Ecosyste.ms: Papers

10.1155/2020/7151634

Deciphering the Molecular Targets and Mechanisms of HGWD in the Treatment of Rheumatoid Arthritis via Network Pharmacology and Molecular Docking
Cited by: 21
Author(s): Wei Liu, Yihua Fan, Chunying Tian, Yue Jin, Shaopeng Du, Ping Zeng, Aihua Wang
Software Mentions: 2
Published: about 4 years ago

10.1038/s41431-020-00728-2

NAA10 p.(N101K) disrupts N-terminal acetyltransferase complex NatA and is associated with developmental delay and hemihypertrophy
Cited by: 6
Author(s): Nina McTiernan, Harinder Gill, Carlos E. Prada, Harry Pachajoa, Juliana Lores, Causes Study, Thomas Arnesen
Software Mentions: 2
Published: about 4 years ago

10.1111/1462-2920.13036

Closing the gaps on the viral photosystem‐ <scp>I</scp> <i> psa <scp>DCAB</scp> </i> gene organization
Cited by: 7
Author(s): Sheila Roitman, José Flores‐Uribe, Alon Philosof, Ben Knowles, Forest Rohwer, J. Cesar Ignacio‐Espinoza, Matthew B. Sullivan, Francisco M. Cornejo‐Castillo, Pablo Sánchez, Silvia G. Acinas, Chris L. Dupont, Oded Béjà
Software Mentions: 2
Published: about 9 years ago

10.1016/j.ejmech.2018.04.035

Aminobenzothiazole derivatives stabilize the thermolabile p53 cancer mutant Y220C and show anticancer activity in p53-Y220C cell lines
Cited by: 52
Author(s): Matthias G. J. Baud, Matthias R. Bauer, Lorena Verduci, Felix A. Dingler, Ketan Patel, Debmalya Roy, A.C. Joerger, Alan R. Fersht
Software Mentions: 2
Published: over 6 years ago

10.1080/22221751.2021.1899770

The preclinical inhibitor GS441524 in combination with GC376 efficaciously inhibited the proliferation of SARS-CoV-2 in the mouse respiratory tract
Cited by: 33
Author(s): Yuejun Shi, Lei Shuai, Zhiyuan Wen, Chong Wang, Yuanyuan Yan, Zhe Jiao, Fenglin Guo, Zhen F. Fu, Huanchun Chen, Zhigao Bu, Guiqing Peng
Software Mentions: 2
Published: almost 4 years ago

10.1080/22221751.2020.1865840

Structure of the multiple functional domains from coronavirus nonstructural protein 3
Cited by: 8
Author(s): Mengxia Li, Gang Ye, Yu Si, Zhou Shen, Zhu Liu, Yuejun Shi, Shaobo Xiao, Zhen F. Fu, Guiqing Peng
Software Mentions: 2
Published: almost 4 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 11 years ago

10.1155/2020/3219840

Screening for a Potential Therapeutic Agent from the Herbal Formula in the 4th Edition of the Chinese National Guidelines for the Initial-Stage Management of COVID-19 via Molecular Docking
Cited by: 13
Author(s): Yue Sun, Angela Wei Hong Yang, Andrew Hung, George Binh Lenon
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2017.01860

Engineering of Fc Fragments with Optimized Physicochemical Properties Implying Improvement of Clinical Potentials for Fc-Based Therapeutics
Cited by: 51
Author(s): Chunpeng Yang, Xinyu Gao, Rui Gong
Software Mentions: 2
Published: almost 7 years ago

10.15252/embr.201847183

Structural basis of <scp>HEAT</scp> ‐kleisin interactions in the human condensin I subcomplex
Cited by: 18
Author(s): Kodai Hara, Kazuhisa Kinoshita, Tomoko Migita, Kei Murakami, Kenichiro Shimizu, K. Takeuchi, Takeshi Hirano, Hiroshi Hashimoto
Software Mentions: 2
Published: over 5 years ago

