Ecosyste.ms: Papers

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

10.1186/s12864-018-4605-1

Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance
Cited by: 26
Author(s): Alison T. Isaacs, Henry Mawejje, Sean Tomlinson, Daniel J. Rigden, Martin J. Donnelly
Software Mentions: 3
Published: over 6 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 7 years ago

10.1128/mBio.03549-20

Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator
Cited by: 23
Author(s): Shruti Nagaraja, Maggi W. Cai, Jingjing Sun, Hugo Varet, Lotem Sarid, Meirav Trebicz-Geffen, Yana Shaulov, Mohit Mazumdar, Rachel Legendre, Jean‐Yves Coppée, Thomas J. Begley, Peter C. Dedon, S. Gourinath, Nancy Guillén, Yumiko Saito‐Nakano, Chikako Shimokawa, Hajime Hisaeda, Serge Ankri
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1008394

Structural and functional insights into a novel two-component endolysin encoded by a single gene in Enterococcus faecalis phage
Cited by: 21
Author(s): Biao Zhou, Xiangkai Zhen, Huan Zhou, Feiyang Zhao, Chao Fan, Vanja Perčulija, Yigang Tong, Zhiqiang Mi, Songying Ouyang
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.ppat.1003403

The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence
Cited by: 65
Author(s): Anne Marie Hansen, Raghothama Chaerkady, Jyoti Sharma, J. Javier Díaz-Mejía, Nidhi Tyagi, Santosh Renuse, Harrys K.C. Jacob, Sneha M. Pinto, Nandini A. Sahasrabuddhe, Min‐Sik Kim, Bernard Delanghe, Narayanaswamy Srinivasan, Andrew Emili, James B. Kaper, Akhilesh Pandey
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.ppat.1002085

The N-Terminus of the RNA Polymerase from Infectious Pancreatic Necrosis Virus Is the Determinant of Genome Attachment
Cited by: 34
Author(s): Stephen C. Graham, L. Peter Sarin, Mohammad W. Bahar, Robert A. Myers, David I. Stuart, Dennis H. Bamford, Jonathan M. Grimes
Software Mentions: 3
Published: over 13 years ago

10.1080/14756366.2021.1931862

Structure-based virtual screening of highly potent inhibitors of the nematode chitinase <i>Ce</i>Cht1
Cited by: 7
Author(s): Wei Chen, Qi Chen, Ashutosh Kumar, Xi Jiang, Kam Y. J. Zhang, Qing Yang
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.ppat.1002957

De novo GTP Biosynthesis Is Critical for Virulence of the Fungal Pathogen Cryptococcus neoformans
Cited by: 53
Author(s): Carl A. Morrow, Eugene Valkov, Anna Stamp, Eve W. L. Chow, I. Russel Lee, Ania Wronski, Simon J. Williams, Jennifer Hill, Julianne T. Djordjevic, Ulrike Kappler, Boštjan Kobe, James S. Fraser
Software Mentions: 3
Published: about 12 years ago

10.1126/sciadv.aaq0762

Structures of monomeric and oligomeric forms of the <i>Toxoplasma gondii</i> perforin-like protein 1
Cited by: 28
Author(s): Ni Tien, Sophie I. Williams, Saša Rezelj, Gregor Anderluh, K. Harlos, Phillip J. Stansfeld, Robert J.C. Gilbert
Software Mentions: 3
Published: over 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 5 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 8 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: over 6 years ago

10.1186/s12915-016-0311-0

Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation
Cited by: 18
Author(s): David S. Rabiger, Jennifer Taylor, Andrew Spriggs, Melanie L. Hand, Steven T. Henderson, Susan D. Johnson, Karsten Oelkers, Mária Hrmová, Keisuke Saito, Go Suzuki, Yasuhiko Mukai, Bernard J. Carroll, Anna M. Koltunow
Software Mentions: 3
Published: about 8 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: over 3 years ago

10.1016/j.jbc.2021.101061

A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase
Cited by: 7
Author(s): Emily Chen, Krystle Reiss, Dilip Shah, R Manjula, Brandon Allen, Eva Murphy, James W. Murphy, Víctor S. Batista, Vineet Bhandari, Elias Lolis, George P. Lisi
Software Mentions: 3
Published: about 3 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 3 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 5 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 9 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 4 years ago

