pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.1016/j.bbrep.2021.100982

Repurposing of approved drugs with potential to interact with SARS-CoV-2 receptor
Cited by: 5
Author(s): Tamim Ahsan, Abu Ashfaqur Sajib
Software Mentions: 2
Published: about 5 years ago

Design, structure prediction and molecular dynamics simulation of a fusion construct containing malaria pre-erythrocytic vaccine candidate, PfCelTOS, and human interleukin 2 as adjuvant
Cited by: 21
Author(s): Shabnam Shamriz, Hamideh Ofoghi
Software Mentions: 2
Published: over 10 years ago

10.1002/prot.26018

<scp>PDB‐tools</scp> web: A user‐friendly interface for the manipulation of <scp>PDB</scp> files
Cited by: 12
Author(s): Brian Jiménez‐García, João M.C. Teixeira, Mikaël Trellet, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
Software Mentions: 2
Published: over 5 years ago

10.1002/prot.25223

The evolution of function within the Nudix homology clan
Cited by: 49
Author(s): John R. Srouji, Anting Xu, Annsea Park, Jack F. Kirsch, Steven E. Brenner
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-12-421

Automated NMR relaxation dispersion data analysis using NESSY
Cited by: 62
Author(s): Martin Bieri, Paul R. Gooley
Software Mentions: 2
Published: over 14 years ago

10.1007/s11120-017-0450-3

Crystal structure of Psb27 from Arabidopsis thaliana determined at a resolution of 1.85 Å
Cited by: 7
Author(s): Xingxing Cheng, Jiuyang Liu, Huan Zhang, Fudong Li, Zhang Shuya, Min Xu, Ke Ruan, Yuhua Wang, Aigen Fu
Software Mentions: 2
Published: over 8 years ago

10.1042/BCJ20160806

Neisseria meningitidis factor H-binding protein bound to monoclonal antibody JAR5: implications for antibody synergy
Cited by: 18
Author(s): E. Malito, Paola Lo Surdo, Daniele Veggi, Laura Santini, Heather Stefek, Brunella Brunelli, Enrico Luzzi, Matthew J. Bottomley, Peter T. Beernink, María Scarselli
Software Mentions: 2
Published: over 9 years ago

10.1042/BCJ20200128

Nek7 conformational flexibility and inhibitor binding probed through protein engineering of the R-spine
Cited by: 10
Author(s): Matthew J. Byrne, Nazia Nasir, Christine Basmadjian, Chitra Bhatia, Rory F. Cunnison, Katherine H. Carr, Corine Mas-Droux, Sharon Yeoh, Céline Cano, Richard Bayliss
Software Mentions: 2
Published: about 6 years ago

10.1107/S2059798320005355

Structural analysis of the PATZ1 BTB domain homodimer
Cited by: 4
Author(s): Sofia Piepoli, Aaron Alt, Canan Atılgan, Erika J. Mancini, Batu Erman
Software Mentions: 2
Published: about 6 years ago

10.1111/pbi.12896

Trans-species synthetic gene design allows resistance pyramiding and broad-spectrum engineering of virus resistance in plants
Cited by: 60
Author(s): Anna Bastet, Baptiste Lederer, Nathalie Giovinazzo, Xavier Arnoux, Sylvie German-Retana, Catherine Reinbold, Véronique Brault, Damien Garcia, Samia Djennane, Sophie Gersch, Olivier Lemaire, Christophe Robaglia, Jean‐Luc Gallois
Software Mentions: 2
Published: over 8 years ago

10.1107/S2059798317007021

High-resolution cryo-EM proteasome structures in drug development
Cited by: 10
Author(s): Edward P. Morris, Paula C. A. da Fonseca
Software Mentions: 2
Published: about 9 years ago

10.1098/rsos.200844

Targeting the glycan of receptor binding domain with jacalin as a novel approach to develop a treatment against COVID-19
Cited by: 3
Author(s): Senthilnathan Rajendaran, Arunchalam Jothi, Anbazhagan Veerappan
Software Mentions: 2
Published: almost 6 years ago

10.1111/tpj.14409

Functional specialization of <scp>UDP</scp>‐glycosyltransferase 73P12 in licorice to produce a sweet triterpenoid saponin, glycyrrhizin
Cited by: 55
Author(s): Yuhta Nomura, Hikaru Seki, Tomonori Suzuki, Kiyoshi Ohyama, Masaharu Mizutani, Takashi Kaku, K Tamura, Eiichiro Ono, Manabu Horikawa, Hiroshi Sudo, Hiroaki Hayashi, Kazuki Saito, Toshiya Muranaka
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0021267