10.15252/embr.201745680

Active site alanine mutations convert deubiquitinases into high‐affinity ubiquitin‐binding proteins
Cited by: 40
Author(s): Marie E. Morrow, Michael T. Morgan, Marcello Clerici, Kateřina Growková, Ming Yan, David Komander, Titia K. Sixma, Michal Šimíček, Cynthia Wolberger
Software Mentions: 2
Published: about 6 years ago

10.15252/embr.201847182

Multiple C2 domains and transmembrane region proteins ( <scp>MCTP</scp> s) tether membranes at plasmodesmata
Cited by: 78
Author(s): Marie Brault, J.P. Petit, Françoise Immel, William J Nicolas, Marie Glavier, Lysiane Brocard, Amèlia Gaston, Mathieu Fouché, Timothy J. Hawkins, Jean-Marc Crowet, Magali Grison, V. Germain, Marion Rocher, Max Kraner, Vikram Alva, Stéphane Claverol, Andrea Paterlini, Yrjö Helariutta, Magali Deleu, Laurence Lins, Jens Tilsner, Emmanuelle Bayer
Software Mentions: 2
Published: over 5 years ago

10.1186/s12900-015-0037-1

Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase
Cited by: 8
Author(s): Norbert Schormann, Surajit Banerjee, Robert P. Ricciardi, Debasish Chattopadhyay
Software Mentions: 2
Published: over 9 years ago

10.15252/emmm.201911248

A high‐affinity, bivalent <scp>PDZ</scp> domain inhibitor complexes <scp>PICK</scp> 1 to alleviate neuropathic pain
Cited by: 16
Author(s): Nikolaj Riis Christensen, Marta De Luca, Michael Brett Lever, Mette Richner, Astrid B Hansen, Gith Noes-Holt, Kathrine L. Jensen, Mette Rathje, Dennis Bo Jensen, Simon Erlendsson, Christian R. O. Bartling, Ina Ammendrup-Johnsen, Sofie Pedersen, Michèle Schönauer, Klaus B. Nissen, Søren Roi Midtgaard, Kaare Teilum, Andreas T. Sørensen, Anders Bach, Kristian Strømgaard, Claire Francesca Meehan, Christian Bjerggaard Vægter, Ulrik Gether, Kenneth L. Madsen
Software Mentions: 2
Published: over 4 years ago

10.15252/embr.201540436

Structure and function of the N‐terminal domain of the human mitochondrial calcium uniporter
Cited by: 80
Author(s): Youngjin Lee, Choon Kee Min, Tae Kyun Kim, Heesang Song, Young‐Hun Lim, Dong-Wook Kim, Kyung Shik Shin, Minji Kang, Jung Youn Kang, Hyung‐Seop Youn, Jung‐Gyu Lee, Jin Yong An, Kyoung Ryoung Park, Jia Jia Lim, Ji Hun Kim, Zee Yong Park, Yeon‐Soo Kim, Jimin Wang, Do Han Kim, Soo Hyun Eom
Software Mentions: 2
Published: about 9 years ago

10.1002/ece3.7582

The complete mitogenome of <i>Phymorhynchus</i> sp. (Neogastropoda, Conoidea, Raphitomidae) provides insights into the deep‐sea adaptive evolution of Conoidea
Cited by: 7
Author(s): Mei Yang, Dong Dong, Xinzheng Li
Software Mentions: 2
Published: over 3 years ago

10.1186/1472-6807-10-16

Structural definition and substrate specificity of the S28 protease family: the crystal structure of human prolylcarboxypeptidase
Cited by: 48
Author(s): S.M. Soisson, Sangita Patel, Pravien Abeywickrema, Noel Byrne, Ronald E. Diehl, Dawn L. Hall, Rachael E. Ford, John C. Reid, Keith Rickert, Jennifer M. Shipman, Sujata Sharma, Kevin J. Lumb
Software Mentions: 2
Published: almost 15 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: over 7 years ago

