10.1107/S1399004714026777

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation
Cited by: 10
Author(s): Alan Gray, Oliver G. Harlen, Sarah A. Harris, Syma Khalid, Yuk Ming Leung, Richard Lonsdale, Adrian J. Mulholland, Arwen R. Pearson, Daniel J. Read, Robin A. Richardson
Software Mentions: 2
Published: almost 11 years ago

10.1016/j.cell.2021.03.055

Antibody evasion by the P.1 strain of SARS-CoV-2
Cited by: 480
Author(s): Wanwisa Dejnirattisai, Daming Zhou, Piyada Supasa, C Liu, Alexander J. Mentzer, H. Ginn, Yuguang Zhao, Duyvesteyn Hme., Aekkachai Tuekprakhon, Rungtiwa Nutalai, Beibei Wang, César López-Camacho, J Slon-Campos, Thomas S. Walter, Donal Skelly, Sue Ann Costa Clemens, Felipe Gomes Naveca, Valdinete Alves do Nascimento, Felipe Franco Nascimento, Cristiano Fernandes da Costa, Paola Cristina Resende, Alex Pauvolid‐Corrêa, Marilda Mendonça Siqueira, Christina Dold, Robert H. Levin, Tao Dong, Andrew J. Pollard, Julian C. Knight, Derrick W. Crook, Teresa Lambe, Elizabeth A. Clutterbuck, Sagida Bibi, Amy Flaxman, Mustapha Bittaye, Sandra Belij‐Rammerstorfer, Sarah C. Gilbert, Miles W. Carroll, Paul Klenerman, Eleanor Barnes, Susanna Dunachie, Neil G. Paterson, Mark A. Williams, ' Hall, Ruben J.G. Hulswit, Thomas A. Bowden, Elizabeth E. Fry, Juthathip Mongkolsapaya, Jingshan Ren, D.I. Stuart, Gavin Screaton
Software Mentions: 2
Published: over 4 years ago

10.1107/S2053230X18002236

Crystal structure of theMSMEG_4306gene product fromMycobacterium smegmatis
Cited by: 1
Author(s): Adarsh Kumar, Subramanian Karthikeyan
Software Mentions: 2
Published: over 7 years ago

10.1016/j.cell.2021.06.020

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum
Cited by: 571
Author(s): C Liu, H. Ginn, Wanwisa Dejnirattisai, Piyada Supasa, Beibei Wang, Aekkachai Tuekprakhon, Rungtiwa Nutalai, Daming Zhou, Alexander J. Mentzer, Yuguang Zhao, Duyvesteyn Hme., César López-Camacho, J Slon-Campos, T S Walter, Donal Skelly, Síle A. Johnson, Thomas G. Ritter, Chris Mason, Sue Ann Costa Clemens, Felipe Gomes Naveca, Valdinete Alves do Nascimento, Fernanda Nascimento, Cristiano Fernandes da Costa, Paola Cristina Resende, Alex Pauvolid‐Corrêa, Marilda Mendonça Siqueira, Christina Dold, Nigel Temperton, Tao Dong, Andrew J. Pollard, Julian C. Knight, Derrick W. Crook, Teresa Lambe, Elizabeth A. Clutterbuck, Sagida Bibi, Amy Flaxman, Mustapha Bittaye, Sandra Belij‐Rammerstorfer, Sarah C. Gilbert, Tariq Malik, Miles W. Carroll, Paul Klenerman, Eleanor Barnes, Susanna Dunachie, Vicky L. Baillie, Natali Serafin, Zanele Ditse, K Da Silva, Neil G. Paterson, Mark A. Williams, David R. Hall, Shabir A. Madhi, Marta C Nunes, Philip Goulder, Elizabeth E. Fry, Juthathip Mongkolsapaya, Jingshan Ren, D.I. Stuart, Gavin Screaton
Software Mentions: 2
Published: over 4 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: about 7 years ago

