cran: Modeler | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0153680

Viral Evolved Inhibition Mechanism of the RNA Dependent Protein Kinase PKR's Kinase Domain, a Structural Perspective
Cited by: 4
Author(s): K. Hari Krishna, Yallamandayya Vadlamudi, Mithilesh Kumar
Software Mentions: 9
Published: over 8 years ago

10.3389/fmicb.2020.594928

Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity
Cited by: 45
Author(s): Sunil K. Raghav, Arup Ghosh, Jyotirmayee Turuk, Satish Kumar, Atimukta Jha, Swati Madhulika, Manasi Priyadarshini, Viplov Kumar Biswas, P. Sushree Shyamli, Balveer Singh, Neha Singh, Deepika Singh, Ankita Datey, Kiran Avula, Shuchi Smita, Jyotsnamayee Sabat, Debdutta Bhattacharya, Jaya Singh Kshatri, Dileep Vasudevan, Amol Ratnakar Suryawanshi, Rupesh Dash, Shantibhusan Senapati, Tushar Kant Beuria, Roy Swain, Soma Chattopadhyay, Gulam Hussain Syed, Anshuman Dixit, Punit Prasad, Sanghamitra Pati, Ajay Parida
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pgen.1009492

A structural signature motif enlightens the origin and diversification of nuclear receptors
Cited by: 8
Author(s): Brice Beinsteiner, Gabriel V. Markov, Stéphane Erb, Yassmine Chebaro, A.G. McEwen, Sarah Cianférani, Vincent Laudet, Dino Moras, I. M. L. Billas
Software Mentions: 6
Published: over 3 years ago

10.3389/fcell.2021.628699

A New Zebrafish Model for Pseudoxanthoma Elasticum
Cited by: 2
Author(s): Dávid Czimer, Klaudia Porok, Dániel Csete, Zsolt Gyüre, Viktória Lavró, Krisztina Fülöp, Zelin Chen, Hella Gyergyák, Gábor Tusnády, Shawn M. Burgess, Attila Mócsai, András Váradi, Máté Varga
Software Mentions: 5
Published: over 3 years ago

10.1186/s13742-016-0134-5

Genome sequence of the olive tree, Olea europaea
Cited by: 158
Author(s): Fernando Cruz, Irene Julca, Jèssica Gómez-Garrido, Damian Loska, Marina Marcet‐Houben, Emilio Cano, Beatriz Galán, Leonor Frías, Paolo Ribeca, Sophia Derdak, Marta Gut, Manuel Sánchez-Fernández, José Luis Garcı́a, Pablo Vargas, Tyler Alioto, Toni Gabaldón
Software Mentions: 5
Published: over 8 years ago

10.3389/fchem.2020.00243

An Innovative Sequence-to-Structure-Based Approach to Drug Resistance Interpretation and Prediction: The Use of Molecular Interaction Fields to Detect HIV-1 Protease Binding-Site Dissimilarities
Cited by: 4
Author(s): Nuno G. Alves, Ana I. Mata, João Luís, Rui M. M. Brito, Carlos J. V. Simões
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-64270-3

PATH - Prediction of Amyloidogenicity by Threading and Machine Learning
Cited by: 17
Author(s): Jakub W Wojciechowski, Małgorzata Kotulska
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2017.01641

Enhanced Killing and Antibiofilm Activity of Encapsulated Cinnamaldehyde against Candida albicans
Cited by: 57
Author(s): Shahper N. Khan, Shakir Khan, Jawaid Iqbal, Rosina Khan, Asad Khan
Software Mentions: 4
Published: about 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

10.1002/humu.23277

MiSynPat: An integrated knowledge base linking clinical, genetic, and structural data for disease-causing mutations in human mitochondrial aminoacyl-tRNA synthetases
Cited by: 34
Author(s): Luc Moulinier, Raymond Ripp, Gaston Castillo, Olivier Poch, Marie Sissler
Software Mentions: 4
Published: over 7 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

10.1016/j.cell.2017.05.029

SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs
Cited by: 162
Author(s): Ryu Suke Nozawa, Lora Boteva, Dinesh C. Soares, Catherine Naughton, Alison R. Dun, Adam Buckle, Bernard Ramsahoye, Peter Christopher Bruton, Rebecca S. Saleeb, María Arnedo, Bill Hill, Rory R. Duncan, Sutherland K. Maciver, Nick Gilbert
Software Mentions: 4
Published: over 7 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

10.1074/jbc.RA119.007709

Structure and interactions of the archaeal motility repression module ArnA–ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius
Cited by: 15
Author(s): Lena Hoffmann, Katrin Anders, Lisa Franziska Bischof, Xing Ye, Julia Reimann, Sunia Khadouma, Trong Khoa Pham, Chris van der Does, Phillip C. Wright, Lars‐Oliver Essen, Sonja‐Verena Albers
Software Mentions: 3
Published: over 5 years ago