Expression of Enzymatically Inactive Wasp Venom Phospholipase A1 in Pichia pastoris
Cited by: 13
Author(s): Irina Borodina, Bettina M. Jensen, Tim Wagner, Maher Abou Hachem, Ib Søndergaard, Lars K. Poulsen
Software Mentions: 2
Published: about 15 years ago

10.1042/BCJ20200507

Fragment-derived modulators of an industrial β-glucosidase
Cited by: 2
Author(s): Eleni Makraki, John F. Darby, Marta G. Carneiro, James D. Firth, Alex Heyam, Eiso Ab, Peter O’Brien, Gregg Siegal, Roderick E. Hubbard
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0071835

Functional Mapping of Human Dynamin-1-Like GTPase Domain Based on X-ray Structure Analyses
Cited by: 60
Author(s): Julia Wenger, Eva Klinglmayr, Chris Fröhlich, Clarissa Eibl, Ana Gimeno, Manuel Hessenberger, Sandra Puehringer, Oliver Daumke, Peter Goettig
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12915-021-01039-8

Characterization of a novel type of carbonic anhydrase that acts without metal cofactors
Cited by: 30
Author(s): Yoshihisa Hirakawa, Masuo Senda, Kodai Fukuda, Hong Yang Yu, Masaki Ishida, M. Taira, Kazushi Kinbara, Toshiya Senda
Software Mentions: 2
Published: about 5 years ago

10.1186/s12915-015-0167-8

Role of electrostatic interactions for ligand recognition and specificity of peptide transporters
Cited by: 47
Author(s): Rajendra Boggavarapu, Jean-Marc Jeckelmann, Daniel Harder, Zöhre Ucurum, Dimitrios Fotiadis
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep39024

Comparative Proteomics Reveals that Phosphorylation of β Carbonic Anhydrase 1 Might be Important for Adaptation to Drought Stress in Brassica napus
Cited by: 31
Author(s): Limin Wang, Xiang Jin, Qingbin Li, Xuchu Wang, Zaiyun Li, Xiaoming Wu
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0020950

Conformational Changes of rBTI from Buckwheat upon Binding to Trypsin: Implications for the Role of the P8′ Residue in the Potato Inhibitor I Family
Cited by: 13
Author(s): Long Wang, Fei Zhao, Mei Li, Hongmei Zhang, Yu Gao, Peng Cao, Xiaowei Pan, Zhuanhua Wang, Wenrui Chang
Software Mentions: 2
Published: about 15 years ago

10.1038/srep40254

Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode
Cited by: 5
Author(s): Tianle Qian, Jing Wo, Yan Zhang, Quanwei Song, Guoqiang Feng, Ray Luo, Shuangjin Lin, Geng Wu, Haifeng Chen
Software Mentions: 2
Published: over 9 years ago

10.1186/1741-7007-5-17

Ab initio modeling of small proteins by iterative TASSER simulations
Cited by: 459
Author(s): Sitao Wu, Jeffrey Skolnick, Yang Zhang
Software Mentions: 2
Published: about 19 years ago

10.1038/srep41487

Identification of a novel selective PPARγ ligand with a unique binding mode and improved therapeutic profile in vitro
Cited by: 15
Author(s): Wei Yi, Jingjing Shi, Guanguan Zhao, Xuemei Zhou, Kelly Suino-Powell, Karsten Melcher, H. Eric Xu
Software Mentions: 2
Published: over 9 years ago

10.1107/S2059798320000339

SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses
Cited by: 8
Author(s): Rafael J. Borges, Kathrin Meindl, Josep Triviño, Massimo Sammito, Ana María Medina, Claudia Millán, Martín Alcorlo, J.A. Hermoso, Marcos R.M. Fontes, Isabel Usón
Software Mentions: 2
Published: over 6 years ago

10.1038/srep41212

Two strategies to engineer flexible loops for improved enzyme thermostability
Cited by: 111
Author(s): Haoran Yu, Yihan Yan, Cheng Zhang, Paul A. Dalby
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pbio.0050297

Fabp7 Maps to a Quantitative Trait Locus for a Schizophrenia Endophenotype
Cited by: 176
Author(s): Akïharu Watanabe, Tomoko Toyota, Yuji Owada, Takeshi Hayashi, Yoshimi Iwayama, Miho Matsumata, Yuichi Ishitsuka, Akihiro Nakaya, Motoko Maekawa, Tetsuo Ohnishi, Ryoichi Arai, K. Sakurai, Kazuo Yamada, Hisatake Kondo, Kenji Hashimoto, Noriko Osumi, Takeo Yoshikawa
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pbio.1000589