10.15252/embj.2019101603

Structures of neurexophilin–neurexin complexes reveal a regulatory mechanism of alternative splicing
Cited by: 15
Author(s): Steven C Wilson, K. Ian White, Qiuhong Zhou, Richard A. Pfuetzner, Ucheor B. Choi, Thomas C. Südhof, Axel T. Brunger
Software Mentions: 2
Published: about 5 years ago

10.15252/embj.2020105127

Identification and characterization of diverse OTU deubiquitinases in bacteria
Cited by: 33
Author(s): Alexander F Schubert, Justine Nguyen, Tyler G. Franklin, Paul P. Geurink, Cameron G Roberts, Daniel J. Sanderson, Lauren N. Miller, Huib Ovaa, Kay Hofmann, Jonathan N. Pruneda, David Komander
Software Mentions: 2
Published: over 4 years ago

10.15252/embj.201797278

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD
Cited by: 51
Author(s): Kiran Bountra, Gregor Hagelueken, Hassanul G. Choudhury, Valentina Corradi, Kamel El Omari, Armin Wagner, Indran Mathavan, Séverine Zirah, Weixiao Yuan Wahlgren, D. Peter Tieleman, Olav Schiemann, Sylvie Rebuffat, Konstantinos Beis
Software Mentions: 2
Published: about 7 years ago

10.15252/embj.2019103889

Proteasomal degradation induced by DPP9‐mediated processing competes with mitochondrial protein import
Cited by: 21
Author(s): Yannik Finger, Markus Habich, Sarah Gerlich, Sophia Urbanczyk, Erik van de Logt, Julian Koch, Laura Schu, Kim Jasmin Lapacz, Muna Ali, Carmelina Petrungaro, Silja Lucia Salscheider, C. Pichlo, Ulrich Baumann, Dirk Mielenz, Jörn Dengjel, Bent Brachvogel, Kay Hofmann, Jan Riemer
Software Mentions: 2
Published: over 4 years ago

10.15252/embj.2019103234

Structural basis for centromere maintenance by <i>Drosophila</i> <scp>CENP</scp> ‐A chaperone <scp>CAL</scp> 1
Cited by: 27
Author(s): Bethan Medina‐Pritchard, Vasiliki Lazou, Juan Zou, Olwyn Byron, Maria Alba Abad, Juri Rappsilber, Patrick Heun, A. Arockia Jeyaprakash
Software Mentions: 2
Published: over 4 years ago

10.1002/ece3.52

Regulatory versus coding signatures of natural selection in a candidate gene involved in the adaptive divergence of whitefish species pairs ( Coregonus spp.)
Cited by: 15
Author(s): Julie Jeukens, Louis Bernatchez
Software Mentions: 2
Published: almost 13 years ago

10.3389/fimmu.2017.00771

Nanobody Technology: A Versatile Toolkit for Microscopic Imaging, Protein–Protein Interaction Analysis, and Protein Function Exploration
Cited by: 142
Author(s): Els Beghein, Jan Gettemans
Software Mentions: 2
Published: over 7 years ago

10.1186/1472-6807-12-29

MTMDAT-HADDOCK: High-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry
Cited by: 11
Author(s): Janosch Hennig, Sjoerd J. de Vries, Klaus Dm Hennig, Leah Randles, Kylie J. Walters, Maria Sunnerhagen, Alexandre M. J. J. Bonvin
Software Mentions: 2
Published: almost 13 years ago

10.1186/1472-6807-12-32

Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme’s active site closure
Cited by: 22
Author(s): Jaeok Park, Yih‐Shyan Lin, Joris W. De Schutter, Youla S. Tsantrizos, Albert M. Berghuis
Software Mentions: 2
Published: almost 12 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: almost 12 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: over 13 years ago