10.1016/j.bpj.2019.07.056

Proton Control of Transitions in an Amino Acid Transporter
Cited by: 10
Author(s): Zhiyi Wu, Irfan Alibay, Simon Newstead, Philip C. Biggin
Software Mentions: 3
Published: about 5 years ago

10.1074/jbc.M117.806893

Negatively charged residues in the first extracellular loop of the L-type CaV1.2 channel anchor the interaction with the CaVα2δ1 auxiliary subunit
Cited by: 16
Author(s): Benoîte Bourdin, Julie Briot, Marie-Philippe Tétreault, Rémy Sauvé, Lucie Parent
Software Mentions: 3
Published: about 7 years ago

10.1186/s12859-019-3097-6

Glycosylator: a Python framework for the rapid modeling of glycans
Cited by: 16
Author(s): Thomas Lemmin, Cinque Soto
Software Mentions: 3
Published: about 5 years ago

10.3389/fchem.2020.593497

A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis
Cited by: 7
Author(s): Ushashi Banerjee, Santhosh Sankar, Amit Singh, Nagasuma Chandra
Software Mentions: 3
Published: almost 4 years ago

10.1073/pnas.1911776116

Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection
Cited by: 14
Author(s): Fiona Whelan, Aleix Lafita, Samuel C. Griffiths, R.E.M. Cooper, J.L. Whittingham, J.P. Turkenburg, Iain W. Manfield, Alexander N. St John, Emanuele Paci, Alex Bateman, Jennifer R. Potts
Software Mentions: 3
Published: almost 5 years ago

10.3389/fnagi.2017.00064

Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease
Cited by: 9
Author(s): Francisco Altimiras, Barbara Uszczyńska-Ratajczak, Francisco Câmara, Anna Vlasova, Emilio Palumbo, Stephen Newhouse, Robert M. J. Deacon, Leandro A. E. Farias, Michael Hurley, David E. Loyola, Rodrigo A. Vásquez, Richard Dobson, Roderic Guigó, Patricia Cogram
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0038595

A Method to Find Longevity-Selected Positions in the Mammalian Proteome
Cited by: 10
Author(s): Jeremy R. Semeiks, Nick V. Grishin
Software Mentions: 3
Published: over 12 years ago

10.1242/jcs.183103

Chromatibody, a novel non-invasive molecular tool to explore and manipulate chromatin in living cells
Cited by: 32
Author(s): Denis Jullien, Julien Vignard, Yoann Fedor, Nicolas Béry, Aurélien Olichon, Michèle Crozatier, Marie Erard, Hervé Cassard, Bernard Ducommun, Bernard Salles, Gladys Mirey
Software Mentions: 3
Published: almost 9 years ago

10.1534/g3.119.400868

Origin and Evolution of Two Independently Duplicated Genes Encoding UDP- Glucose: Glycoprotein Glucosyltransferases in<i>Caenorhabditis</i>and Vertebrates
Cited by: 6
Author(s): Diego A. Caraballo, Lucila I Buzzi, Carlos P. Modenutti, Ana Acosta-Montalvo, Olga Castro, María Susana Rossi
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj.7514

The adipokinetic hormones and their cognate receptor from the desert locust, Schistocerca gregaria: solution structure of endogenous peptides and models of their binding to the receptor
Cited by: 11
Author(s): Graham E. Jackson, Elumalai Pavadai, Gerd GÄde, N.H. Andersen
Software Mentions: 3
Published: about 5 years ago

10.1128/JVI.00828-17

Cooperation between Strain-Specific and Broadly Neutralizing Responses Limited Viral Escape and Prolonged the Exposure of the Broadly Neutralizing Epitope
Cited by: 35
Author(s): Colin Anthony, Talita York, Valerie Bekker, David Matten, Philippe Selhorst, Roux-Cil. Ferreria, Nigel Garrett, Salim S. Abdool Karim, Lynn Morris, Natasha T. Wood, Penny L. Moore, Carolyn Williamson
Software Mentions: 3
Published: about 7 years ago

10.1074/jbc.M116.770271

Nanostructure and stability of calcitonin amyloids
Cited by: 14
Author(s): Federica Rigoldi, Pierangelo Metrangolo, Alberto Redaelli, Alfonso Gautieri
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pntd.0004710

Cholesterol Corrects Altered Conformation of MHC-II Protein in Leishmania donovani Infected Macrophages: Implication in Therapy
Cited by: 22
Author(s): Koushik Roy, Sapan Mandloi, Saikat Chakrabarti, Syamal Roy
Software Mentions: 3
Published: over 8 years ago