10.1074/jbc.RA118.004469

Discovery of peptide ligands targeting a specific ubiquitin-like domain–binding site in the deubiquitinase USP11
Cited by: 24
Author(s): Anastasios Spiliotopoulos, Lia Blokpoel Ferreras, Ruth M Densham, Simon G. Caulton, Ben C. Maddison, Joanna R. Morris, James E. Dixon, Kevin C. Gough, Ingrid Dreveny
Software Mentions: 3
Published: almost 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 4 years ago

10.1074/jbc.M117.776476

Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab
Cited by: 57
Author(s): Anna M. Davies, Elizabeth G. Allan, Anthony H. Keeble, Jean Delgado, Benjamin P. Cossins, A.N. Mitropoulou, M.O.Y. Pang, Tom Ceska, Andrew J. Beavil, Graham Craggs, Marta Westwood, Alistair J. Henry, James M. McDonnell, Brian J. Sutton
Software Mentions: 3
Published: over 7 years ago

10.1074/jbc.M115.671586

Structure and Function of the Escherichia coli Tol-Pal Stator Protein TolR
Cited by: 30
Author(s): Justyna Aleksandra Wojdyla, Erin E. Cutts, Renata Kaminska, Grigorios Papadakos, Jonathan T. S. Hopper, Phillip J. Stansfeld, David Staunton, Carol V. Robinson, Colin Kleanthous
Software Mentions: 3
Published: about 9 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

10.1016/j.jbc.2021.100384

Bacillus subtilis YngB contributes to wall teichoic acid glucosylation and glycolipid formation during anaerobic growth
Cited by: 8
Author(s): Chih-Hung Wu, Jeanine Rismondo, Rhodri M. L. Morgan, Yang Shen, Martin J. Loessner, Gérald Larrouy-Maumus, Paul S. Freemont, Angelika Gründling
Software Mentions: 3
Published: almost 4 years ago

10.1534/g3.119.400224

Contraction of the ROS Scavenging Enzyme Glutathione<i>S</i>-Transferase Gene Family in Cetaceans
Cited by: 11
Author(s): Ran Tian, Inge Seim, Wenhua Ren, Shixia Xu
Software Mentions: 3
Published: over 5 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 5 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 4 years ago

10.3389/fpls.2016.01810

The Eucalyptus Tonoplast Intrinsic Protein (TIP) Gene Subfamily: Genomic Organization, Structural Features, and Expression Profiles
Cited by: 9
Author(s): Marcela Iara Rodrigues, Agnes Alessandra Sekijima Takeda, Juliana Pereira Bravo, Ivan de Godoy Maia
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2105-13-S14-S13

High-Throughput parallel blind Virtual Screening using BINDSURF
Cited by: 142
Author(s): Irene Sánchez-Linares, Horacio Pérez‐Sánchez, José M. Cecilia, José M. García
Software Mentions: 3
Published: about 12 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 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: over 7 years ago

10.1074/jbc.M114.621789

Complex Structure and Biochemical Characterization of the Staphylococcus aureus Cyclic Diadenylate Monophosphate (c-di-AMP)-binding Protein PstA, the Founding Member of a New Signal Transduction Protein Family
Cited by: 47
Author(s): Ivan Campeotto, Yong Everett Zhang, Miroslav Mladenov, Paul S. Freemont, Angelika Gründling
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.jbc.2021.100700

ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis
Cited by: 8
Author(s): Jitender Mehla, George W. Liechti, Randy M. Morgenstein, J. Harry Caufield, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Norman Goodacre, Mary R. Brockett, Neha Sakhawalkar, Mohan Babu, Rong Xiao, Gaetano T. Montelione, S.M. Vorobiev, T. den Blaauwen, J.F. Hunt, Peter Uetz
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0043245

A Bioinformatic Strategy for the Detection, Classification and Analysis of Bacterial Autotransporters
Cited by: 62
Author(s): Nemin Celik, Chaille T Webb, Denisse L. Leyton, Kathryn E. Holt, Eva Heinz, Rebecca J. Gorrell, Terry Kwok, Thomas Naderer, Richard A. Strugnell, Terence P. Speed, Rohan D. Teasdale, Vladimir A Likić, Trevor Lithgow
Software Mentions: 3
Published: over 12 years ago

10.1093/jxb/ery353

Homology modeling and<i>in vivo</i>functional 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: about 6 years ago

10.1371/journal.pone.0140934

Rubisco Activase Is Also a Multiple Responder to Abiotic Stresses in Rice
Cited by: 40
Author(s): Yue Chen, Xiaoman Wang, Li Zhou, Yi He, Dun Wang, Yanhua Qi, Dongxiang Jiang
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0082341

