10.1016/j.cell.2020.01.010

Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody
Cited by: 89
Author(s): Philipp Schommers, Henning Gruell, Morgan E. Abernathy, My-Kim Tran, Adam S. Dingens, Harry B. Gristick, Christopher O. Barnes, Till Schoofs, Maike Schlotz, Kanika Vanshylla, Christoph Kreer, Daniela Weiland, Udo Holtick, Christof Scheid, Markus M. Valter, Marit J. van Gils, Rogier W. Sanders, Jörg Janne Vehreschild, Oliver A. Cornely, Clara Lehmann, Gerd Fätkenheuer, Michael S. Seaman, Jesse D Bloom, Pamela J. Björkman, Florian Klein
Software Mentions: 2
Published: over 6 years ago

10.6026/97320630017212

Molecular docking of potential inhibitors with the mTOR protein
Cited by: 3
Author(s): Jh Shazia Fathima, Selvaraj Jayaraman, Venkatacalam Sivabalan, Umapathy Vidhya Rekha, Ponnulakshmi Rajagopal, V. Vishnupriya, Malathi Kullappan, Radhika Nalinakumari Sreekandan, Surapaneni Krishna Mohan, Periyasamy Vijayalakshmi
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-12-207

HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information
Cited by: 39
Author(s): Rong Liu, Jianjun Hu
Software Mentions: 2
Published: about 15 years ago

10.1016/j.cell.2018.10.037

Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design
Cited by: 52
Author(s): Yin Dong, Hua Wang, A.C.W. Pike, Stephen A. Cochrane, Sadra Hamedzadeh, Filip J. Wyszyński, S.R. Bushell, Sylvain Royer, David A. Widdick, Andaleeb Sajid, Helena I. Boshoff, Yumi Park, Ricardo Dantas de Lucas, Weimin Liu, Seung Seo Lee, Takuya Machida, Leanne Minall, Shahid Mehmood, Katsiaryna Belaya, Weiwei Liu, Amy Chu, L. Shrestha, Shubhashish M.M. Mukhopadhyay, Claire Strain-Damerell, R. Chalk, N. Burgess-Brown, Mervyn J. Bibb, Clifton E. Barry, Carol V. Robinson, David Beeson, Benjamin G. Davis, E.P. Carpenter
Software Mentions: 2
Published: over 7 years ago

10.3390/cancers12020456

An Epitope on EGFR Loading Catastrophic Internalization Serve as a Novel Oncotarget for Hepatocellular Carcinoma Therapy
Cited by: 0
Author(s): Dianshuai Huang, Qingjie Fan, Zhiyi Liu, Shuqin Zhang, Wei Huang, Hongrui Li, Chaozhao Liang, Fenyong Sun
Software Mentions: 2
Published: over 6 years ago

10.1107/S0907444911014302

Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain
Cited by: 7
Author(s): Gretchen Meinke, Paul J. Phelan, Amélie Fradet-Turcotte, Jacques Archambault, Peter A. Bullock
Software Mentions: 2
Published: about 15 years ago

10.3390/cancers12061523

New Anti-Cancer Strategy to Suppress Colorectal Cancer Growth Through Inhibition of ATG4B and Lysosome Function
Cited by: 13
Author(s): Yuanyuan Fu, Qianqian Gu, Li Luo, Jiangang Xu, Yuping Luo, Fan Xia, Fanghai Han, Hong Liu, Xiao Ming Yin, Zhiying Huang, Min Li
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers12040813

Ensartinib (X-396) Effectively Modulates Pharmacokinetic Resistance Mediated by ABCB1 and ABCG2 Drug Efflux Transporters and CYP3A4 Biotransformation Enzyme
Cited by: 19
Author(s): Dimitrios Vagiannis, Eva Novotná, Adam Skarka, Sarah Kammerer, Jan-Heiner Küpper, Si Chen, Lei Guo, František Štaud, Jakub Hofman
Software Mentions: 2
Published: over 6 years ago