10.1016/j.cell.2020.10.004

SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses
Cited by: 394
Author(s): Abhik Banerjee, Mario R. Blanco, Emily A. Bruce, Drew D. Honson, Linlin M. Chen, Amy Chow, Prashant Bhat, Noah Ollikainen, Sofia A. Quinodoz, Colin Loney, Jasmine Thai, Zachary D. Miller, Aaron E. Lin, Madaline M Schmidt, Douglas G. Stewart, Daniel Goldfarb, Giuditta De Lorenzo, Suzannah J. Rihn, R.M. Voorhees, Jason Botten, Devdoot Majumdar, Mitchell Guttman
Software Mentions: 3
Published: about 4 years ago

10.1021/acs.inorgchem.0c02971

Rationalizing the Decavanadate(V) and Oxidovanadium(IV) Binding to G-Actin and the Competition with Decaniobate(V) and ATP
Cited by: 26
Author(s): Giuseppe Sciortino, Manuel Aureliano, Eugenio Garribba
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1003115

Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus
Cited by: 69
Author(s): Annalisa Nuccitelli, C. Daniela Rinaudo, Barbara Brogioni, Roberta Cozzi, Mario Ferrer-Navarro, Daniel Yero, John L. Telford, Guido Grandi, Xavier Daura, Martin Zacharias, Domenico Maione
Software Mentions: 3
Published: over 11 years ago

10.1016/j.bpj.2018.03.040

Evaluating Anti-CD32b F(ab) Conformation Using Molecular Dynamics and Small-Angle X-Ray Scattering
Cited by: 3
Author(s): Emma J. Sutton, Richard T. Bradshaw, Christian M. Orr, Björn Frendéus, Gunilla Larsson, Ingrid Teige, Mark S. Cragg, Ivo Tews, Jonathan W. Essex
Software Mentions: 3
Published: over 6 years ago

10.1016/j.cell.2018.11.025

The Molecular Mechanism of Transport by the Mitochondrial ADP/ATP Carrier
Cited by: 206
Author(s): Jonathan J. Ruprecht, Martin King, Thomas Zögg, Antoniya A. Aleksandrova, Els Pardon, Paul G. Crichton, Jan Steyaert, Edmund R. S. Kunji
Software Mentions: 3
Published: almost 6 years ago

10.1038/srep38564

Structure and dynamics of a constitutively active neurotensin receptor
Cited by: 55
Author(s): Brian E. Krumm, Sangbae Lee, Supriyo Bhattacharya, Istvan Botos, Courtney F. White, Haijuan Du, Nagarajan Vaidehi, Reinhard Grisshammer
Software Mentions: 3
Published: almost 8 years ago

10.1016/j.str.2013.10.013

Structure and Self-Assembly of the Calcium Binding Matrix Protein of Human Metapneumovirus
Cited by: 45
Author(s): C. Leyrat, Max Renner, K. Harlos, Juha T. Huiskonen, Jonathan M. Grimes
Software Mentions: 3
Published: almost 11 years ago

10.1093/gigascience/giab066

A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.
Cited by: 6
Author(s): Aundrea K. Westfall, Rory S. Telemeco, Mariana B. Grizante, Damien S. Waits, Amanda D. Clark, Dasia Y. Simpson, Randy L. Klabacka, Alexis Sullivan, George H. Perry, Michael W. Sears, Christian L. Cox, Robert M. Cox, Matthew E. Gifford, Henry B. John‐Alder, Tracy Langkilde, Michael J. Angilletta, Adam D. Leaché, Marc Tollis, Kenro Kusumi, Tonia S. Schwartz
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2021.647565

Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting
Cited by: 6
Author(s): Meshack O Juma, Arun Sankaradoss, Redcliff Ndombi, Patrick Mwaura, Tina Damodar, Junaid Nazir, Awadhesh Pandit, Rupsy Khurana, Moses Masika, Ruth Chirchir, John Gachie, Sudhir Krishna, Ramanathan Sowdhamini, Omu Anzala, Iyer Meenakshi
Software Mentions: 3
Published: over 3 years ago

10.3389/fmolb.2020.00040

Computational Investigation of Voltage-Gated Sodium Channel β3 Subunit Dynamics
Cited by: 4
Author(s): William G. Glass, Anna L. Duncan, Philip C. Biggin
Software Mentions: 3
Published: over 4 years ago

10.1074/jbc.M117.809657

Prodomain–growth factor swapping in the structure of pro-TGF-β1
Cited by: 29
Author(s): Bo Zhao, Shutong Xu, Xiao Dong, Chafen Lu, Timothy A. Springer
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12870-021-02858-1