10.1186/1472-6807-13-17

Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a β-solenoid structure
Cited by: 9
Author(s): Metaxia Vlassi, Katharina Brauns, Miguel A. Andrade‐Navarro
Software Mentions: 2
Published: almost 12 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: over 13 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: about 12 years ago

10.1371/journal.pone.0154046

Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics
Cited by: 2
Author(s): Gloria Ruiz-Gómez, John C. Hawkins, Patrick Jenny, Georg Künze, Robert Wodtke, Reik Löser, Karim Fahmy, M. Teresa Pisabarro
Software Mentions: 2
Published: over 8 years ago

10.1186/s12900-018-0096-1

Deciphering evolution of immune recognition in antibodies
Cited by: 4
Author(s): Harmeet Kaur, Neetu Sain, Debasisa Mohanty, Dinakar M. Salunke
Software Mentions: 2
Published: almost 6 years ago

10.1107/S1744309111016551

Structures of the rat complement regulator CrrY
Cited by: 4
Author(s): Pietro Roversi, Steven Johnson, Joseph Caesar, Florence McLean, K.J. Leath, Stefanos A. Tsiftsoglou, B. Paul Morgan, Claire L. Harris, Robert B. Sim, Susan M. Lea
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0067536

Towards Ligand Docking Including Explicit Interface Water Molecules
Cited by: 58
Author(s): Gordon Lemmon, Jens Meiler
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0119760

In Silico Screening for Novel Inhibitors of DNA Polymerase III Alpha Subunit of Mycobacterium tuberculosis (MtbDnaE2, H37Rv)
Cited by: 14
Author(s): Alka Jadaun, Raja Sudhakar D, Naidu Subbarao, Aparna Dixit
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0206143

Primary structures of different isoforms of buffalo pregnancy-associated glycoproteins (BuPAGs) during early pregnancy and elucidation of the 3-dimensional structure of the most abundant isoform BuPAG 7
Cited by: 7
Author(s): Masoud Lotfan, Suman Choudhary, Munna Lal Yadav, Sudarshan Kumar, Surender Singh, Shveta Bathla, Preeti Rawat, Jai K. Kaushik, Ashok Kumar Mohanty
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0114903

An Integrative Computational Approach for Prioritization of Genomic Variants
Cited by: 7
Author(s): Inna Dubchak, Sandhya Balasubramanian, Sheng Wang, Cem Meyden, Dinanath Sulakhe, Alexander Poliakov, Daniela Börnigen, Bingqing Xie, Andrew Taylor, Jianzhu Ma, Alex R. Paciorkowski, Ghayda Mirzaa, Paul Dave, Gady Agam, Jinbo Xu, Lihadh Al‐Gazali, Christopher E. Mason, M. Elizabeth Ross, Natalia Maltsev, T. Conrad Gilliam
Software Mentions: 2
Published: almost 10 years ago

10.1242/dmm.043307

Temperature sensitive SMA-causing point mutations lead to SMN instability, locomotor defects, and premature lethality in Drosophila
Cited by: 4
Author(s): Amanda C. Raimer, S. S. Singh, Maina R. Edula, Tamara Paris-Davila, Vasudha Vandadi, Ashlyn M. Spring, A. Gregory Matera
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0170260

Targeted Deletion of a Plasmodium Site-2 Protease Impairs Life Cycle Progression in the Mammalian Host
Cited by: 5
Author(s): Konstantinos Koussis, Evi Goulielmaki, Anna Chalari, Chrislaine Withers‐Martinez, Inga Sidén‐Kiamos, Kai Matuschewski, Thanasis G. Loukeris
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0029406

Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII
Cited by: 21
Author(s): Melanie I. Stefan, David P. Marshall, Nicolas Le Novère
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0062021

Structure of the Non-Catalytic Domain of the Protein Disulfide Isomerase-Related Protein (PDIR) Reveals Function in Protein Binding
Cited by: 20
Author(s): R. Vinaik, Guennadi Kozlov, Kalle Gehring
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0251067