10.1016/j.cell.2017.06.025

Development of a Novel Lead that Targets M. tuberculosis Polyketide Synthase 13
Cited by: 115
Author(s): Anup Aggarwal, Maloy Kumar Parai, N.D. Shetty, Deeann Wallis, Lisa K. Woolhiser, Courtney Hastings, Noton K. Dutta, Stacy Galaviz, Ramesh Dhakal, Rupesh Shrestha, Shoko Wakabayashi, Chris Walpole, David J. Matthews, David M. Floyd, Paul Scullion, Jennifer Riley, Ola Epemolu, Suzanne Norval, Thomas Snavely, Gregory T. Robertson, Eric J. Rubín, Thomas R. Ioerger, F A Sirgel, Ruben van der Merwe, Paul D. van Helden, Peter M. Keller, Erik C. Böttger, Petros C. Karakousis, Anne J. Lenaerts, James C. Sacchettini
Software Mentions: 2
Published: about 9 years ago

10.1107/S2053230X15008766

Structural characterization of the principal mRNA-export factor Mex67–Mtr2 from<i>Chaetomium thermophilum</i>
Cited by: 8
Author(s): Shintaro Aibara, Eugene Valkov, Meindert H. Lamers, Lyudmila Dimitrova, Ed Hurt, Murray Stewart
Software Mentions: 2
Published: about 11 years ago

10.1186/1745-6150-1-25

The signaling helix: a common functional theme in diverse signaling proteins
Cited by: 124
Author(s): Vivek Anantharaman, S. Balaji, L. Aravind
Software Mentions: 2
Published: almost 20 years ago

10.3389/fmicb.2020.01178

Structural and Functional Characterization of a Unique AP Endonuclease From Deinococcus radiodurans
Cited by: 6
Author(s): Yuan He, Yiyi Wang, Qin Chen, Ying Xu, Kaiying Cheng, Hong Xu, Bing Teng, Ye Zhao, Liangyan Wang, Yuejin Hua
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2105-13-55

CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure
Cited by: 13
Author(s): Jan-Oliver Janda, Markus Busch, Fabian Kück, Mikhail Porfenenko, Rainer Merkl
Software Mentions: 2
Published: over 14 years ago

10.1186/s13062-019-0232-2

Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions
Cited by: 24
Author(s): S Jayashree, Pavalam Murugavel, Ramanathan Sowdhamini, Narayanaswamy Srinivasan
Software Mentions: 2
Published: over 7 years ago

10.3390/cancers6031464

Phosphorylation of Large T Antigen Regulates Merkel Cell Polyomavirus Replication
Cited by: 19
Author(s): José Ángel Menéndez Díaz, Xin Wang, Sabrina H. Tsang, Jing Jiao, Jianxin You
Software Mentions: 2
Published: about 12 years ago

10.3389/fmicb.2018.01468

Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase From Shigella flexneri
Cited by: 15
Author(s): Xiaopan Gao, Zhixia Mu, Xia Yu, Bo Qin, Justyna Aleksandra Wojdyla, Meitian Wang, Sheng Cui
Software Mentions: 2
Published: about 8 years ago

10.3390/cancers13112843

Elevated Expression of the RAGE Variant-V in SCLC Mitigates the Effect of Chemotherapeutic Drugs
Cited by: 4
Author(s): Bindhu K. Madhavan, Zhe Han, B.K. Singh, Nico Bordt, Serap Kaymak, Obul Reddy Bandapalli, Lars Kihm, Khurrum Shahzad, Berend Isermann, Stephan Herzig, Peter P. Nawroth, Vaijayanti A. Kumar
Software Mentions: 2
Published: about 5 years ago

10.3390/biom11050642

The ‘Shape-Shifter’ Peptide from the Disulphide Isomerase PmScsC Shows Context-Dependent Conformational Preferences
Cited by: 1
Author(s): Lorna J. Smith, Chloe W. Green, Christina Redfield
Software Mentions: 2
Published: about 5 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

10.3390/cancers11121828

Synergy of Ginkgetin and Resveratrol in Suppressing VEGF-Induced Angiogenesis: A Therapy in Treating Colorectal Cancer
Cited by: 49
Author(s): Weihui Hu, Gallant Kar-Lun Chan, Ran Duan, Huaiyou Wang, Xiangpeng Kong, Tina Tingxia Dong, Karl Wah-Keung Tsim
Software Mentions: 2
Published: over 6 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

10.1107/S2053230X19009786

Crystal structure of the Schizosaccharomyces pombe U7BR E2-binding region in complex with Ubc7
Cited by: 1
Author(s): Z.S. Hann, Meredith B. Metzger, Allan M. Weissman, Christopher D. Lima
Software Mentions: 2
Published: almost 7 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