Structural Basis of Response Regulator Dephosphorylation by Rap Phosphatases
Cited by: 86
Author(s): Vijay Parashar, Nicolas Mirouze, David Dubnau, Matthew B. Neiditch
Software Mentions: 2
Published: over 15 years ago

10.1186/s12915-017-0372-8

Ion- and water-binding sites inside an occluded hourglass pore of a trimeric intracellular cation (TRIC) channel
Cited by: 4
Author(s): Xiaomin Ou, Jing Guo, Long Wang, Hongxin Yang, Xiuying Liu, Jianyuan Sun, Zhongfan Liu
Software Mentions: 2
Published: about 9 years ago

10.3390/biom10050789

MARK4 Inhibited by AChE Inhibitors, Donepezil and Rivastigmine Tartrate: Insights into Alzheimer’s Disease Therapy
Cited by: 66
Author(s): Anas Shamsi, Saleha Anwar, Taj Mohammad, Mohamed F. Alajmi, Afzal Hussain, Tabish Rehman, Gulam Mustafa Hasan, Asimul Islam, Md. Imtaiyaz Hassan
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pbio.1002480

The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation
Cited by: 39
Author(s): Sohail Khoshnevis, Isabel Askenasy, Matthew C. Johnson, Maria D. Dattolo, Crystal L. Young-Erdos, M. Elizabeth Stroupe, Katrin Karbstein
Software Mentions: 2
Published: about 10 years ago

10.3390/biom11081083

The Right-Handed Parallel β-Helix Topology of Erwinia chrysanthemi Pectin Methylesterase Is Intimately Associated with Both Sequential Folding and Resistance to High Pressure
Cited by: 3
Author(s): Jessica Guillerm, Jean‐Marie Frère, Filip Meersman, André Matagne
Software Mentions: 2
Published: almost 5 years ago

10.1038/srep42711

Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage ΦAB6 tailspike protein
Cited by: 37
Author(s): I‐Ming Lee, I-Fan Tu, Yang Fu, Tzu‐Ping Ko, Jiahn-Haur Liao, Ning Lin, Chung‐Yi Wu, Chien‐Tai Ren, Andrew H.‐J. Wang, Ching-Ming Chang, Kai‐Fa Huang, Shih‐Hsiung Wu
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pbio.1001226

Structural Basis of Response Regulator Inhibition by a Bacterial Anti-Activator Protein
Cited by: 52
Author(s): Melinda D. Baker, Matthew B. Neiditch
Software Mentions: 2
Published: over 14 years ago

10.1107/S1399004713030149

Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex
Cited by: 29
Author(s): Jacob Lauwring Andersen, Tenna Juul Schrøder, Søren Christensen, Dorthe Strandbygård, Lone Tjener Pallesen, María García-Alai, Samsa Lindberg, Morten Langgård, Jørgen Eskildsen, Laurent David, Lena Tagmose, Klaus B. Simonsen, Philip Maltas, Lars Christian B. Rønn, Inge E.M. de Jong, Ibrahim Malik, Jan Egebjerg, Jens-Jacob Karlsson, U. Srinivas, Durga Rao Sakumudi, Pradheep Eradi, Steven P. Watson, Søren Thirup
Software Mentions: 2
Published: over 12 years ago

10.1107/S2059798315024110

Data-collection strategy for challenging native SAD phasing
Cited by: 40
Author(s): V. Oliéric, T. Weinert, Aaron D. Finke, Carolin Anders, Dianfan Li, Natacha Olieric, Camelia N. Borca, Michel O. Steinmetz, Martin Caffrey, Martin Jinek, Meitian Wang
Software Mentions: 2
Published: over 10 years ago

10.1038/srep43318

ACCORD: an assessment tool to determine the orientation of homodimeric coiled-coils
Cited by: 6
Author(s): Byeong Won Kim, Yang Ouk Jung, Min Kyung Kim, Do Hoon Kwon, Si Hoon Park, Jun Hoe Kim, Yong Boo Kuk, Sun Joo Oh, Leehyeon Kim, Bong Heon Kim, Woo Seok Yang, Hyun Kyu Song
Software Mentions: 2
Published: over 9 years ago