Heterogeneous multimeric structure of isocitrate lyase in complex with succinate and itaconate provides novel insights into its inhibitory mechanism
Cited by: 4
Author(s): Sunghoon Kwon, Hye Lin Chun, Hyekyung Ha, So Yeon Lee, Hyun Ho Park
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0092636

In-Silico Analysis of Binding Site Features and Substrate Selectivity in Plant Flavonoid-3-O Glycosyltransferases (F3GT) through Molecular Modeling, Docking and Dynamics Simulation Studies
Cited by: 12
Author(s): Ranu Sharma, Priyabrata Panigrahi, C.G. Suresh
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0239702

SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique
Cited by: 7
Author(s): Timothy R. Stachowski, M. Elizabeth Snell, Edward H. Snell
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0128225

Structural and Biochemical Characterization of the Francisella tularensis Pathogenicity Regulator, Macrophage Locus Protein A (MglA)
Cited by: 8
Author(s): Bonnie J. Cuthbert, Richard G. Brennan, Maria A. Schumacher
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0008949

An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome
Cited by: 26
Author(s): Danny A. Bitton, Duncan L. Smith, Yvonne Connolly, Paul J. Scutt, Crispin Miller
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12862-015-0581-0

Analysis of the erythropoietin of a Tibetan Plateau schizothoracine fish (Gymnocypris dobula) reveals enhanced cytoprotection function in hypoxic environments
Cited by: 26
Author(s): Qianghua Xu, Chi Zhang, Dongsheng Zhang, Huapeng Jiang, Syd S. Peng, Yang Liu, Kai Zhao, Congcong Wang, Liangbiao Chen
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0082484

Structure-Based Analysis of A19D, a Variant of Transthyretin Involved in Familial Amyloid Cardiomyopathy
Cited by: 5
Author(s): Priscila S. Ferreira, Oliveira Sant’Anna, Nathalia Varejão, Cristina Ferreira Lima, Sérgio A. P. Novis, Renata V. Barbosa, Concy M. Caldeira, Franklin David Rumjanek, Salvador Ventura, Márcia Waddington Cruz, Débora Foguel
Software Mentions: 2
Published: almost 11 years ago

10.1107/S0907444912051670

Structural studies of<i>Pseudomonas</i>and<i>Chromobacterium</i>ω-aminotransferases provide insights into their differing substrate specificity
Cited by: 50
Author(s): C. Sayer, Michail N. Isupov, Aaron Westlake, Jennifer A. Littlechild
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2148-8-336

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?
Cited by: 77
Author(s): Véronique Douard, Frédéric Brunet, Bastien Boussau, Isabelle Ahrens-Fath, Virginie Vlaeminck-Guillem, Bernard Haendler, Vincent Laudet, Yann Guiguen
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0026251

Structural Analysis of Prolyl Oligopeptidases Using Molecular Docking and Dynamics: Insights into Conformational Changes and Ligand Binding
Cited by: 28
Author(s): Sushmita Kaushik, Ramanathan Sowdhamini
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0123195

An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor β (RARβ, NR1B2) Selective Agonist
Cited by: 12
Author(s): Nadendla EswarKumar, Catherine Teyssier, V. Delfosse, Valérie Vivat, Krishnasamy Gunasekaran, Hinrich Gronemeyer, William Bourguet, Pierre Germain
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0081753

Heterologous Expression of Mycobacterial Esx Complexes in Escherichia coli for Structural Studies Is Facilitated by the Use of Maltose Binding Protein Fusions
Cited by: 22
Author(s): M.A. Arbing, Sammy Chan, L.R. Harris, E. Kuo, T. Zhou, Christine J. Ahn, Ludivine David NGuyen, Cyndi Qixin He, Jamie Lu, Phuong T. Menchavez, Ae Sun Shin, Thomas Holton, M.R. Sawaya, Duilio Cascio, David Eisenberg
Software Mentions: 2
Published: almost 11 years ago