10.1007/s10858-019-00247-3

Characterization of H/D exchange in type 1 pili by proton-detected solid-state NMR and molecular dynamics simulations
Cited by: 4
Author(s): Songhwan Hwang, Carl Öster, Veniamin Chevelkov, Karin Giller, Adam Lange, Stefan Becker, Adam Lange
Software Mentions: 2
Published: over 6 years ago

10.1016/j.cell.2010.05.037

A Comprehensive Comparison of Transmembrane Domains Reveals Organelle-Specific Properties
Cited by: 467
Author(s): Hayley J. Sharpe, Tim J. Stevens, Sean Munro
Software Mentions: 2
Published: over 15 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: over 14 years ago

10.1083/jcb.201910059

Molecular basis of MKLP2-dependent Aurora B transport from chromatin to the anaphase central spindle
Cited by: 23
Author(s): Michela Serena, Ricardo Bastos, P.R. Elliott, Francis A. Barr
Software Mentions: 2
Published: over 5 years ago

10.1038/cddis.2016.255

Kinsenoside screening with a microfluidic chip attenuates gouty arthritis through inactivating NF-κB signaling in macrophages and protecting endothelial cells
Cited by: 33
Author(s): Han Qiao, Bing Wang, Dong Yin, Hua Li, Shihe Li, Yongri Zheng, Xiaozhe Han, Yugang Wang, Qing Fan, Shuo Yang, Tingting Tang
Software Mentions: 2
Published: about 9 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: over 5 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: over 11 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 5 years ago

10.1186/1758-2946-4-17

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
Cited by: 5,518
Author(s): Marcus D. Hanwell, Donald Curtis, David Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey Hutchison
Software Mentions: 2
Published: over 13 years ago

10.3390/cancers12061412

A H-REV107 Peptide Inhibits Tumor Growth and Interacts Directly with Oncogenic KRAS Mutants
Cited by: 10
Author(s): Chang Woo Han, Mi Suk Jeong, Soonhoi Ha, Se Bok Jang
Software Mentions: 2
Published: over 5 years ago

10.1186/1753-6561-9-S6-S5

MoFlow: visualizing conformational changes in molecules as molecular flow improves understanding
Cited by: 7
Author(s): Shareef M Dabdoub, R. Wolfgang Rumpf, Amber D. Shindhelm, William C. Ray
Software Mentions: 2
Published: over 10 years ago

10.1107/S0907444913025250

Improvements in the order, isotropy and electron density of glypican-1 crystals by controlled dehydration
Cited by: 13
Author(s): W. Awad, Gabriel Svensson Birkedal, Marjolein M.G.M. Thunnissen, Katrin Mani, D.T. Logan
Software Mentions: 2
Published: almost 12 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 5 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 4 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: over 4 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: over 4 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: about 14 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: almost 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: over 5 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: about 12 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: almost 6 years ago

10.1038/s41419-018-0689-4

The cyclohexene derivative MC-3129 exhibits antileukemic activity via RhoA/ROCK1/PTEN/PI3K/Akt pathway-mediated mitochondrial translocation of cofilin
Cited by: 8
Author(s): Yi Zheng, Qin Ouyang, Ruoqiu Fu, Lei Liu, Hongwei Zhang, Xiaoye Hu, Yanxia Liu, Ying‐Chun Chen, Ning Gao
Software Mentions: 2
Published: over 7 years ago

10.1289/ehp.1306902

Mimicking of Estradiol Binding by Flame Retardants and Their Metabolites: A Crystallographic Analysis
Cited by: 79
Author(s): R.A. Gosavi, Gabriel A. Knudsen, Linda S. Birnbaum, Lars C. Pedersen
Software Mentions: 2
Published: about 12 years ago

10.3389/fpls.2017.01878

Novel Ribonuclease Activity Differs between Fibrillarins from Arabidopsis thaliana
Cited by: 9
Author(s): Ulises Rodríguez-Corona, Alejandro Pereira-Santana, Margarita Sobol, Luis Carlos Rodríguez-Zapata, Pavel Hozák, Enrique Castaño
Software Mentions: 2
Published: about 8 years ago