10.1371/journal.pone.0256141

Genomics-guided identification of potential modulators of SARS-CoV-2 entry proteases, TMPRSS2 and Cathepsins B/L
Cited by: 12
Author(s): Kartikay Prasad, Suliman Yousef Alomar, Eman Abdullah Almuqri, Hassan Ahmed Rudayni, Vijay Kumar
Software Mentions: 2
Published: almost 5 years ago

10.3390/biom11081218

Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars
Cited by: 3
Author(s): Atieh Moradi, Shuaijian Dai, Emily Oi Ying Wong, Guang Zhu, Fengchao Yu, Hon‐Ming Lam, Zhiyong Wang, A. L. Burlingame, Lin Chen, Alireza Afsharifar, Weichuan Yu, Tingliang Wang, Ning Li
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0248394

Anti-asthmatic effect of nitric oxide metallo-donor FOR811A [cis-[Ru(bpy)2(2-MIM)(NO)](PF6)3] in the respiratory mechanics of Swiss mice
Cited by: 6
Author(s): Paula Priscila Correia Costa, Stefanie Bressan Waller, Gilvan Ribeiro dos Santos, Fladimir de Lima Gondim, Daniel Silveira Serra, Francisco Sales Ávila Cavalcante, Florêncio Sousa Gouveia Júnior, Valdir Ferreira de Paula Júnior, Eduardo Henrique Silva Sousa, Luiz Gonzaga de França Lopes, Wesley Lyeverton Correia Ribeiro, Helena Serra Azul Monteiro
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0050769

Using RosettaLigand for Small Molecule Docking into Comparative Models
Cited by: 38
Author(s): Kristian Kaufmann, Jens Meiler
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0245358

Insights into structure and dynamics of extracellular domain of Toll-like receptor 5 in Cirrhinus mrigala (mrigala): A molecular dynamics simulation approach
Cited by: 8
Author(s): Ajaya Kumar Rout, Varsha Acharya, Diptimayee Maharana, Budheswar Dehury, Sheela Rani Udgata, Rajkumar Jena, Bhaskar Behera, Pranaya Kumar Parida, Bijay Kumar Behera
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0209420

Deciphering the ATP-binding mechanism(s) in NLRP-NACHT 3D models using structural bioinformatics approaches
Cited by: 22
Author(s): Jitendra Maharana, Debashis Panda, Sachinandan De
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0122512

Crystal Structure of a Two-Subunit TrkA Octameric Gating Ring Assembly
Cited by: 2
Author(s): Marc C. Deller, Hope A. Johnson, Mitchell D. Miller, Glen Spraggon, Marc‐André Elsliger, Ian A. Wilson, Scott A. Lesley
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0103099

In Silico Modeling of Human α2C-Adrenoreceptor Interaction with Filamin-2
Cited by: 11
Author(s): Marcin Pawłowski, Saras Saraswathi, Hanaa K. B. Motawea, Maqsood A. Chotani, Andrzej Kloczkowski
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0105984

Cleavage Specificity Analysis of Six Type II Transmembrane Serine Proteases (TTSPs) Using PICS with Proteome-Derived Peptide Libraries
Cited by: 46
Author(s): Olivier Barré, Antoine Dufour, Ulrich Eckhard, Reinhild Kappelhoff, François Béliveau, Richard Leduc, Christopher M. Overall
Software Mentions: 2
Published: almost 12 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

10.1016/j.cell.2021.01.037

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
Cited by: 508
Author(s): Emma C. Thomson, Laura E. Rosen, James G. Shepherd, Roberto Spreafico, Ana da Silva Filipe, Jason A. Wojcechowskyj, Chris Davis, Luca Piccoli, David Pascall, Josh R Dillen, Spyros Lytras, Nadine Czudnochowski, Rajiv Shah, Marcel Meury, Natasha Jesudason, Anna De Marco, Kathy Li, Jessica Bassi, Áine O’Toole, Dora Pinto, Rachel Colquhoun, Katja Culap, Ben Jackson, Fabrizia Zatta, Andrew Rambaut, Stefano Jaconi, Vattipally B Sreenu, Jay C. Nix, Ivy Zhang, Ruth F. Jarrett, William G. Glass, Martina Beltramello, Kyriaki Nomikou, Matteo Samuele Pizzuto, L. Tong, Elisabetta Cameroni, Tristan I. Croll, Natasha Johnson, Julia di Iulio, Arthur Wickenhagen, Alessandro Ceschi, Aoife M Harbison, Daniel Mair, Paolo Ferrari, Katherine Smollett, Federica Sallusto, Stephen Carmichael, Christian Garzoni, Jenna Nichols, Massimo Galli, Joseph Hughes, Agostino Riva, Antonia Ho, Marco Schiuma, Malcolm G Semple, Peter Openshaw, Elisa Fadda, J Kenneth Baillie, John D. Chodera, Suzannah J. Rihn, Samantha Lycett, Herbert W. Virgin, Amalio Telenti, Davide Corti, David L. Robertson, Gyorgy Snell
Software Mentions: 2
Published: over 5 years ago