10.1080/10717544.2018.1428245

HSA-based multi-target combination therapy: regulating drugs’ release from HSA and overcoming single drug resistance in a breast cancer model
Cited by: 31
Author(s): Yanzi Gou, Zhenlei Zhang, Dongyang Li, Lei Zhao, Meiling Cai, Zhigang Sun, Yongping Li, Yao Zhang, Hina Khan, Hongbing Sun, Tao Wang, Hong Liang, Feng Yang
Software Mentions: 2
Published: almost 7 years ago

10.3389/fimmu.2021.625808

Structural Basis of VSIG3: The Ligand for VISTA
Cited by: 11
Author(s): Xiaoxue Xie, Caiping Chen, Wenting Chen, Jingwei Jiang, Lanlan Wang, Tingting Li, Hongbin Sun, Jun Li
Software Mentions: 2
Published: over 3 years ago

10.1016/j.jbc.2021.100713

The mycobacterial proteasomal ATPase Mpa forms a gapped ring to engage the 20S proteasome
Cited by: 3
Author(s): Yuanyuan Yin, Amanda Kovach, Hao-Chi Hsu, K. Heran Darwin, Huilin Li
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0086050

Tracking Molecular Recognition at the Atomic Level with a New Protein Scaffold Based on the OB-Fold
Cited by: 18
Author(s): John D. Steemson, Matthias Baake, Jasna Rakonjac, Vickery L. Arcus, Mark T. Liddament
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0039850

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

10.1371/journal.pone.0076355

Crystal Structure of the Human Short Coiled Coil Protein and Insights into SCOC-FEZ1 Complex Formation
Cited by: 6
Author(s): Caroline Behrens, Beyenech Binotti, Carla Schmidt, Carol V. Robinson, John Jia En Chua, Karin Kühnel
Software Mentions: 2
Published: about 11 years ago

10.1107/S2053230X15008584

Structure of human saposin A at lysosomal pH
Cited by: 11
Author(s): C.P. Hill, Randy J. Read, Janet E. Deane
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0044124

Complex Structure of Engineered Modular Domains Defining Molecular Interaction between ICAM-1 and Integrin LFA-1
Cited by: 3
Author(s): Sungkwon Kang, Chae Un Kim, Xiaoling Gu, Róisı́n M. Owens, Sarah J. van Rijn, Vanissra Boonyaleepun, Yuxin Mao, Timothy A. Springer, Moonsoo M. Jin
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0081526

Structural Insights into the Mechanism for Recognizing Substrate of the Cytochrome P450 Enzyme TxtE
Cited by: 18
Author(s): Feng Yu, Minjun Li, Chunyan Xu, Zhijun Wang, Huan Zhou, Min Yang, Yaxing Chen, Lin Tang, Jianhua He
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0099408

Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes
Cited by: 16
Author(s): Laura J. Kingsley, Markus A. Lill
Software Mentions: 2
Published: over 10 years ago

10.1186/s12906-018-2116-x

Computational investigations of physicochemical, pharmacokinetic, toxicological properties and molecular docking of betulinic acid, a constituent of Corypha taliera (Roxb.) with Phospholipase A2 (PLA2)
Cited by: 37
Author(s): Mohammad Firoz Khan, Nusrat Nahar, Ridwan Bin Rashid, A. K. Chowdhury, Mohammad A. Rashid
Software Mentions: 2
Published: almost 7 years ago

10.1107/S2059798316007907

Structural basis for acyl-group discrimination by human Gcn5L2
Cited by: 44
Author(s): Alison E. Ringel, Cynthia Wolberger
Software Mentions: 2
Published: over 8 years ago

10.1107/S2059798321000826

<i>Vagabond</i>: bond-based parametrization reduces overfitting for refinement of proteins
Cited by: 8
Author(s): H. Ginn
Software Mentions: 2
Published: over 3 years ago