10.1186/s13321-020-00460-5

Molecular representations in AI-driven drug discovery: a review and practical guide
Cited by: 176
Author(s): Laurianne David, Amol Thakkar, Rocío Mercado, Ola Engkvist
Software Mentions: 2
Published: about 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: almost 7 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: almost 5 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: about 11 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 10 years ago

10.1186/s12870-019-2136-9

Defining the function of SUMO system in pod development and abiotic stresses in Peanut
Cited by: 11
Author(s): Yiyang Liu, Jianqing Zhu, Sheng Sun, Feng Cui, Han Yan, Zhenying Peng, Xuejie Zhang, Shubo Wan, Guowei Li
Software Mentions: 2
Published: almost 6 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: over 11 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: over 13 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: over 12 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: over 10 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 14 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: about 5 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: over 5 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 7 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: about 10 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 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: over 14 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: over 6 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: over 7 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: almost 9 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: almost 12 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: about 6 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: about 14 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: about 11 years ago

10.18632/aging.103396

Identification of cardiovascular health gene variants related to longevity in a Chinese population
Cited by: 3
Author(s): Li Zhang, Chen Bai, Chao Nie, Xiaoquan Zhu, Huiping Yuan, Liang Sun, Qi Zhou, Xiaoling Li, Xuan Xian, Fan Yang, Guo‐Fang Pang, Yuan Lv, Xiaolin Ni, Chengping Hu, Ze Yang
Software Mentions: 2
Published: about 5 years ago

10.1107/S2059798317016618

Molecular architectures of benzoic acid-specific type III polyketide synthases
Cited by: 11
Author(s): Charles Stewart, Kate Woods, Greg Macias, Andrew C. Allan, Roger P. Hellens, Joseph P. Noel
Software Mentions: 2
Published: almost 8 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: over 5 years ago

10.18632/aging.103775

Coupled immune stratification and identification of therapeutic candidates in patients with lung adenocarcinoma
Cited by: 9
Author(s): Wenquan Hu, Guosheng Wang, Yundi Chen, Lonny Yarmus, Biao Liu, Yuan Wan
Software Mentions: 2
Published: about 5 years ago

10.1107/S205979832001133X

Helical ensembles outperform ideal helices in molecular replacement
Cited by: 2
Author(s): Filomeno Sánchez Rodríguez, Adam J Simpkin, Owen R. Davies, Ronan Keegan, Daniel J. Rigden
Software Mentions: 2
Published: about 5 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: about 11 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: over 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: about 4 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: about 12 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: over 10 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: over 8 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: about 13 years ago

10.1371/journal.pone.0036526

Structural Analyses of the Slm1-PH Domain Demonstrate Ligand Binding in the Non-Canonical Site
Cited by: 21
Author(s): K. Anand, Kenji Maeda, Anne‐Claude Gavin
Software Mentions: 2
Published: over 13 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: over 7 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: about 12 years ago

10.1371/journal.pone.0064363

Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability
Cited by: 65
Author(s): Bryan S. Der, Christien Kluwe, Aleksandr E. Miklos, Ron Jacak, Sergey Lyskov, Jeffrey J. Gray, George Georgiou, Andrew D. Ellington, Brian Kuhlman
Software Mentions: 2
Published: over 12 years ago

10.1107/S0907444913027534

Extending molecular-replacement solutions with<i>SHELXE</i>
Cited by: 80
Author(s): Andrea Thorn, George M. Sheldrick
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0006820

The Crystal Structure of the Escherichia coli Autoinducer-2 Processing Protein LsrF
Cited by: 17
Author(s): Zamia Diaz, Karina B. Xavier, Stephen T. Miller
Software Mentions: 2
Published: about 16 years ago

