/s43141-021-00120-7

Molecular docking studies of some selected gallic acid derivatives against five non-structural proteins of novel coronavirus
Cited by: 26
Author(s): Haruna Isiyaku Umar, Bushra Siraj, Adeola Ajayi, Tajudeen O. Jimoh, Prosper Obed Chukwuemeka
Software Mentions: 4
Published: almost 4 years ago

10.3389/fphar.2020.00753

Leishmanicidal Potential of Hardwickiic Acid Isolated From Croton sylvaticus
Cited by: 16
Author(s): Justice Afrifa Crentsil, Lauve Rachel Tchokouaha Yamthé, Barbara Anibea, Emmanuel Broni, Samuel K. Kwofie, John Tetteh, Dorcas Osei‐Safo
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-55199-3

Evaluation of binding and inhibition mechanism of dietary phytochemicals with sphingosine kinase 1: Towards targeted anticancer therapy
Cited by: 51
Author(s): Preeti Gupta, Taj Mohammad, Rashmi Dahiya, Sonam Roy, Omar M. Noman, Mohamed F. Alajmi, Afzal Hussain, Md. Imtaiyaz Hassan
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-019-54935-z

Identification of potential chemosignals in the European water vole Arvicola terrestris
Cited by: 8
Author(s): Patricia Nagnan‐Le Meillour, Amandine Descamps, Chrystelle Le Danvic, Maurane Grandmougin, Jean‐Michel Saliou, Christophe Klopp, Marine Milhes, Coralie Bompard, Didier Chesneau, Kévin Poissenot, Matthieu Keller
Software Mentions: 4
Published: almost 5 years ago

10.1128/mBio.01408-18

Heterosubtypic Protections against Human-Infecting Avian Influenza Viruses Correlate to Biased Cross-T-Cell Responses
Cited by: 23
Author(s): Min Zhao, Kefang Liu, Jiejian Luo, Shuguang Tan, Chuansong Quan, Shuijun Zhang, Yan Chai, Jianxun Qi, Yan Li, Yang Bi, Haixia Xiao, Gary Wong, Jianfang Zhou, Taijiao Jiang, Wenjun Liu, Hongjie Yu, Jinghua Yan, Yingxia Liu, Yuelong Shu, Guizhen Wu, Aiping Wu, George F. Gao, William J. Liu
Software Mentions: 4
Published: about 6 years ago

10.1126/sciadv.aax8286

Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity
Cited by: 53
Author(s): Ni Tien, Fang Jiao, Xiulian Yu, Saša Aden, Lucy Ginger, Sophie I. Williams, Fangfang Bai, Vojtěch Pražák, Dimple Karia, Phillip J. Stansfeld, Peijun Zhang, George P. Munson, Gregor Anderluh, Simon Scheuring, R.J.C. Gilbert
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13062-020-00267-2

AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4
Cited by: 87
Author(s): Mario S. Valdés-Tresanco, Mario E. Valdés‐Tresanco, Pedro A. Valiente, Ernesto Moreno
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0092721

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners
Cited by: 134
Author(s): Carlo Baldassi, Marco Zamparo, Christoph Feinauer, Andrea Procaccini, Riccardo Zecchina, Martin Weigt, Andrea Pagnani
Software Mentions: 4
Published: over 10 years ago

10.3389/fgene.2021.608936

Whole Genome Level Analysis of the Wnt and DIX Gene Families in Mice and Their Coordination Relationship in Regulating Cardiac Hypertrophy
Cited by: 6
Author(s): Zhongchao Gai, Yujiao Wang, Lü Tian, Guoli Gong, Jieqiong Zhao
Software Mentions: 4
Published: over 3 years ago

10.1155/2020/8886914

An Integrative Analysis Reveals the Potential Mechanism between Herbal Medicine Yinchen and Immunoregulation in Hepatocellular Carcinoma
Cited by: 3
Author(s): Zhuomao Mo, Zhirui Cao, Ling Yu, Yongdan Wang, Pan Li, You-Wu Lin, Shijun Zhang
Software Mentions: 4
Published: almost 4 years ago

10.1038/s42003-020-01419-w

Distortion of the bilayer and dynamics of the BAM complex in lipid nanodiscs
Cited by: 27
Author(s): M.G. Iadanza, Bob Schiffrin, Paul White, Matthew Watson, Jim E. Horne, A.J. Higgins, Antonio N. Calabrese, David J. Brockwell, Roman Tůma, Antreas C. Kalli, Sheena E. Radford, Neil A. Ranson
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.cell.2019.10.010

Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors
Cited by: 143
Author(s): Simon R. Foster, Alexander S. Hauser, Line Vedel, Ryan T. Strachan, Xi Ping Huang, Ariana C. Gavin, Sushrut D. Shah, Ajay P. Nayak, Linda M. Haugaard‐Kedström, Raymond B. Penn, Bryan L. Roth, Hans Bräuner‐Osborne, David E. Gloriam
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2021.665080

Bioinformatics, Molecular Docking and Experiments In Vitro Analyze the Prognostic Value of CXC Chemokines in Breast Cancer
Cited by: 14
Author(s): Fei Wang, Chong Yuan, Wu H, Bo Liu, Yong Yang
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0231714

Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software application
Cited by: 0
Author(s): Kai Pua, Daisuke Yuhara, Sho Ayuba, Kenji Yasuoka
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0225368

Computational analysis of functional single nucleotide polymorphisms associated with SLC26A4 gene
Cited by: 18
Author(s): Mirza Jawad ul Hasnain, Muhammad Shoaib, Salman Qadri, Bakhtawar Afzal, Tehreem Anwar, Syed Hassan Abbas, Amina Sarwar, Hafiz Muhammad Talha Malik, Muhammad Tariq Pervez
Software Mentions: 4
Published: almost 5 years ago