Targeting a Cross-Reactive Gly m 5 Soy Peptide as Responsible for Hypersensitivity Reactions in a Milk Allergy Mouse Model
Cited by: 21
Author(s): Renata Curciarello, Paola Lorena Smaldini, Ángela María Candreva, Vicente Ferreira González, Gustavo Parisi, Ana Cauerhff, Ivana Analía Barrios, Luis Enrique Bruno Blanch, Carlos A. Fossati, Silvana Petruccelli, Guillermo Horacio Docena
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0088229

Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts
Cited by: 29
Author(s): Dallas Thomas, Abdul G. Lone, L. Brent Selinger, Eduardo N. Taboada, Richard R. E. Uwiera, D. Wade Abbott, G. Douglas Inglis
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0097817

Exploring the Functional Residues in a Flavin-Binding Fluorescent Protein Using Deep Mutational Scanning
Cited by: 12
Author(s): HyeonSeok Shin, Yoobok Cho, Donghui Choe, Yu‐Jin Jeong, Suhyung Cho, Sun Chang Kim, Byung-Kwan Cho
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0150634

Computational Identification Raises a Riddle for Distribution of Putative NACHT NTPases in the Genome of Early Green Plants
Cited by: 4
Author(s): Preeti Arya, Vishal Acharya
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0217164

Three genetically distinct ferlaviruses have varying effects on infected corn snakes (Pantherophis guttatus)
Cited by: 7
Author(s): Michael Pees, Volker Schmidt, Tibor Papp, Ákos Gellért, Maha Diekan Abbas, J. Matthias Starck, Annkatrin Neul, Rachel E. Marschang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0029237

Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster
Cited by: 19
Author(s): Constância Flávia Junqueira Ayres, Pie Müller, Naomi Dyer, Craig S. Wilding, Daniel J. Rigden, Martin J. Donnelly
Software Mentions: 3
Published: almost 13 years ago

10.1186/1471-2105-9-352

Alignment of protein structures in the presence of domain motions
Cited by: 48
Author(s): Roberto Mosca, Barbara Brannetti, Thomas R. Schneider
Software Mentions: 3
Published: about 16 years ago

10.1186/1471-2105-10-153

Tableau-based protein substructure search using quadratic programming
Cited by: 11
Author(s): Alex Stivala, Anthony Wirth, Peter J. Stuckey
Software Mentions: 3
Published: over 15 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 6 years ago

10.1107/S0907444912001308

Towards automated crystallographic structure refinement with <i>phenix.refine</i>
Cited by: 4,334
Author(s): Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Nathaniel Echols, Jeffrey J. Headd, Nigel W. Moriarty, Marat Mustyakimov, Thomas C. Terwilliger, Alexandre Urzhumtsev, Peter H. Zwart, Paul D. Adams
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0035974

The Hepatitis E Virus Polyproline Region Is Involved in Viral Adaptation
Cited by: 74
Author(s): Michael A. Purdy, James Lara, Yury Khudyakov
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0078059

Perturbation Centrality and Turbine: A Novel Centrality Measure Obtained Using a Versatile Network Dynamics Tool
Cited by: 25
Author(s): Kristóf Z. Szalay, Péter Csermely
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0140359

Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein-Protein Interactions
Cited by: 20
Author(s): Andrea Bazzoli, Simon Kelow, John Karanicolas
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0172743

Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin
Cited by: 35
Author(s): Akshay Sridhar, Gregory A. Ross, Philip C. Biggin
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0165020

Genome-Wide Analysis, Classification, Evolution, and Expression Analysis of the Cytochrome P450 93 Family in Land Plants
Cited by: 32
Author(s): Hongwu Du, Feng Ran, Hongli Dong, Jing Wen, Jiana Li, Zhe Liang
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0156067

Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana
Cited by: 0
Author(s): Yuan Xie, Li Mei, Wenrui Chang
Software Mentions: 3
Published: over 8 years ago

10.1107/S1399004715005210

<i>In meso in situ</i> 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 9 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 3 years ago

10.1371/journal.pgen.1009215

Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae
Cited by: 12
Author(s): Joshua J. Black, Richa Sardana, Ezzeddine W. Elmir, Arlen Johnson
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1008140

A steady-state model of microbial acclimation to substrate limitation
Cited by: 13
Author(s): John R. Casey, Michael J. Follows
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1002708