10.15252/emmm.201404077

Efficient transduction and optogenetic stimulation of retinal bipolar cells by a synthetic adeno‐associated virus capsid and promoter
Cited by: 142
Author(s): Thérèse Cronin, Luk Vandenberghe, Péter Hantz, Josephine Jüttner, Andreas Reimann, Ágota–Enikő Kacsó, Rachel M. Huckfeldt, Volker Busskamp, Hubertus Kohler, Pamela S. Lagali, Botond Roska, Jean Bennett
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0069833

An Activating Mutation Reveals a Second Binding Mode of the Integrin α2 I Domain to the GFOGER Motif in Collagens
Cited by: 29
Author(s): Federico Carafoli, Samir Hamaia, Dominique Bihan, Erhard Hohenester, Richard W. Farndale
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0123996

Novel Non-Peptide Inhibitors against SmCL1 of Schistosoma mansoni: In Silico Elucidation, Implications and Evaluation via Knowledge Based Drug Discovery
Cited by: 5
Author(s): Atif Zafar, Sameena Ahmad, Asim Rizvi, Masood Ahmad
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0017624

Structure and Function of the First Full-Length Murein Peptide Ligase (Mpl) Cell Wall Recycling Protein
Cited by: 24
Author(s): Debanu Das, Mireille Hervé, Julie Feuerhelm, Carol L. Farr, Hsiu‐Ju Chiu, Marc‐André Elsliger, Mark W. Knuth, Heath E. Klock, Mitchell D. Miller, Adam Godzik, Scott A. Lesley, Ashley M. Deacon, Dominique Mengin‐Lecreulx, Ian A. Wilson
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0195355

Solution scattering study of the Bacillus subtilis PgdS enzyme involved in poly-γ-glutamic acids degradation
Cited by: 1
Author(s): Jumei Zeng, Yipeng Jin, Zhongchuan Liu
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0130888

Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies
Cited by: 16
Author(s): Shannon E. Hill, Rebecca K. Donegan, Elaine Nguyen, Tanay M. Desai, Raquel L. Lieberman
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0107000

Crystal Structure of the Mineralocorticoid Receptor DNA Binding Domain in Complex with DNA
Cited by: 39
Author(s): William Henry Hudson, Christine Youn, Eric A. Ortlund
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0140984

Improving the pH-stability of Versatile Peroxidase by Comparative Structural Analysis with a Naturally-Stable Manganese Peroxidase
Cited by: 40
Author(s): Verónica Sáez-Jiménez, Elena Fernández‐Fueyo, F.J. Medrano, Antonio Romero, Ángel T. Martínez, Francisco J. Ruíz-Dueñas
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0201556

Deciphering the targets of retroviral protease inhibitors in Plasmodium berghei
Cited by: 16
Author(s): Noah Machuki Onchieku, Reagan M. Mogire, Loise Ndung’u, Peter Mwitari, Francis Kimani, Damaris Matoke-Muhia, Daniel Kiboi, Gabriel Magoma
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0052642

Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases
Cited by: 6
Author(s): Cédric Grauffel, Angèle Abboud, Glen Liszczak, Ronen Marmorstein, Thomas Arnesen, Nathalie Reuter
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0024227

Get Phases from Arsenic Anomalous Scattering: de novo SAD Phasing of Two Protein Structures Crystallized in Cacodylate Buffer
Cited by: 22
Author(s): Xiang Liu, Heng Zhang, Wang Xiao-jun, Lanfen Li, Xiao‐Dong Su
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0224753

Streptococcal phosphotransferase system imports unsaturated hyaluronan disaccharide derived from host extracellular matrices
Cited by: 8
Author(s): Shigetoshi Oiki, Yusuke Nakamichi, Yukie Maruyama, Bunzo Mikami, Kousaku Murata, Wataru Hashimoto
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0121494