10.1038/srep44341

Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability
Cited by: 36
Author(s): Marcin Wolny, Matthew Batchelor, Gail J. Bartlett, Emily G. Baker, Marta Kurzawa, Peter J. Knight, Lorna Dougan, Derek N. Woolfson, Emanuele Paci, Michelle Peckham
Software Mentions: 2
Published: over 9 years ago

10.1107/S2059798319010866

Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms
Cited by: 8
Author(s): C.D. Radka, Shaunivan Labiuk, Lawrence J. DeLucas, Stephen G. Aller
Software Mentions: 2
Published: almost 7 years ago

10.1038/srep45224

Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics
Cited by: 10
Author(s): Hannah A. Davies, Daniel J. Rigden, Marie M. Phelan, Jillian Madine
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pbio.2003145

Uncovering protein–protein interactions through a team-based undergraduate biochemistry course
Cited by: 14
Author(s): David L. Cookmeyer, Emily S. Winesett, Bashkim Kokona, Adam R. Huff, Sabina Aliev, Noah B. Bloch, Joshua A. Bulos, Irene L. Evans, Christian Fagre, Kerilyn N. Godbe, Maryna Khromava, Daniel Konstantinovsky, Alexander E. Lafrance, Alexandra J. Lamacki, Robert C. Parry, Jeanne M. Quinn, Alana M. Thurston, Kathleen J. S. Tsai, Aurelio Mollo, Max J. Cryle, Robert Fairman, Louise K. Charkoudian
Software Mentions: 2
Published: over 8 years ago

10.1107/S2059798320000212

3D domain swapping in the TIM barrel of the α subunit ofStreptococcus pneumoniaetryptophan synthase
Cited by: 3
Author(s): K. Michalska, Marcin Kowiel, L. Bigelow, M. Endres, Mirosław Gilski, Mariusz Jaskólski, A. Joachimiak
Software Mentions: 2
Published: over 6 years ago

10.1107/S2059798318006356

Crystal structure of the spliceosomal DEAH-box ATPase Prp2
Cited by: 21
Author(s): Andreas Schmitt, Florian Hamann, Piotr Neumann, Ralf Ficner
Software Mentions: 2
Published: about 8 years ago

10.1186/1741-7007-9-48

Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1
Cited by: 49
Author(s): Alexei Korennykh, Pascal F. Egea, А.A. Коростелев, J. Finer-Moore, Robert M. Stroud, Chao Zhang, Kevan M. Shokat, Peter Walter
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0052421

Head-Head Interactions of Resting Myosin Crossbridges in Intact Frog Skeletal Muscles, Revealed by Synchrotron X-Ray Fiber Diffraction
Cited by: 14
Author(s): Kazuteru Oshima, Yoshiaki Sugimoto, Thomas C. Irving, Katsuzo Wakabayashi
Software Mentions: 2
Published: over 13 years ago

10.1038/srep45505

Global evolutionary history and spatio-temporal dynamics of dengue virus type 2
Cited by: 29
Author(s): Kaifa Wei, Yuhan Li
Software Mentions: 2
Published: over 9 years ago

10.1186/s12915-017-0397-z

Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues
Cited by: 93
Author(s): Rohan Bythell-Douglas, Carl J. Rothfels, Dennis Stevenson, Sean W. Graham, Gane Ka‐Shu Wong, David C. Nelson, Tom Bennett
Software Mentions: 2
Published: about 9 years ago

10.1107/S1399004715002308

Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array
Cited by: 67
Author(s): A.Y. Lyubimov, Thomas D. Murray, Antoine Koehl, Ismail Emre Araci, Monarin Uervirojnangkoorn, Oliver B. Zeldin, Aina E. Cohen, S. Michael Soltis, E.L. Baxter, Aaron S. Brewster, Nicholas K. Sauter, Axel T. Brunger, James M. Berger
Software Mentions: 2
Published: over 11 years ago

10.1038/srep08560

The catalytic role of the M2 metal ion in PP2Cα
Cited by: 16
Author(s): Chang Pan, Junyi Tang, Yaping Xu, Xiao Peng, Hongda Liu, Hao-an Wang, Wenbo Wang, Fanyue Meng, Xiao Yu, Junying Sun
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0043985

Stapled BH3 Peptides against MCL-1: Mechanism and Design Using Atomistic Simulations
Cited by: 37
Author(s): Thomas L. Joseph, David P. Lane, Chandra Verma
Software Mentions: 2
Published: almost 14 years ago