10.1093/database/baab013

MENSAdb: a thorough structural analysis of membrane protein dimers
Cited by: 1
Author(s): Pedro Matos-Filipe, António Preto, Panagiotis I. Koukos, Joana Mourão, Alexandre M. J. J. Bonvin, Irina S. Moreira
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12977-015-0148-6

An integrated map of HIV genome-wide variation from a population perspective
Cited by: 83
Author(s): Guangdi Li, Supinya Piampongsant, Nuno Rodrigues Faria, Arnout Voet, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Philippe Lemey, Anne‐Mieke Vandamme, Kristof Theys
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0074165

Spatiotemporal Dynamics and Epistatic Interaction Sites in Dengue Virus Type 1: A Comprehensive Sequence-Based Analysis
Cited by: 12
Author(s): Pei‐Yu Chu, Guan-Ming Ke, Po-Chih Chen, Li‐Teh Liu, Yen-Chun Tsai, Jih‐Jin Tsai
Software Mentions: 4
Published: about 11 years ago

10.3390/ijms22126345

Association between Predicted Effects of TP53 Missense Variants on Protein Conformation and Their Phenotypic Presentation as Li-Fraumeni Syndrome or Hereditary Breast Cancer
Cited by: 3
Author(s): Yaxuan Liu, Olga Axell, Tom Van Leeuwen, Robert Konrat, Pedram Kharaziha, Catharina Larsson, Anthony P. H. Wright, Svetlana Lagercrantz
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.36629

Structure of the CLC-1 chloride channel from Homo sapiens
Cited by: 80
Author(s): Eunyong Park, Roderick MacKinnon
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1005848

A Founder Mutation in VPS11 Causes an Autosomal Recessive Leukoencephalopathy Linked to Autophagic Defects
Cited by: 47
Author(s): Jinglan Zhang, Véronik Lachance, Adam D. Schaffner, Xianting Li, Anastasia Fedick, Lauren E. Kaye, Jun Liao, Jill A. Rosenfeld, Naomi Yachelevich, Mary Lynn Chu, Wendy G. Mitchell, Richard G. Boles, Ellen Moran, Mari Tokita, Elizabeth Gorman, Kaytee Bagley, Wei Zhang, Fan Xia, Magalie S. Leduc, Yaping Yang, Christine M. Eng, Lee Jun Wong, Raphael Schiffmann, George A. Diaz, Ruth Kornreich, Ryan Thummel, Melissa P. Wasserstein, Zhenyu Yue, Lisa Edelmann
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.65282

Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake
Cited by: 31
Author(s): Marc A. Schureck, Joseph E. Darling, Alan Merk, Jinfeng Shao, Geervani Daggupati, Prakash Srinivasan, Paul Dominic B. Olinares, Michael P. Rout, Brian T. Chait, Kurt Wollenberg, Sriram Subramaniam, Sanjay A. Desai
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-017-14959-9

Crystal Structure of Borrelia turicatae protein, BTA121, a differentially regulated gene in the tick-mammalian transmission cycle of relapsing fever spirochetes
Cited by: 2
Author(s): Zhipu Luo, Alan Kelleher, Rabih Darwiche, Elissa M. Hudspeth, Oluwatosin Kudirat Shittu, Aparna Krishnavajhala, Roger Schneiter, Job E. López, Oluwatoyin A. Asojo
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0242677

Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats
Cited by: 16
Author(s): Sara Sajko, Irina Grishkovskaya, Július Košťan, Melissa A. Graewert, Kim Setiawan, Linda Trübestein, Korbinian Niedermüller, Charlotte Gehin, Antonio Sponga, Martin Puchinger, Anne‐Claude Gavin, Thomas A. Leonard, D. I. Svergun, Terry Smith, Brooke Morriswood, Kristina Djinović-Carugo
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.66662

Homo-oligomerization of the human adenosine A2A receptor is driven by the intrinsically disordered C-terminus
Cited by: 9
Author(s): Khanh D. Nguyen, Michael Vigers, Eric Sefah, Susanna Seppälä, Jennifer Paige Hoover, Nicole S. Schonenbach, Blake Mertz, Michelle O’Malley, Songi Han
Software Mentions: 4
Published: over 3 years ago

10.1093/bioinformatics/bty347

Applying graph theory to protein structures: an Atlas of coiled coils
Cited by: 15
Author(s): Jack W. Heal, Gail J. Bartlett, Christopher W. Wood, Andrew Thomson, Derek N. Woolfson
Software Mentions: 4
Published: over 6 years ago

10.3389/fnmol.2019.00241

A TBR1-K228E Mutation Induces Tbr1 Upregulation, Altered Cortical Distribution of Interneurons, Increased Inhibitory Synaptic Transmission, and Autistic-Like Behavioral Deficits in Mice
Cited by: 21
Author(s): Chaehyun Yook, Kyungdeok Kim, Doyoun Kim, Hyojin Kang, Sun-Gyun Kim, Eunjoon Kim, Soo Young Kim
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2021.569295

Resveratrol Mediates the Apoptosis of Triple Negative Breast Cancer Cells by Reducing POLD1 Expression
Cited by: 18
Author(s): Zheng Liang, Yu Wan, Dandan Zhu, Mengxin Wang, Hong-Mian Jiang, Deng-Shing Huang, Lifeng Luo, Mao-jian Chen, Weiping Yang, Hong-Mian Li, Changyuan Wei
Software Mentions: 4
Published: over 3 years ago