Crystal Structures of the Kinase Domain of the Sulfate-Activating Complex in Mycobacterium tuberculosis
Cited by: 9
Author(s): Ömer Poyraz, Katharina Brunner, Bernhard Lohkamp, Hanna Axelsson, Lars G.J. Hammarström, R. Schnell, Günter Schneider
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0216979

Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis
Cited by: 2
Author(s): Ke Shi, Chong-Min Kyung, Kelly G. Aukema, Thomas Lee, Asim K. Bera, Jennifer L. Seffernick, Lawrence P. Wackett, Hideki Aihara
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0042473

Crystal Structures of the Network-Forming Short-Arm Tips of the Laminin β1 and γ1 Chains
Cited by: 51
Author(s): Federico Carafoli, Sadaf-Ahmahni Hussain, Erhard Hohenester
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0097015

Structural Studies of an Anti-Inflammatory Lectin from Canavalia boliviana Seeds in Complex with Dimannosides
Cited by: 22
Author(s): G.A. Bezerra, Roland Viertlmayr, Tales Rocha de Moura, P. Delatorre, B.A.M. Rocha, Kyria S. Nascimento, Jozi Godoy Figueiredo, Ingrid Gonçalves Bezerra, C.S. Teixeira, Rafael Conceição Simões, Celso Shiniti Nagano, Nylane Maria Nunes de Alencar, Karl Gruber, Benildo S. Cavada
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0106936

Atomic Resolution Structure of a Protein Prepared by Non-Enzymatic His-Tag Removal. Crystallographic and NMR Study of GmSPI-2 Inhibitor
Cited by: 8
Author(s): Edyta Kopera, Wojciech Bal, Martina Lenarčič Živković, A. S. Dvornyk, Barbara Kłudkiewicz, Krystyna Grzelak, Igor Zhukov, Włodzimierz Zagórski-Ostoja, Mariusz Jaskólski, Szymon Krzywda
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0023582

Flanking Bases Influence the Nature of DNA Distortion by Platinum 1,2-Intrastrand (GG) Cross-Links
Cited by: 18
Author(s): Debadeep Bhattacharyya, Srinivas Ramachandran, Sanjai Sharma, Wimal Pathmasiri, Candice L. King, Irene Abraham, Gunnar Boysen, James A. Swenberg, Sharon L. Campbell, Nikolay V. Dokholyan, Stephen G. Chaney
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0104878

Molecular Analysis of Aedes aegypti Classical Protein Tyrosine Phosphatases Uncovers an Ortholog of Mammalian PTP-1B Implicated in the Control of Egg Production in Mosquitoes
Cited by: 7
Author(s): Débora Monteiro Moretti, Lalima G. Ahuja, Rodrigo Dutra Nunes, Cecília Oliveira Cudischevitch, Carlos Renato de Oliveira Daumas-Filho, Priscilla Medeiros-Castro, Guilherme Ventura-Martins, Willy Jablonka, Felipe Gazos-Lopes, Raquel Senna, Marcos Henrique Ferreira Sorgine, Klaus Hartfelder, Margareth Lara Capurro, Geórgia C. Atella, Rafael D. Mesquita, Mário A.C. Silva-Neto
Software Mentions: 2
Published: almost 12 years ago

10.1107/S1399004713033841

Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting
Cited by: 46
Author(s): Lei Chen, Tian Liu, Yong Zhou, Qi Chen, Xu Shen, Qing Yang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0223464

Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding
Cited by: 15
Author(s): Rumbidzai Chitongo, Adetayo Emmanuel Obasa, Sello Given Mikasi, Graeme Brendon Jacobs, Ruben Cloete
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0076793

Variation in One Residue Associated with the Metal Ion-Dependent Adhesion Site Regulates αIIbβ3 Integrin Ligand Binding Affinity
Cited by: 3
Author(s): Joel Raborn, Ting Fu, Xue Wu, Zhilong Xiu, Guohui Li, Bing Hao Luo
Software Mentions: 2
Published: almost 13 years ago

10.1107/S2053230X15015939

An active site–tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase
Cited by: 7
Author(s): Jesse Murphy, Stefano Donini, T.J. Kappock
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0160694

Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA
Cited by: 15
Author(s): Yinglu Zhang, Katarzyna Rataj, Gordon G. Simpson, Liang Tong
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0005479

Vaccinia Virus G8R Protein: A Structural Ortholog of Proliferating Cell Nuclear Antigen (PCNA)
Cited by: 13
Author(s): Melissa Da Silva, Chris Upton
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0186840

Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins
Cited by: 11
Author(s): Mykhaylo O. Debelyy, Patrice Waridel, Manfredo Quadroni, Roger Schneiter, Andreas Conzelmann
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-14-S3-S12

Concomitant prediction of function and fold at the domain level with GO-based profiles
Cited by: 4
Author(s): Daniel López, Florencio Pazos
Software Mentions: 2
Published: over 13 years ago

10.1107/S2053230X16017891

The crystal structure of the endoglucanase Cel10, a family 8 glycosyl hydrolase from<i>Klebsiella pneumoniae</i>
Cited by: 9
Author(s): Ayman Attigani, Lifang Sun, Qing Wang, Yadan Liu, Ding-Ping Bai, Shengping Li, Xiaohong Huang
Software Mentions: 2
Published: over 9 years ago

10.1107/S2053230X19006472

Structure of the Prx6-subfamily 1-Cys peroxiredoxin from <i>Sulfolobus islandicus</i>
Cited by: 5
Author(s): Sander Stroobants, Inge Van Molle, Queen Saidi, Karl Jonckheere, Dominique Maes, Eveline Peeters
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0227287

Two novel mutations in MSX1 causing oligodontia
Cited by: 5
Author(s): Yang Le, Jia Liang, Haitang Yue, Zhuan Bian
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0067158

Characterization of PUD-1 and PUD-2, two proteins up-regulated in a long-lived daf-2 mutant.
Cited by: 8
Author(s): Yue-He Ding, Yunguang Du, Shukun Luo, Yuxin Li, Tie-Mei Li, Sawako Yoshina, Xing Wang, Karsten Klage, Shohei Mitani, Keqiong Ye, Meng‐Qiu Dong
Software Mentions: 2
Published: over 13 years ago

10.1155/2019/6125068

Structural Basis for the Selective Inhibition of Cdc2-Like Kinases by CX-4945
Cited by: 17
Author(s): Joo Youn Lee, Ji-Sook Yun, Woo‐Keun Kim, Hang-Suk Chun, Hyeonseok Jin, Sungchan Cho, Jeong Ho Chang
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2105-15-56

iview: an interactive WebGL visualizer for protein-ligand complex
Cited by: 54
Author(s): Hongjian Li, Kwong‐Sak Leung, Takanori Nakane, Man Hon Wong
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0167755

Biophysical Studies of the Induced Dimerization of Human VEGF Receptor 1 Binding Domain by Divalent Metals Competing with VEGF-A
Cited by: 10
Author(s): Jonathan Gaucher, Marie Reille‐Seroussi, Nathalie Gagey‐Eilstein, Sylvain Broussy, Pascale Coric, Bili Seijo, Marie-Bernard Lascombe, Benoît Gautier, Wang-Quing Liu, Florent Huguenot, Nicolas Inguimbert, Serge Bouaziz, Michel Vidal, Isabelle Broutin
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-14-77

GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures
Cited by: 24
Author(s): Björn Hammesfahr, Florian Odronitz, Stefanie Mühlhausen, Stephan Waack, Martin Kollmar
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0215555

Heavy-atom labeling of RNA by PLOR for de novo crystallographic phasing
Cited by: 6
Author(s): Jason R. Stagno, Ping Yü, Marcin Dyba, Yun‐Xing Wang, Yu Liu
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0131077

Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening
Cited by: 19
Author(s): Harini Krishnan, Ramanathan Sowdhamini
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0018413

Co-Crystal Structures of PKG Iβ (92–227) with cGMP and cAMP Reveal the Molecular Details of Cyclic-Nucleotide Binding
Cited by: 51
Author(s): Jeong Joo Kim, Darren E. Casteel, Gary B. Huang, Tai Hun Kwon, Ronnie Kuo Ren, Peter H. Zwart, Jeffrey J. Headd, Nicholas G. Brown, Dar Chone Chow, Timothy Palzkill, Choel Kim
Software Mentions: 2
Published: about 15 years ago