10.1038/s41598-017-00147-2

PRL3 phosphatase active site is required for binding the putative magnesium transporter CNNM3
Cited by: 41
Author(s): Huizhi Zhang, Guennadi Kozlov, Xinlu Li, Howie Wu, Irina Gulerez, Kalle Gehring
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-01186-5

Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine
Cited by: 12
Author(s): Cha San Koh, Rohini Madireddy, Timothy J. Beane, Phillip D. Zamore, А.A. Коростелев
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-00917-y

A bacterial ABC transporter enables import of mammalian host glycosaminoglycans
Cited by: 21
Author(s): Shigetoshi Oiki, Bunzo Mikami, Yukie Maruyama, Kousaku Murata, Wataru Hashimoto
Software Mentions: 2
Published: about 9 years ago

10.1186/s12915-017-0438-7

An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook
Cited by: 7
Author(s): Clive S. Barker, Irina V. Meshcheryakova, Alla S. Kostyukova, Peter L. Freddolino, Fadel A. Samatey
Software Mentions: 2
Published: over 8 years ago

10.1107/S2059798318001365

Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination
Cited by: 25
Author(s): Claudia Millán, Massimo Sammito, Airlie J. McCoy, Andrey Fabricio Ziem Nascimento, Giovanna Petrillo, Robert D. Oeffner, T. Dominguez-Gil, J.A. Hermoso, Randy J. Read, Isabel Usón
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-01057-z

Structural investigations on orotate phosphoribosyltransferase from Mycobacterium tuberculosis, a key enzyme of the de novo pyrimidine biosynthesis
Cited by: 22
Author(s): Stefano Donini, Davide M. Ferraris, Riccardo Miggiano, Alberto Massarotti, Menico Rizzi
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0232757

Characterization of a human monoclonal antibody generated from a B-cell specific for a prefusion-stabilized spike protein of Middle East respiratory syndrome coronavirus
Cited by: 10
Author(s): Jang Hoon Choi, Hye Min Woo, Tae Young Lee, So Young Lee, Sang Mu Shim, Woo Jung Park, Jeong Sun Yang, Joo Ae Kim, Mi Ran Yun, Dae Won Kim, Sung Soon Kim, Yi Zhang, Wei Shi, Lingshu Wang, Barney S. Graham, John R. Mascola, Nanshuang Wang, Jason S. McLellan, Joo Yeon Lee, Hansaem Lee
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-017-01989-6

Structural studies of the periplasmic portion of the diguanylate cyclase CdgH from Vibrio cholerae
Cited by: 8
Author(s): Min Xu, Yizhi Wang, Xiu‐An Yang, Tao Jiang, Wei Xie
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pbio.3000347

Assembling a plug-and-play production line for combinatorial biosynthesis of aromatic polyketides in Escherichia coli
Cited by: 32
Author(s): Matthew Cummings, Anna Peters, George F. S. Whitehead, Binuraj R. K. Menon, Jason Micklefield, Simon J. Webb, Eriko Takano
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.bpj.2021.01.012

Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein
Cited by: 49
Author(s): Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham Dokainish, Suyong Re, Yuji Sugita
Software Mentions: 2
Published: over 5 years ago

10.1186/2046-1682-5-7

Arbitrary protein−protein docking targets biologically relevant interfaces
Cited by: 37
Author(s): Juliette Martin, Richard Lavery
Software Mentions: 2
Published: about 14 years ago

10.1038/s41598-017-02823-9

Efficient Generation of Bispecific Murine Antibodies for Pre-Clinical Investigations in Syngeneic Rodent Models
Cited by: 31
Author(s): Aran F. Labrijn, Joyce Meesters, Matthew W. Bunce, Anthony A. Armstrong, Sandeep Somani, Tom Nesspor, Mark L. Chiu, Işıl Altıntaş, Sandra Verploegen, Janine Schuurman, Paul W.H.I. Parren
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pbio.1001776

Segmental Helical Motions and Dynamical Asymmetry Modulate Histidine Kinase Autophosphorylation
Cited by: 97
Author(s): A.E. Mechaly, Nathalie Sassoon, Jean‐Michel Betton, Pedro M. Alzari
Software Mentions: 2
Published: over 12 years ago

10.1038/s41598-017-02805-x

A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases
Cited by: 32
Author(s): Rubén M. Buey, David Fernández‐Justel, Íñigo Marcos‐Alcalde, Graeme Winter, Paulino Gómez‐Puertas, José M. de Pereda, José Luis Revuelta
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-02803-z