10.1186/s12866-018-1190-z

Beta-defensin derived cationic antimicrobial peptides with potent killing activity against gram negative and gram positive bacteria
Cited by: 30
Author(s): Ming Yang, Chunye Zhang, Michael Z. Zhang, Shuping Zhang
Software Mentions: 2
Published: over 7 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: about 8 years ago

10.1371/journal.pone.0170232

NOD1CARD Might Be Using Multiple Interfaces for RIP2-Mediated CARD-CARD Interaction: Insights from Molecular Dynamics Simulation
Cited by: 15
Author(s): Jitendra Maharana, Sukanta Kumar Pradhan, Sachinandan De
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0040066

The Crystal Structures of Dystrophin and Utrophin Spectrin Repeats: Implications for Domain Boundaries
Cited by: 27
Author(s): M. Muthu, Kylie A. Richardson, Andrew J. Sutherland-Smith
Software Mentions: 2
Published: over 13 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: over 9 years ago

10.1371/journal.pone.0188267

Antigenicity of the 2015–2016 seasonal H1N1 human influenza virus HA and NA proteins
Cited by: 44
Author(s): Amelia Clark, Marta L. DeDiego, Christopher Anderson, Jiong Wang, Hongmei Yang, Aitor Nogales, Luis Martinez‐Sobrido, Martin S. Zand, Mark Y. Sangster, David J. Topham
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0248634

Prediction of LncRNA-encoded small peptides in glioma and oligomer channel functional analysis using in silico approaches
Cited by: 6
Author(s): Yipeng Cao, Rui Yang, Imshik Lee, Wenwen Zhang, Jiana Sun, Xiangfei Meng, Wei Wang
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0188005

Crystal structures of ternary complexes of archaeal B-family DNA polymerases
Cited by: 36
Author(s): H.M. Kropp, Karin Betz, Johannes Wirth, Kay Diederichs, Andreas Marx
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0140953

Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain
Cited by: 4
Author(s): Wenjie Wang, Cheng Wang, Ming Luo, Qingyu Yan, Gino Yu, Qiong Li, Dong Cao, Shengfeng Huang, Anlong Xu, Roy A. Mariuzza, Yuxing Chen, Cong‐Zhao Zhou
Software Mentions: 2
Published: about 10 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 7 years ago

10.1371/journal.pone.0143876

The First Extracellular Domain Plays an Important Role in Unitary Channel Conductance of Cx50 Gap Junction Channels
Cited by: 12
Author(s): Xiaoling Tong, Hiroshi Aoyama, Swathy Sudhakar, Honghong Chen, Brian H. Shilton, Donglin Bai
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0063370

Structural Basis for the Oligomerization-State Switch from a Dimer to a Trimer of an Engineered Cortexillin-1 Coiled-Coil Variant
Cited by: 2
Author(s): Saša Bjelić, Mara M. Wieser, Daniel Frey, Christian U. Stirnimann, Mark R. Chance, Rolf Jaussi, Michel O. Steinmetz, Richard A. Kammerer
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0184627

Structure-based design, synthesis and crystallization of 2-arylquinazolines as lipid pocket ligands of p38α MAPK
Cited by: 10
Author(s): Mike Bührmann, Bianca Wiedemann, Matthias Müller, Julia Hardick, Mary Ecke, Daniel Rauh
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0195442

An antibody with Fab-constant domains exchanged for a pair of CH3 domains
Cited by: 9
Author(s): Gordana Wozniak‐Knopp, Gerhard Stadlmayr, Jan Walther Perthold, Katharina Stadlbauer, Mathias Gotsmy, Stefan Becker, Florian Rüker
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0174284

Structural insights into the regulation of Bacillus subtilis SigW activity by anti-sigma RsiW
Cited by: 19
Author(s): Shankar Raj Devkota, Eunju Kwon, Soonhoi Ha, Hyeun Wook Chang, Dong Young Kim
Software Mentions: 2
Published: over 8 years ago