10.1107/S2053230X15003337

High-resolution crystal structure of a polyextreme GH43 glycosidase from<i>Halothermothrix orenii</i>with α-<scp>L</scp>-arabinofuranosidase activity
Cited by: 7
Author(s): Noor Hassan, Lokesh D. Kori, Rosaria Gandini, Bharat K. C. Patel, Christina Divne, T.C. Tan
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0235990

Drug targeting CYP2E1 for the treatment of early-stage alcoholic steatohepatitis
Cited by: 18
Author(s): Torsten Diesinger, Vyacheslav Buko, Alfred Lautwein, Radovan Dvorský, Elena Belonovskaya, Oksana Lukivskaya, Elena Naruta, Siarhei Kirko, В. П. Андреев, Dominik Buckert, Sebastian Bergler, Christian Renz, Edith Schneider, Florian Kuchenbauer, Mukesh Kumar, Çagatay Güneş, Berthold Büchele, Thomas Simmet, Dieter Müller‐Enoch, Thomas Wirth, Thomas Haehner
Software Mentions: 2
Published: almost 6 years ago

10.1107/S139900471400830X

Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site
Cited by: 35
Author(s): Thanuja Gangi Setty, Christine Cho, Sowmya Govindappa, Michael A. Apicella, S. Ramaswamy
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0237999

Spectrum of clinical features and genetic variants in mevalonate kinase (MVK) gene of South Indian families suffering from Hyperimmunoglobulin D Syndrome
Cited by: 11
Author(s): Geeta Govindaraj, Abhinav Jain, Geetha Peethambaran, Rahul C. Bhoyar, Shamsudheen Karuthedath Vellarikkal, Arvind Ganapati, Pulukool Sandhya, Athulya Edavazhippurath, Dhananjayan Dhanasooraj, Jayakrishnan Machinary Puthenpurayil, Krishnan Chakkiyar, Anushree Mishra, Arushi Batra, Anu Punnen, Sathish Kumar, Sridhar Sivasubbu
Software Mentions: 2
Published: almost 6 years ago

10.3390/biomedicines8050119

Discovery of Hordenine as a Potential Inhibitor of Pyruvate Dehydrogenase Kinase 3: Implication in Lung Cancer Therapy
Cited by: 66
Author(s): Saleha Anwar, Taj Mohammad, Anas Shamsi, Aarfa Queen, Shabana Parveen, Suaib Luqman, Gulam Mustafa Hasan, Khalid A. Alamry, Naved Azum, Abdullah M. Asiri, Md. Imtaiyaz Hassan
Software Mentions: 2
Published: about 6 years ago

10.1107/S2053230X15019986

Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking
Cited by: 28
Author(s): Tobias Rumpf, S. Gerhardt, Oliver Einsle, Manfred Jung
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-15-75

Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis
Cited by: 1
Author(s): Debanu Das, Alexey G. Murzin, Neil D. Rawlings, Alex Bateman, Penelope Coggill, Alex Bateman, Adam Godzik, L. Aravind
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0196642

Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance
Cited by: 9
Author(s): Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean Johnson
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0072368

SCMCRYS: Predicting Protein Crystallization Using an Ensemble Scoring Card Method with Estimating Propensity Scores of P-Collocated Amino Acid Pairs
Cited by: 73
Author(s): Phasit Charoenkwan, Watshara Shoombuatong, Hua Chin Lee, Jeerayut Chaijaruwanich, Hui Ling Huang, Shinn‐Ying Ho
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2105-7-14

Local protein structure prediction using discriminative models
Cited by: 64
Author(s): Oliver Sander, Iris E. Sommer, Thomas Lengauer
Software Mentions: 2
Published: over 20 years ago

10.1186/1471-2105-11-429

Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models
Cited by: 50
Author(s): Kasper Stovgaard, Christian Andreetta, Jesper Ferkinghoff‐Borg, Thomas Hamelryck
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0043019

Structures of Human DPP7 Reveal the Molecular Basis of Specific Inhibition and the Architectural Diversity of Proline-Specific Peptidases
Cited by: 23
Author(s): G.A. Bezerra, E. Dobrovetsky, Aiping Dong, Almagul Seitova, Lissete Crombett, Lisa M. Shewchuk, Annie M. Hassell, Sharon Sweitzer, Thomas D. Sweitzer, Patrick McDevitt, Kyung Johanson, Karen M. Kennedy-Wilson, D. Cossar, A. Bochkarev, Karl Gruber, Sirano Dhe‐Paganon
Software Mentions: 2
Published: almost 14 years ago