The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality
Cited by: 25
Author(s): I. S. E. Bally, Aureliano Bombarely, Alan H. Chambers, Yuval Cohen, Natalie Dillon, David J. Innes, María A. Islas-Osuna, David N. Kuhn, Lukas A. Mueller, Ron Ophir, Aditi Rambani, Amir Sherman, Haidong Yan
Software Mentions: 2
Published: over 3 years ago

10.1074/jbc.RA118.002792

Cell surface expression of homomeric GABAA receptors depends on single residues in subunit transmembrane domains
Cited by: 14
Author(s): Swarnali Ahmed Hannan, Trevor G. Smart
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pbio.2005821

Genome-wide functional analyses of plant coiled–coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity
Cited by: 48
Author(s): Tadeusz Wróblewski, Laurentiu N. Spiridon, Eliza C. Martin, Andrei-José Petrescu, Keri Cavanaugh, María José Truco, Haiping Xu, Dariusz Gozdowski, Krzysztof Pawłowski, Richard W. Michelmore, Frank L. W. Takken
Software Mentions: 2
Published: almost 6 years ago

10.1074/jbc.M116.758300

Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry
Cited by: 28
Author(s): Kaveesha J. Wijesinghe, Sarah Urata, Nisha Bhattarai, Edgar E. Kooijman, Bernard S. Gerstman, Prem P. Chapagain, Sheng Li, Robert V. Stahelin
Software Mentions: 2
Published: over 7 years ago

10.1074/jbc.M117.779496

Genetically encoded photocross-linkers determine the biological binding site of exendin-4 peptide in the N-terminal domain of the intact human glucagon-like peptide-1 receptor (GLP-1R)
Cited by: 43
Author(s): Cassandra Koole, Christopher A. Reynolds, Juan Carlos Mobarec, Caroline A. Hick, Patrick M. Sexton, Thomas P. Sakmar
Software Mentions: 2
Published: over 7 years ago

10.1074/jbc.M115.684142

Unique Role of the WD-40 Repeat Protein 5 (WDR5) Subunit within the Mixed Lineage Leukemia 3 (MLL3) Histone Methyltransferase Complex
Cited by: 21
Author(s): Stephen A. Shinsky, Michael S. Cosgrove
Software Mentions: 2
Published: about 9 years ago

10.1074/jbc.M114.630681

Analysis of Human Dopamine D3 Receptor Quaternary Structure
Cited by: 23
Author(s): Sara Marsango, Gianluigi Caltabiano, Chantévy Pou, María José Varela Liste, Graeme Milligan
Software Mentions: 2
Published: over 9 years ago

10.1074/jbc.M115.685222

The Evolutionarily Conserved Tre2/Bub2/Cdc16 (TBC), Lysin Motif (LysM), Domain Catalytic (TLDc) Domain Is Neuroprotective against Oxidative Stress
Cited by: 44
Author(s): Mattéa J. Finelli, Luis Sánchez‐Pulido, Kevin X. Liu, Kay E. Davies, Peter L. Oliver
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.immuni.2018.10.015

Inference of the HIV-1 VRC01 Antibody Lineage Unmutated Common Ancestor Reveals Alternative Pathways to Overcome a Key Glycan Barrier
Cited by: 59
Author(s): Mattia Bonsignori, Eric Scott, Kevin Wiehe, David Easterhoff, S. Munir Alam, Kwan‐Ki Hwang, Melissa Cooper, Shi-Mao Xia, Ruijun Zhang, David C. Montefiori, Rory Henderson, Xin Nie, Garnett Kelsoe, M. Anthony Moody, Xuejun Chen, Michael Joyce, Peter D. Kwong, Mark Connors, John R. Mascola, Andrew T. McGuire, Leonidas Stamatatos, Max Medina-Ramírez, Rogier W. Sanders, Kevin O. Saunders, Thomas B. Kepler, Barton F. Haynes
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0115409

Characterization of M. tuberculosis SerB2, an Essential HAD-Family Phosphatase, Reveals Novel Properties
Cited by: 12
Author(s): Gaya P. Yadav, Sonal Shree, Ruchi Maurya, Niyati Rai, Diwakar Singh, Kirti Srivastava, Ravishankar Ramachandran
Software Mentions: 2
Published: almost 10 years ago

10.3390/biom9100633

Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations
Cited by: 20
Author(s): Jure Borišek, Andrea Saltalamacchia, Anna Gallì, Giulia Palermo, Elisabetta Molteni, Luca Malcovati, Alessandra Magistrato
Software Mentions: 2
Published: about 5 years ago

10.3390/antiox10060950

Implications of Oxidative Stress in Glioblastoma Multiforme Following Treatment with Purine Derivatives
Cited by: 11
Author(s): Marta Orlicka-Płocka, Agnieszka Fedoruk-Wyszomirska, Dorota Gurda, Paweł Pawelczak, Patrycja Krawczyk, Małgorzata Giel-Pietraszuk, Grzegorz Framski, Tomasz Ostrowski, Eliza Wyszko
Software Mentions: 2
Published: over 3 years ago