10.1107/S1399004714022755

Structural implications of the C-terminal tail in the catalytic and stability properties of manganese peroxidases from ligninolytic fungi
Cited by: 33
Author(s): Elena Fernández‐Fueyo, Sandra Acebes, Francisco J. Ruíz-Dueñas, Marı́a Jesús Martı́nez, Antonio Romero, F.J. Medrano, Vı́ctor Guallar, Ángel T. Martı́nez
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0128310

Structural Studies of the HIV-1 Integrase Protein: Compound Screening and Characterization of a DNA-Binding Inhibitor
Cited by: 15
Author(s): Peter K. Quashie, Ying-Shan Han, Said Hassounah, Thibault Mésplède, Mark A. Wainberg
Software Mentions: 2
Published: over 10 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: over 7 years ago

10.1371/journal.pone.0114373

Crystal Structure of the Fibre Head Domain of the Atadenovirus Snake Adenovirus 1
Cited by: 15
Author(s): Abhimanyu Singh, Rosa Menéndez-Conejero, Carmen San Martín, Mark J. van Raaij
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0193028

Folic acid derived-P5779 mimetics regulate DAMP-mediated inflammation through disruption of HMGB1:TLR4:MD-2 axes
Cited by: 13
Author(s): Shan Sun, Mingzhu He, Yongjun Wang, Huan Yang, Yousef Al‐Abed
Software Mentions: 2
Published: over 7 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 4 years ago

10.1371/journal.pone.0134084

Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes
Cited by: 12
Author(s): Radhika Ganu, Yasuko Ishida, Markos Koutmos, Sergios‐Orestis Kolokotronis, Alfred L. Roca, Timothy A. Garrow, Lawrence B. Schook
Software Mentions: 2
Published: over 10 years ago

10.1107/S2059798320000212

3D domain swapping in the TIM barrel of the α subunit of<i>Streptococcus pneumoniae</i>tryptophan synthase
Cited by: 3
Author(s): K. Michalska, Marcin Kowiel, L. Bigelow, M. Endres, Mirosław Gilski, Mariusz Jaskólski, A. Joachimiak
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0075446

A Purine Analog Synergizes with Chloroquine (CQ) by Targeting Plasmodium falciparum Hsp90 (PfHsp90)
Cited by: 23
Author(s): Dea Shahinas, Asongna Folefoc, Tony Taldone, Gabriela Chiosis, Ian Crandall, Dylan R. Pillai
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0242383

The crystal structure of mouse IRG1 suggests that cis-aconitate decarboxylase has an open and closed conformation
Cited by: 4
Author(s): Hye Lin Chun, So Yeon Lee, Ki-Hwa Kim, Chang Sup Lee, Tae‐Jin Oh, Hyun Ho Park
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0181551

Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain
Cited by: 8
Author(s): Amélie Wallenhammar, Madhanagopal Anandapadamanaban, Alexander Lemak, Claudio Mirabello, Patrik Lundström, Björn Wallner, Maria Sunnerhagen
Software Mentions: 2
Published: over 8 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: about 6 years ago

10.1371/journal.pone.0234869

Whole-genome sequencing reveals origin and evolution of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018
Cited by: 7
Author(s): Xiaonan Zhao, Han-Ju Zhang, Duo Li, Ji Zhou, Y. Chen, Yanhong Sun, Adeniyi C. Adeola, Xiaoqing Fu, Yong Shao, Meiling Zhang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0081904

New Conformational State of NHERF1-CXCR2 Signaling Complex Captured by Crystal Lattice Trapping
Cited by: 10
Author(s): Yuanyuan Jiang, Guorong Lu, Laura Trescott, Yuning Hou, Xiaoqing Guan, Shuo Wang, Angelique Stamenkovich, J.S. Brunzelle, Nualpun Sirinupong, Chunying Li, Zhe Yang
Software Mentions: 2
Published: almost 12 years ago