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
Cited by: 908
Author(s): Eva Chovancová, Antonín Pavelka, Petr Beneš, Ondřej Strnad, Jan Brezovský, Barbora Kozlíková, Artur Góra, Vilém Šustr, Martin Klvaňa, Petr Medek, Lada Biedermannová, Jiří­ Sochor, Jiřı́ Damborský
Software Mentions: 3
Published: about 12 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: almost 8 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 9 years ago

10.1371/journal.pcbi.1003478

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor
Cited by: 69
Author(s): Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pcbi.1004805

Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications
Cited by: 73
Author(s): Vaclav Cvicek, William A. Goddard, Ravinder Abrol
Software Mentions: 3
Published: over 8 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 14 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 5 years ago

10.1371/journal.pcbi.1006722

Identifying individual risk rare variants using protein structure guided local tests (POINT)
Cited by: 8
Author(s): Rachel West, Wenbin Lu, Daniel M. Rotroff, Mélaine A. Kuenemann, Sheng Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger‐Reif, Denis Fourches, Jung Ying Tzeng
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0083496

Exploration of Virtual Candidates for Human HMG-CoA Reductase Inhibitors Using Pharmacophore Modeling and Molecular Dynamics Simulations
Cited by: 17
Author(s): Maeng-Hyun Son, Ayoung Baek, Sugunadevi Sakkiah, Chanin Park, John Strouboulis, Keun Woo Lee
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0236894

A chemical interpretation of protein electron density maps in the worldwide protein data bank
Cited by: 5
Author(s): Sen Yao, Hunter N. B. Moseley
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008964

The evolution and functional divergence of the histone H2B family in plants
Cited by: 42
Author(s): Dazong Jiang, Michael Borg, Zdravko J. Lorković, Sean A. Montgomery, Akihisa Osakabe, Ramesh Yelagandula, Elin Axelsson, Frédéric Berger
Software Mentions: 3
Published: over 4 years ago

10.1038/srep13652

Dimeric interactions and complex formation using direct coevolutionary couplings
Cited by: 72
Author(s): Ricardo Nascimento dos Santos, Faruck Morcos, Biman Jana, Adriano D. Andricopulo, José N. Onuchic
Software Mentions: 3
Published: about 9 years ago

10.1107/S090744491301576X

Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein
Cited by: 17
Author(s): Tianyu Wang, Jingjin Ding, Ying Zhang, Dacheng Wang, Wei Liu
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0077995

Structural and Enzymatic Characterization of the Phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes
Cited by: 52
Author(s): Guillaume Gotthard, Julien Hiblot, Daniel H. González, Mikael Elias, Éric Chabrière
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0214440

A DNA aptamer reveals an allosteric site for inhibition in metallo-β-lactamases
Cited by: 17
Author(s): Nazmul H Khan, Anthony A. Bui, Yang Xiao, R. Bryan Sutton, Robert W. Shaw, Benjamin J. Wylie, Michael P. Latham
Software Mentions: 3
Published: over 5 years ago

10.1107/S0907444910029690

Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from <i>Bacillus anthracis</i>
Cited by: 19
Author(s): Ekaterina Morgunova, Boris Illarionov, Sabine Saller, Aleksander Popov, Thota Sambaiah, Adelbert Bacher, Mary Cushman, Markus Fischer, Rudolf Ladenstein
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0196484

Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches
Cited by: 71
Author(s): Abbas Khan, Muhammad Junaid, Aman Chandra Kaushik, Arif Ali, Syed Shujait Ali, Aamir Mehmood, Dong‐Qing Wei
Software Mentions: 3
Published: over 6 years ago

10.1107/S0907444910000272

Rapid chain tracing of polypeptide backbones in electron-density maps
Cited by: 5
Author(s): Thomas C. Terwilliger
Software Mentions: 3
Published: almost 15 years ago

10.1186/1471-2105-13-S4-S16

Intuitive representation of surface properties of biomolecules using BioBlender
Cited by: 59
Author(s): Raluca Andrei, Marco Callieri, Maria Francesca Zini, Tiziana Loni, Giuseppe Maraziti, Mike Pan, Monica Zoppè
Software Mentions: 3
Published: over 12 years ago

10.6026/97320630015784

Molecular docking based virtual screening of the breast cancer target NUDT5
Cited by: 6
Author(s): Razia Sultana, Monjia Islam, Md Azizul Haque, Fatematuz Zuhura Evamoni, Zahid Mohammad Imran, Jabunnesa Khanom, Adnan Munim
Software Mentions: 3
Published: almost 5 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 3 years ago