10.3390/biom10020231

A Thermolabile Phospholipase B from Talaromyces marneffei GD-0079: Biochemical Characterization and Structure Dynamics Study
Cited by: 16
Author(s): Rabia Durrani, Faez Iqbal Khan, Shahid Ali, Yonghua Wang, Bo Yang
Software Mentions: 2
Published: almost 5 years ago

10.1074/jbc.M114.561787

Structural Insights into the Activation of the RhoA GTPase by the Lymphoid Blast Crisis (Lbc) Oncoprotein
Cited by: 9
Author(s): Marc Lenoir, Masaaki Sugawara, Jaswant Kaur, Linda Ball, Michael Overduin
Software Mentions: 2
Published: over 10 years ago

10.1186/s12866-021-02244-9

Structural insights into acyl-ACP selective recognition by the Aeromonas hydrophila AHL synthase AhyI
Cited by: 0
Author(s): Lan Jin, Jingjiao Bao, Yu Chen, Wenge Yang, Wenyi Du
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0054630

Prediction of Structure of Human WNT-CRD (FZD) Complex for Computational Drug Repurposing
Cited by: 7
Author(s): Qurrat Ul Ain, Umair Seemab, Sajid Rashid, Muhammad Sulaman Nawaz, Mohammad Amjad Kamal
Software Mentions: 2
Published: almost 12 years ago

10.3390/molecules24101951

Computational Screening and Analysis of Lung Cancer Related Non-Synonymous Single Nucleotide Polymorphisms on the Human Kirsten Rat Sarcoma Gene
Cited by: 27
Author(s): Qiankun Wang, Aamir Mehmood, Heng Wang, Qin Xu, Yi Xiong, Dong‐Qing Wei
Software Mentions: 2
Published: over 5 years ago

10.1038/s41438-021-00467-5

Functional conservation of the grapevine candidate gene INNER NO OUTER for ovule development and seed formation
Cited by: 12
Author(s): Valentina di Rienzo, Zahra Imanifard, Isabella Mascio, Charles S. Gasser, Debra J. Skinner, Ciro Leonardo Pierri, Martina Marini, Valentina Fanelli, Wilma Sabetta, Cinzia Montemurro, Diana Bellin
Software Mentions: 2
Published: almost 4 years ago

10.1074/jbc.M114.557900

Engagement of Nucleotide-binding Oligomerization Domain-containing Protein 1 (NOD1) by Receptor-interacting Protein 2 (RIP2) Is Insufficient for Signal Transduction
Cited by: 24
Author(s): Sophie Mayle, Joseph P. Boyle, Eiki Sekine, Birte Zurek, Thomas A. Kufer, Tom P. Monie
Software Mentions: 2
Published: over 10 years ago

10.1074/jbc.M116.729806

Composition and Activity of the Non-canonical Gram-positive SecY2 Complex
Cited by: 8
Author(s): Mikaila Bandara, Robin A. Corey, Remy Martin, J. Mark Skehel, Ariel Blocker, Howard F. Jenkinson, Ian Collinson
Software Mentions: 2
Published: about 8 years ago

10.3389/fphar.2015.00017

Optimization of the cyclotide framework to improve cell penetration properties
Cited by: 26
Author(s): Yen‐Hua Huang, Stephanie Chaousis, Olivier Cheneval, David J. Craik, Sónia Troeira Henriques
Software Mentions: 2
Published: almost 10 years ago

10.1016/j.bpj.2018.12.014

Influence of Transmembrane Helix Mutations on Cytochrome P450-Membrane Interactions and Function
Cited by: 20
Author(s): Ghulam Mustafa, Prajwal P. Nandekar, Tyler Camp, Neil J. Bruce, Michael C. Gregory, Stephen G. Sligar, Rebecca C. Wade
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmolb.2020.00029

Molecular Simulation of Oncostatin M and Receptor (OSM–OSMR) Interaction as a Potential Therapeutic Target for Inflammatory Bowel Disease
Cited by: 19
Author(s): Qingqing Du, Qian Yan, Weiwei Xue
Software Mentions: 2
Published: over 4 years ago

10.1016/j.bpj.2015.02.013

Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation
Cited by: 71
Author(s): Sonya M. Hanson, Simon Newstead, Kenton J. Swartz, Mark S.P. Sansom
Software Mentions: 2
Published: over 9 years ago