Construction of novel repeat proteins with rigid and predictable structures using a shared helix method
Cited by: 22
Author(s): Suk-Jun Youn, Nayoung Kwon, Ji Hyun Lee, Jin Hong Kim, Jin‐Woo Choi, Hayyoung Lee, Jie‐Oh Lee
Software Mentions: 2
Published: about 9 years ago

10.1186/2046-1682-6-10

Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies
Cited by: 8
Author(s): Anke Steinbach, Christine K. Maurer, Elisabeth Weidel, Claudia Henn, Christian Brengel, Rolf W. Hartmann, Matthias Negri
Software Mentions: 2
Published: almost 13 years ago

10.1038/s41598-017-03220-y

Bacterial protease uses distinct thermodynamic signatures for substrate recognition
Cited by: 13
Author(s): G.A. Bezerra, Yuko Ohara‐Nemoto, Irina Cornaciu, Sofiya Fedosyuk, Guillaume Hoffmann, Adam Round, José Antonio Márquez, Takayuki Nemoto, Kristina Djinović-Carugo
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0026278

A Novel Metagenomic Short-Chain Dehydrogenase/Reductase Attenuates Pseudomonas aeruginosa Biofilm Formation and Virulence on Caenorhabditis elegans
Cited by: 108
Author(s): P. Bijtenhoorn, Hubert Mayerhofer, Jochen Müller-Dieckmann, Christian Utpatel, Christina Schipper, C. Hornung, Matthias Szesny, Stephanie Grond, Andrea Thürmer, Elżbieta Brzuszkiewicz, Rolf Daniel, Katja Dierking, Hinrich Schulenburg, Wolfgang R. Streit
Software Mentions: 2
Published: over 14 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 11 years ago

10.1016/j.bpj.2015.06.061

Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains
Cited by: 26
Author(s): James Krieger, İvet Bahar, Ingo H. Greger
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0074788

The Structural Basis of Erwinia rhapontici Isomaltulose Synthase
Cited by: 17
Author(s): Zheng Xu, Sha Li, Jie Li, Yan Li, Xiaohai Feng, Renxiao Wang, Hong Xu, Jiahai Zhou
Software Mentions: 2
Published: almost 13 years ago

10.1038/s41598-017-03664-2

Antibacterial and detoxifying activity of NZ17074 analogues with multi-layers of selective antimicrobial actions against Escherichia coli and Salmonella enteritidis
Cited by: 48
Author(s): Na Yang, Xuehui Liu, Da Teng, Zhanzhan Li, Xiumin Wang, Ruoyu Mao, Xiao Wang, Ya Hao, Jianhua Wang
Software Mentions: 2
Published: about 9 years ago

10.1186/s13628-018-0048-y

Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments
Cited by: 6
Author(s): Aslı Yıldırım, Nathalie Brenner, Robert Sutherland, Michael Feig
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pbio.3001148

Molecular basis of F-actin regulation and sarcomere assembly via myotilin
Cited by: 9
Author(s): Július Košťan, Miha Pavšič, Vid Puž, Thomas C. Schwarz, Friedel Drepper, Sibylle Molt, Melissa A. Graewert, Claudia Schreiner, Sara Sajko, Peter F.M. van der Ven, Adekunle Onipe, Dmitri I. Svergun, Bettina Warscheid, Robert Konrat, Dieter O. Fürst, Brigita Lenarčič, Kristina Djinović-Carugo
Software Mentions: 2
Published: over 5 years ago

10.1107/S2059798317013043

Conformational dynamics of the essential sensor histidine kinase WalK
Cited by: 26
Author(s): Yongfei Cai, Mingyang Su, Ashfaq Ahmad, Xiaojie Hu, Jiayan Sang, Ling-Yuan Kong, Xingqiang Chen, Chen Wang, Jianwei Shuai, Aidong Han
Software Mentions: 2
Published: almost 9 years ago

10.1007/s41048-018-0073-z

Significant expansion and red-shifting of fluorescent protein chromophore determined through computational design and genetic code expansion
Cited by: 6
Author(s): Li Wang, Xian Chen, Xuzhen Guo, Jiasong Li, Qi Liu, Fuying Kang, Xudong Wang, Cheng Hu, Haiping Li, Weimin Gong, Wei Zhuang, Liu Xiao-hong, Jiangyun Wang
Software Mentions: 2
Published: almost 8 years ago