10.1155/2013/185282

Elucidation of Novel Structural Scaffold in Rohu TLR2 and Its Binding Site Analysis with Peptidoglycan, Lipoteichoic Acid and Zymosan Ligands, and Downstream MyD88 Adaptor Protein
Cited by: 20
Author(s): Bikash R. Sahoo, Madhubanti Basu, Bichitrananda Swain, Manas Ranjan Dikhit, P. Jayasankar, Mrinal Samanta
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0145053

Synergistic Interactions of Eugenol-tosylate and Its Congeners with Fluconazole against Candida albicans
Cited by: 57
Author(s): Aijaz Ahmad, Mohmmad Younus Wani, Amber Khan, Nikhat Manzoor, Julitha Molepo
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-019-40762-9

Meta-analysis suggests evidence of novel stress-related pathway components in Orsay virus - Caenorhabditis elegans viral model
Cited by: 3
Author(s): Prachi Mishra, Jessica Ngo, Jahanshah Ashkani, Frédéric Pio
Software Mentions: 3
Published: over 5 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 6 years ago

10.1038/s41598-021-97871-7

Deep mutational scanning of the plasminogen activator inhibitor-1 functional landscape
Cited by: 7
Author(s): Zachary M. Huttinger, Laura M. Haynes, Andrew Yee, Colin A. Kretz, Matthew L. Holding, David Siemieniak, Daniel A. Lawrence, David Ginsburg
Software Mentions: 3
Published: about 3 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 5 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 5 years ago

10.12688/f1000research.12301.2

In silico analysis of natural compounds targeting structural and nonstructural proteins of chikungunya virus
Cited by: 16
Author(s): Jaspreet Jain, Anchala Kumari, Pallavi Somvanshi, Abhinav Grover, S. Somnath Pai, Sujatha Sunil
Software Mentions: 3
Published: almost 7 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 3 years ago

10.1038/s41598-020-58138-9

Structural characterization and in-silico analysis of Momordica charantia 7S globulin for stability and ACE inhibition
Cited by: 26
Author(s): Pooja Kesari, Shivendra Pratap, Poonam Dhankhar, Vikram Dalal, Manisha Mishra, Pradyumna Kumar Singh, Harsh Chauhan, Pravindra Kumar
Software Mentions: 3
Published: almost 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 5 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: about 6 years ago

10.1016/j.jmb.2013.10.039

Structural Determinants of Unique Properties of Human IgG4-Fc
Cited by: 95
Author(s): Anna M. Davies, Theo Rispens, Pleuni Ooijevaar-de Heer, Hannah J. Gould, Royston Jefferis, Rob C. Aalberse, Brian J. Sutton
Software Mentions: 3
Published: almost 11 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 4 years ago

10.1098/rsob.200237

Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential
Cited by: 55
Author(s): J.G.M. Rack, Valentina Zorzini, Zihan Zhu, M. Schuller, Dragana Ahel, Ivan Ahel
Software Mentions: 3
Published: about 4 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 5 years ago

10.1107/S1600577516016362

Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
Cited by: 36
Author(s): Kazuya Hasegawa, Keitaro Yamashita, Taichi Murai, Nipawan Nuemket, Kunio Hirata, Go Ueno, Hideo Ago, Toru Nakatsu, Takashi Kumasaka, Masaki Yamamoto
Software Mentions: 3
Published: almost 8 years ago

10.1002/mgg3.1571

Compound hemizygous variants in <i>SERPINA7</i> gene cause thyroxine‐binding globulin deficiency
Cited by: 3
Author(s): Yuan Fang, Hong Chen, Qingqing Chen, Chunlin Wang, Li Liang
Software Mentions: 3
Published: almost 4 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: over 3 years ago

10.1371/journal.pone.0232846

Diversity in kinetics correlated with structure in nano body-stabilized LacY
Cited by: 3
Author(s): Atul Kumar Johri, J. Finer-Moore, И. Н. Смирнова, Vladimir N. Kasho, Els Pardon, Jan Steyaert, H. Ronald Kaback, Robert M. Stroud
Software Mentions: 3
Published: over 4 years ago

10.1007/s10969-014-9188-8

Crystal structures of the S6K1 kinase domain in complexes with inhibitors
Cited by: 12
Author(s): Hideaki Niwa, Junko Mikuni, Shunta Sasaki, Yuri Tomabechi, Keiko Honda, Mariko Ikeda, Noboru Ohsawa, Motoaki Wakiyama, N. Handa, Mikako Shirouzu, Teruki Honma, Akiko Tanaka, Shigeyuki Yokoyama
Software Mentions: 3
Published: over 10 years ago