10.3389/fphys.2013.00320

The N-terminal cytoplasmic region of NCBE displays features of an intrinsic disordered structure and represents a novel target for specific drug screening
Cited by: 3
Author(s): Kaare Bjerregaard-Andersen, Harmonie Perdreau‐Dahl, Hanne Guldsten, Jeppe Prætorius, Jan K. Jensen, J. Preben Morth
Software Mentions: 2
Published: almost 12 years ago

10.3390/molecules24112075

In Silico Identification of Potential Inhibitor Against a Fungal Histone Deacetylase, RPD3 from Magnaporthe Oryzae
Cited by: 4
Author(s): Gnanendra Shanmugam, Taehyeon Kim, Junhyun Jeon
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0039850

Structural Modeling and DNA Binding Autoinhibition Analysis of Ergp55, a Critical Transcription Factor in Prostate Cancer
Cited by: 3
Author(s): S.P. Gangwar, Sharmistha Dey, Ajay K. Saxena
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0181665

Novel fine-scale aerial mapping approach quantifies grassland weed cover dynamics and response to management
Cited by: 5
Author(s): Carolyn M. Malmström, H. Scott Butterfield, Laura Planck, Christopher Long, Valerie T. Eviner
Software Mentions: 2
Published: about 7 years ago

10.6026/97320630013122

Linear epitope prediction in HPV type 16 E7 antigen and their docked interaction with human TMEM 50A structural model
Cited by: 2
Author(s): Upasna Srivastava, Satendra Singh, Budhayash Gautam, Pramod Kumar Yadav, Madhu Yadav, George Thomas, Gurmit Singh
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2020.579521

α-Galactosidase and Sucrose-Kinase Relationships in a Bi-functional AgaSK Enzyme Produced by the Human Gut Symbiont Ruminococcus gnavus E1
Cited by: 7
Author(s): Mickaël Lafond, Alexandra Tauzin, Laëtitia Bruel, Élisabeth Laville, Vincent Lombard, Jérémy Esque, Isabelle André, Nicolás Vidal, Frédérique Pompeo, Nathalie Quinson, Josette Perrier, Michel Fons, Gabrielle Potocki-Véronèse, Thierry Giardina
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2020.560667

Non-adaptive Evolution of Trimeric Autotransporters in Brucellaceae
Cited by: 3
Author(s): Mohammad Reza Rahbar, Mahboubeh Zarei, Abolfazl Jahangiri, Saeed Khalili, Navid Nezafat, Manica Negahdaripour, Yaser Fattahian, Amir Savardashtaki, Younes Ghasemi
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2021.631297

The Archaeal Elongation Factor EF-2 Induces the Release of aIF6 From 50S Ribosomal Subunit
Cited by: 4
Author(s): Giada Lo Gullo, Maria Luisa De Santis, Alessandro Paiardini, Serena Rosignoli, Alice Romagnoli, Anna La Teana, Paola Londei, Dario Benelli
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2018.03102

Plumbagin Ameliorates Collagen-Induced Arthritis by Regulating Treg/Th17 Cell Imbalances and Suppressing Osteoclastogenesis
Cited by: 12
Author(s): Tingyu Wang, Han Qiao, Zanjing Zhai, Jun Zhang, Jianwei Tu, Xinyi Zheng, Nan Qian, Hong Zhou, Eryi Lu, Tingting Tang
Software Mentions: 2
Published: almost 6 years ago

10.1093/molbev/msz060

Emergence of a Thrombospondin Superfamily at the Origin of Metazoans
Cited by: 5
Author(s): Deborah K. Shoemark, Berenice Ziegler, Hiroshi Watanabe, Jennifer Strompen, Richard P. Tucker, Suat Özbek, Josephine C. Adams
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.720313

A Functional Variant of CXCL16 Is Associated With Predisposition to Sepsis and MODS in Trauma Patients: Genetic Association Studies
Cited by: 2
Author(s): Jianhui Sun, Huacai Zhang, Di Liu, Li Cui, Qiang Wang, Lebin Gan, Dalin Wen, Jun Wang, Juan Du, Hong Huang, Anqiang Zhang, Jin Deng, Jianxin Jiang, Ling Zeng
Software Mentions: 2
Published: about 3 years ago

10.3389/fimmu.2018.02213

Immuno-informatics Analysis to Identify Novel Vaccine Candidates and Design of a Multi-Epitope Based Vaccine Candidate Against Theileria parasites
Cited by: 26
Author(s): Prajna Parimita Kar, Anand Srivastava
Software Mentions: 2
Published: about 6 years ago

10.1038/s41435-020-00120-6

Evolutionary and structural analysis of SARS-CoV-2 specific evasion of host immunity
Cited by: 35
Author(s): Irfan Hussain, Nashaiman Pervaiz, Abbas Khan, Shoaib Saleem, Huma Shireen, Dong‐Qing Wei, Viviane Labrie, Yīmíng Bào, Amir Ali Abbasi
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0089913