10.1186/1472-6750-11-85

Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)
Cited by: 36
Author(s): Gustavo R. Oliveira, Maria C. M. Silva, Wagner Alexandre Lucena, Erich Yukio Tempel Nakasu, Alexandre Augusto Pereira Firmino, Magda Aparecida Beneventi, Djair S.L. Souza, José Erick Galindo Gomes, José Dijair Antonino, Daniel J. Rigden, H. B. Ramos, Carlos Ricardo Soccol, Maria Fátima Grossi‐de‐Sá
Software Mentions: 2
Published: almost 15 years ago

10.1107/S1744309111019312

Conservation of a crystallographic interface suggests a role for β-sheet augmentation in influenza virus NS1 multifunctionality
Cited by: 9
Author(s): Philip S. Kerry, Eric C. Long, Margaret Taylor, Rosemary Russell
Software Mentions: 2
Published: almost 15 years ago

10.1107/S139900471402776X

Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove
Cited by: 24
Author(s): Marina E. Ivanova, Georgina Fletcher, Nicola O’Reilly, A. Purkiss, B. J. Thompson, Neil Q. McDonald
Software Mentions: 2
Published: over 11 years ago

10.3390/cancers13153847

Identification of Cancer Hub Gene Signatures Associated with Immune-Suppressive Tumor Microenvironment and Ovatodiolide as a Potential Cancer Immunotherapeutic Agent
Cited by: 23
Author(s): Jiahong Chen, Alexander T.H. Wu, Bashir Lawal, David T.W. Tzeng, Jih‐Chin Lee, Ching–Liang Ho, Tsu‐Yi Chao
Software Mentions: 2
Published: almost 5 years ago

10.1107/S2059798318018442

The atypical thiol–disulfide exchange protein α-DsbA2 fromWolbachia pipientisis a homotrimeric disulfide isomerase
Cited by: 4
Author(s): Patricia Walden, Andrew E. Whitten, Lakshmanane Premkumar, Maria A. Halili, Begoña Heras, G. J. King, Jennifer L. Martin
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-05234-y

Structural and Biochemical Characterization of Apicomplexan Inorganic Pyrophosphatases
Cited by: 2
Author(s): Abhishek Jamwal, Manickam Yogavel, M. Z. Abdin, Swatantra Kumar Jain, Amit Sharma
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-05509-4

Structure of polyhydroxyalkanoate (PHA) synthase PhaC from Chromobacterium sp. USM2, producing biodegradable plastics
Cited by: 69
Author(s): Min Fey Chek, Sunyong Kim, Tomoyuki Mori, Hasni Arsad, Mohammed Razip Samian, Kumar Sudesh, Toshio Hakoshima
Software Mentions: 2
Published: almost 9 years ago

10.3390/cancers13040909

Role of PFKFB3 and PFKFB4 in Cancer: Genetic Basis, Impact on Disease Development/Progression, and Potential as Therapeutic Targets
Cited by: 53
Author(s): Krzysztof Kotowski, Jakub Rosik, Filip Machaj, Stanisław Supplitt, Daniel Wiczew, Karolina Jabłońska, Emilia Wiecheć, Saeid Ghavami, Piotr Dzięgiel
Software Mentions: 2
Published: over 5 years ago

10.1042/BSR20170001

Crystal structure of thermostable alkylsulfatase SdsAP from Pseudomonas sp. S9
Cited by: 3
Author(s): Lifang Sun, Pu Chen, Su Y, Zhixiong Cai, Lingwei Ruan, Xun Xu, Yunkun Wu
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-05657-7

Plasticity in the Oxidative Folding Pathway of the High Affinity Nerita Versicolor Carboxypeptidase Inhibitor (NvCI)
Cited by: 4
Author(s): Sebastián Esperante, Giovanni Covaleda, Sebastián A. Trejo, Sílvia Bronsoms, Francesc X. Aviles, Salvador Ventura
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pbio.3000277

Structural insights into histone chaperone Chz1-mediated H2A.Z recognition and histone replacement
Cited by: 17
Author(s): Yunyun Wang, Sheng Liu, Lu Sun, Ning Xu, Shan Shan, Fei Wu, Xiaoping Liang, Yingzi Huang, Ed Luk, Carl Wu, Zheng Zhou
Software Mentions: 2
Published: about 7 years ago

10.3390/cancers13061244

3D Pharmacophore-Based Discovery of Novel KV10.1 Inhibitors with Antiproliferative Activity
Cited by: 5
Author(s): Žan Toplak, Louise Antonia Hendrickx, Špela Gubič, Štefan Možina, Bojana Žegura, Alja Štern, Matjaž Novak, Xiaoyi Shi, Steve Peigneur, Jan Tytgat, Tihomir Tomašič, Luis A. Pardo, Lucíja Peterlin Mašič
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-017-05627-z