10.1107/S2053230X17008093

Crystal structure of a family 6 cellobiohydrolase from the basidiomycetePhanerochaete chrysosporium
Cited by: 8
Author(s): Mikako Tachioka, Akihiko Nakamura, Takuya Ishida, Kiyohiko Igarashi, Masahiro Samejima
Software Mentions: 2
Published: about 9 years ago

10.1155/2016/7562368

Identification of Deleterious Mutations in<i>Myostatin</i>Gene of Rohu Carp (<i>Labeo rohita</i>) Using Modeling and Molecular Dynamic Simulation Approaches
Cited by: 8
Author(s): Kiran D. Rasal, Vemulawada Chakrapani, Swagat Kumar Patra, SD Mohapatra, S.K. Nayak, Sasmita Jena, Jitendra Kumar Sundaray, P. Jayasankar, Hirak Kumar Barman
Software Mentions: 2
Published: over 10 years ago

10.1007/s13205-017-0858-7

Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana
Cited by: 32
Author(s): Bong-Gyu Mun, Sang-Uk Lee, Eung‐Jun Park, Hyunho Kim, Adil Hussain, Qari Muhammad Imran, In‐Jung Lee, Byung‐Wook Yun
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0226657

Biophysical analysis of Plasmodium falciparum Hsp70-Hsp90 organising protein (PfHop) reveals a monomer that is characterised by folded segments connected by flexible linkers
Cited by: 11
Author(s): Stanley Makumire, Tawanda Zininga, Juha Vahokoski, Inari Kursula, Addmore Shonhai
Software Mentions: 2
Published: about 6 years ago

10.1107/S139900471401267X

Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein
Cited by: 16
Author(s): James A. J. Arpino, P.J. Rizkallah, D. Dafydd Jones
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0201234

How does binding of agonist ligands control intrinsic molecular dynamics in human NMDA receptors?
Cited by: 5
Author(s): Zoltan Palmai, Kimberley Houenoussi, Sylvia Cohen‐Kaminsky, Luba Tchertanov
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-13-S4-S2

PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL
Cited by: 130
Author(s): Emanuele Bramucci, Alessandro Paiardini, Francesco Bossa, Stefano Pascarella
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0090915

Crystal Structures of the Novel Cytosolic 5′-Nucleotidase IIIB Explain Its Preference for m7GMP
Cited by: 13
Author(s): Thomas Monecke, Juliane Buschmann, Piotr Neumann, Elmar Wahle, Ralf Ficner
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0175723

Soaking suggests “alternative facts”: Only co-crystallization discloses major ligand-induced interface rearrangements of a homodimeric tRNA-binding protein indicating a novel mode-of-inhibition
Cited by: 31
Author(s): F.R. Ehrmann, Johann Stojko, A. Metz, François Debaene, Luzi Jakob Barandun, A. Heine, François Diederich, Sarah Cianférani, Klaus Reuter, G. Klebe
Software Mentions: 2
Published: about 9 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: over 11 years ago

10.1371/journal.pone.0191610

Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii
Cited by: 1
Author(s): Bhumika S. Shah, Heather E. Ashwood, S.J. Harrop, Daniel N. Farrugia, Ian T. Paulsen, Bridget C. Mabbutt
Software Mentions: 2
Published: over 8 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

10.1371/journal.pone.0082705

New Insights into the Phylogeny and Molecular Classification of Nicotinamide Mononucleotide Deamidases
Cited by: 7
Author(s): Guiomar Sánchez-Carrón, Ana Belén Martínez-Moñino, Agustín Sola-Carvajal, Hideto Takami, Francisco García-Carmona, Álvaro Sánchez‐Ferrer
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0041710

Predicting HLA Class I Non-Permissive Amino Acid Residues Substitutions
Cited by: 21
Author(s): T.A. Binkowski, Susana R. Marino, A. Joachimiak
Software Mentions: 2
Published: almost 14 years ago

10.3390/biom10040615

Insight into the RssB-Mediated Recognition and Delivery of σs to the AAA+ Protease, ClpXP
Cited by: 10
Author(s): Dimce Micevski, Kornelius Zeth, Terrence D. Mulhern, Verena J. Schuenemann, Jessica E. Zammit, Kaye N. Truscott, David A. Dougan
Software Mentions: 2
Published: about 6 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