Using Stochastic Gradient Boosting to Infer Stopover Habitat Selection and Distribution of Hooded Cranes Grus monacha during Spring Migration in Lindian, Northeast China
Cited by: 13
Author(s): Tianlong Cai, Falk Huettmann, Yumin Guo
Software Mentions: 2
Published: over 10 years ago

10.1186/1752-0509-8-70

NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules
Cited by: 14
Author(s): Hsueh-Chien Cheng, B. Angermann, Fengkai Zhang, Martin Meier‐Schellersheim
Software Mentions: 2
Published: over 10 years ago

10.3389/fcell.2021.730095

Connective Tissue Growth Factor From Periosteal Tartrate Acid Phosphatase-Positive Monocytes Direct Skeletal Stem Cell Renewal and Fate During Bone Healing
Cited by: 1
Author(s): Yun Bai, Tao Yu, Jiaying Deng, Ying Yang, Jiulin Tan, Qijie Dai, Zehua Zhang, Shiwu Dong, Jiake Xu
Software Mentions: 2
Published: about 3 years ago

10.3389/fchem.2017.00100

Discovering Novel Alternaria solani Succinate Dehydrogenase Inhibitors by in Silico Modeling and Virtual Screening Strategies to Combat Early Blight
Cited by: 13
Author(s): Sehrish Iftikhar, Ahmad Ali Shahid, Sobia Ahsan Halim, Pieter J. Wolters, Vivianne G. A. A. Vleeshouwers, Ajmal Khan, Ahmed Al‐Harrasi, Shahbaz Ahmad
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2164-8-388

EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome
Cited by: 6
Author(s): Françoise Thibaud‐Nissen, Matthew A. Campbell, John Hamilton, Wei Zhu, C. Robin Buell
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0188037

Comparison of histone-like HU protein DNA-binding properties and HU/IHF protein sequence alignment
Cited by: 31
Author(s): Dmitri Kamashev, Yu. K. Agapova, С. М. Расторгуев, Anna A. Talyzina, K.М. Boyko, D.A. Korzhenevskiy, Anna V. Vlaskina, Р. Г. Василов, В. И. Тимофеев, Tatiana V. Rakitina
Software Mentions: 2
Published: about 7 years ago

10.1016/j.bbrep.2021.100998

Effect of magnesium sulfate in oxidized lipid bilayers properties by using molecular dynamics
Cited by: 2
Author(s): Miguel Ángel Lorenzo Fernández, Reinaldo Marı́n, Fulgencio Proverbio, Fernando Ruette
Software Mentions: 2
Published: over 3 years ago

10.1074/mcp.M116.058016

Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions
Cited by: 85
Author(s): Kshitij Khatri, Joshua Klein, Mitchell R. White, Oliver C. Grant, Nancy Leymarie, Robert J. Woods, Kevan L. Hartshorn, Joseph Zaia
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0142606

Biochemical Analysis of CagE: A VirB4 Homologue of Helicobacter pylori Cag-T4SS
Cited by: 27
Author(s): Mohd Shariq, Navin Kumar, Rajesh Kumari, Amarjeet Kumar, Naidu Subbarao, Gauranga Mukhopadhyay
Software Mentions: 2
Published: about 9 years ago

10.3389/fbioe.2020.00532

On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective
Cited by: 17
Author(s): Konda Mani Saravanan, Haiping Zhang, Huiling Zhang, Wenhui Xi, Yanjie Wei
Software Mentions: 2
Published: over 4 years ago

10.6026/97320630013380

Insights from the protein-protein interaction network analysis of Mycobacterium tuberculosis toxinantitoxin systems
Cited by: 11
Author(s): Zoozeal Thakur, Renu Dharra, Vandana Saini, Ajit Kumar, Promod K Mehta
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0005031

Autocatalytic Activation of the Furin Zymogen Requires Removal of the Emerging Enzyme's N-Terminus from the Active Site
Cited by: 27
Author(s): Katarzyna Gawlik, Sergey A. Shiryaev, Wenhong Zhu, Khatereh Motamedchaboki, Roxane Desjardins, Robert Day, Albert G. Remacle, Boguslaw Stec, Alex Y. Strongin
Software Mentions: 2
Published: over 15 years ago

10.1186/s12900-014-0025-x

In vitro histone lysine methylation by NSD1, NSD2/MMSET/WHSC1 and NSD3/WHSC1L
Cited by: 33
Author(s): Masaki Morishita, Damiaan E. H. F. Mevius, Eric di Luccio
Software Mentions: 2
Published: almost 10 years ago