X-ray crystallographic structure of a bacterial polysialyltransferase provides insight into the biosynthesis of capsular polysialic acid
Cited by: 12
Author(s): Christian Lizak, L.J. Worrall, Lars Baumann, Moritz M. Pfleiderer, Gesa Volkers, Tianjun Sun, Lyann Sim, Warren W. Wakarchuk, Stephen G. Withers, N.C.J. Strynadka
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0059798

2,2′-Diphenyl-3,3′-Diindolylmethane: A Potent Compound Induces Apoptosis in Breast Cancer Cells by Inhibiting EGFR Pathway
Cited by: 32
Author(s): Arijit Bhowmik, N. K. Das, Samir Kumar Pal, Mihirbaran Mandal, Samir Bhattacharya, Moumita Sarkar, Parasuraman Jaisankar, Nakul C. Maiti, Mrinal K. Ghosh
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0032518

Loss and Gain of Function in SERPINB11: An Example of a Gene under Selection on Standing Variation, with Implications for Host-Pathogen Interactions
Cited by: 17
Author(s): Susana Seixas, Nevyana Ivanova, Zélia Ferreira, Jorge Rocha, Bruno L. Victor
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0165074

Kinetic Controlled Tag-Catcher Interactions for Directed Covalent Protein Assembly
Cited by: 49
Author(s): Lee Ling Tan, Shawn Hoon, Fong Tian Wong
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0060610

Structural and Phylogenetic Studies with MjTX-I Reveal a Multi-Oligomeric Toxin – a Novel Feature in Lys49-PLA2s Protein Class
Cited by: 17
Author(s): Daniela P. Marchi-Salvador, Carlos A. H. Fernandes, Ângelo J. Magro, Daniela P. Marchi-Salvador, Walter Luís Garrido Cavalcante, Roberto Fernández, Márcia Gallacci, Andreimar M. Soares, Cristiano L. P. Oliveira, Marcos R.M. Fontes
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0112677

Advantages and Versatility of Fluorescence-Based Methodology to Characterize the Functionality of LDLR and Class Mutation Assignment
Cited by: 32
Author(s): Aitor Etxebarria, Asier Benito‐Vicente, Ana Catarina Alves, Helena Ostolaza, Mafalda Bourbon, César Martín
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0026794

The Molecular Basis for the Broad Substrate Specificity of Human Sulfotransferase 1A1
Cited by: 50
Author(s): Ilana Berger Fridman, Chen Guttman, Dotan Amar, Raz Zarivach, Amir Aharoni
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0176444

Aromatic amino acids in the cellulose binding domain of Penicillium crustosum endoglucanase EGL1 differentially contribute to the cellulose affinity of the enzyme
Cited by: 3
Author(s): Jiangke Yang, Wei Xiong, Fangyuan Chen, Li Xu, Zhenggang Han
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0104592

Anticancer Activities of Pterostilbene-Isothiocyanate Conjugate in Breast Cancer Cells: Involvement of PPARγ
Cited by: 21
Author(s): Kumar Nikhil, Shruti Sharan, Abhimanyu Singh, Ajanta Chakraborty, Partha Roy
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0171727

MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding
Cited by: 5
Author(s): Kaori Asamitsu, Takatsugu Hirokawa, Takashi Okamoto
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0074281

Transmembrane and Juxtamembrane Structure of αL Integrin in Bicelles
Cited by: 17
Author(s): Wahyu Surya, Yan Li, Óscar Millet, Tammo Diercks, Jaume Torres
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0035962

Structure of Bradavidin – C-Terminal Residues Act as Intrinsic Ligands
Cited by: 8
Author(s): Jenni Leppiniemi, Toni Grönroos, Juha Määttä, Mark S. Johnson, Markku S. Kulomaa, Vesa P. Hytönen, Tomi T. Airenne
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0003201

The Difficult Case of Crystallization and Structure Solution for the ParC55 Breakage-Reunion Domain of Topoisomerase IV from Streptococcus pneumoniae
Cited by: 2
Author(s): Maninder K. Sohi, D. A. Veselkov, Ivan Laponogov, Xiao-Su Pan, L. Mark Fisher, Mark Sanderson
Software Mentions: 1
Published: almost 18 years ago

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Papers Mentioning PyMOL 8,266