10.1016/j.dib.2017.10.045

Data for the homology modelling of the red pigment-concentrating hormone receptor (Dappu-RPCHR) of the crustacean Daphnia pulex , and docking of its cognate agonist (Dappu-RPCH)
Cited by: 2
Author(s): Graham E. Jackson, Elumalai Pavadai, Gerd GÄde, Zaheer Timol, Niels H. Andersen
Software Mentions: 2
Published: almost 7 years ago

10.3389/fbioe.2020.00642

A Broad Temperature Active Lipase Purified From a Psychrotrophic Bacterium of Sikkim Himalaya With Potential Application in Detergent Formulation
Cited by: 32
Author(s): Anil Kumar, Srijana Mukhia, Neeraj Kumar, Vishal Acharya, Sanjay Kumar, Rakshak Kumar
Software Mentions: 2
Published: over 4 years ago

10.1128/AEM.00449-17

Rational Engineering of a Cold-Adapted α-Amylase from the Antarctic Ciliate Euplotes focardii for Simultaneous Improvement of Thermostability and Catalytic Activity
Cited by: 31
Author(s): Guang Yang, Hua Yang, Matteo Mozzicafreddo, Patrizia Ballarini, Sandra Pucciarelli, Cristina Miceli
Software Mentions: 2
Published: over 7 years ago

10.3389/fmolb.2019.00147

Glucose-6-Phosphate Upregulates Txnip Expression by Interacting With MondoA
Cited by: 4
Author(s): Xueyun Zhang, Tao Fu, Qian He, Xiang Gao, Yan Luo
Software Mentions: 2
Published: almost 5 years ago

10.3389/fchem.2018.00437

Adaptive Steered Molecular Dynamics Combined With Protein Structure Networks Revealing the Mechanism of Y68I/G109P Mutations That Enhance the Catalytic Activity of D-psicose 3-Epimerase From Clostridium Bolteae
Cited by: 18
Author(s): Jianxun Zhu, Yang Li, Jinzhi Wang, Zeyang Yu, Ye Liu, Yi Tong, Wei Han
Software Mentions: 2
Published: about 6 years ago

10.3389/fphar.2016.00107

Cysteine Proteases: Modes of Activation and Future Prospects as Pharmacological Targets
Cited by: 168
Author(s): Sonia Verma, Rajnikant Dixit, Kailash C. Pandey
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0008311

Bi-Directional SIFT Predicts a Subset of Activating Mutations
Cited by: 34
Author(s): William Lee, Yan Zhang, Kiran Mukhyala, Robert A. Lazarus, Zemin Zhang
Software Mentions: 2
Published: almost 15 years ago

10.1038/s41419-020-2344-0

Deguelin suppresses non-small cell lung cancer by inhibiting EGFR signaling and promoting GSK3β/FBW7-mediated Mcl-1 destabilization
Cited by: 34
Author(s): Feng Gao, Xinfang Yu, Ming Li, Liqun Zhou, Wenbin Liu, Wei Li, Haidan Liu
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0256704

Identification and in-silico characterization of taxadien-5α-ol-O-acetyltransferase (TDAT) gene in Corylus avellana L.
Cited by: 1
Author(s): Mona Raeispour Shirazi, Sara Alsadat Rahpeyma, Sajad Rashidi Monfared, Jafar Zolala, Azadeh Lohrasbi‐Nejad
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0248479

Ayurveda botanicals in COVID-19 management: An in silico multi-target approach
Cited by: 48
Author(s): Swapnil Borse, M. P. Joshi, Akash Saggam, Vedika Bhat, Safal Walia, Aniket Marathe, Sneha R. Sagar, Preeti Chavan‐Gautam, Aboli Girme, Lal Hingorani, Girish Tillu
Software Mentions: 2
Published: over 3 years ago

10.1038/s41421-021-00278-x

Discovery of a cooperative mode of inhibiting RIPK1 kinase
Cited by: 11
Author(s): Huyan Meng, Guowei Wu, Xinsuo Zhao, Anhui Wang, Dekang Li, Yilun Tong, Teng Jin, Ye Cao, Bing Shan, Shichen Hu, Ying Liu, Lifeng Pan, Xiaoxu Tian, Ping Wu, Chao Peng, Junying Yuan, Guohui Li, Tan Li, Zhaoyin Wang, Ying Li
Software Mentions: 2
Published: over 3 years ago

10.1038/cddis.2016.255

Kinsenoside screening with a microfluidic chip attenuates gouty arthritis through inactivating NF-κB signaling in macrophages and protecting endothelial cells
Cited by: 33
Author(s): Han Qiao, Bing Wang, Dong Yin, Hua Li, Shihe Li, Yongri Zheng, Xiaozhe Han, Yugang Wang, Qing Fan, Shuo Yang, Tingting Tang
Software Mentions: 2
Published: about 8 years ago

Projects: cran: Modeler

Papers Mentioning Modeler 310