10.1107/S2053230X15001351

Improved crystallization and diffraction of caffeine-induced death suppressor protein 1 (Cid1)
Cited by: 1
Author(s): Luke A. Yates, Benjamin P. Durrant, M. Barber, K. Harlos, Sophie Fleurdépine, Chris J. Norbury, Robert J.C. Gilbert
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0245822

Sequence and structure comparison of ATP synthase F0 subunits 6 and 8 in notothenioid fish
Cited by: 3
Author(s): Gunjan Katyal, Brad Ebanks, Magnus Lucassen, Chiara Papetti, Lisa Chakrabarti
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0045379

BioFET-SIM Web Interface: Implementation and Two Applications
Cited by: 10
Author(s): Martin R. Hediger, Jan H. Jensen, Luca De Vico
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0175758

Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages
Cited by: 8
Author(s): Qi Chen, Michał Vieth, David E. Timm, Christine Humblet, Dina Stroopinsky, Ilan E. Chemmama, Andrej Šali, Wei Zeng, Jirong Lu, Ling Liu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0165917

Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes
Cited by: 14
Author(s): Norbert Schormann, Chapelle A. Ayres, Fry Alexandra, Todd Green, Surajit Banerjee, Glen C. Ulett, Debasish Chattopadhyay
Software Mentions: 2
Published: about 8 years ago

10.1107/S2053230X15024437

Crystal structure of the flavoenzyme PA4991 fromPseudomonas aeruginosa
Cited by: 0
Author(s): Agata Jacewicz, R. Schnell, Ylva Lindqvist, Günter Schneider
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0039993

Analysis of Conformational Variation in Macromolecular Structural Models
Cited by: 6
Author(s): Sandeep Srivastava, S Gayathri, Babu A. Manjasetty, B. Gopal
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0075992

Ligand Pose and Orientational Sampling in Molecular Docking
Cited by: 123
Author(s): Ryan G. Coleman, Michael Carchia, Teague Sterling, John J. Irwin, Brian K. Shoichet
Software Mentions: 2
Published: about 11 years ago

10.1107/S2059798320010505

Crystal structures of human ENPP1 in apo and bound forms
Cited by: 18
Author(s): Matthew L. Dennis, Janet Newman, Olan Dolezal, Meghan Hattarki, Regina Surjadi, Stewart D. Nuttall, Tam Pham, Thomas Nebl, Michelle Camerino, Poh Sim Khoo, Brendon J. Monahan, T.S. Peat
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0242686

Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ
Cited by: 12
Author(s): William C. Scott, Brian Lowrance, Alexander C Anderson, Joel T. Weadge
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0061327

Prospecting for Novel Plant-Derived Molecules of Rauvolfia serpentina as Inhibitors of Aldose Reductase, a Potent Drug Target for Diabetes and Its Complications
Cited by: 46
Author(s): Shivalika Pathania, Vinay Randhawa, Ganesh Bagler
Software Mentions: 2
Published: over 11 years ago

10.1107/S2053230X17001376

Crystal structure of the type IV secretion system component CagX fromHelicobacter pylori
Cited by: 7
Author(s): Jin Zhang, Fan Fei, Yunmeng Zhao, Lifang Sun, Yadan Liu, Ronan Keegan, Michail N. Isupov, Yunkun Wu
Software Mentions: 2
Published: over 7 years ago

10.1107/S1399004714025188

Analysis of the HindIII-catalyzed reaction by time-resolved crystallography
Cited by: 2
Author(s): Takashi Kawamura, Tomoki Kobayashi, Nobuhisa Watanabe
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0020864

Identification of the Allosteric Regulatory Site of Insulysin
Cited by: 36
Author(s): Nicholas Noinaj, Sonia K. Bhasin, Eun Suk Song, Kirsten E. Scoggin, María A. Juliano, Luiz Juliano, Louis B. Hersh, David W. Rodgers
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0193760

MIP diversity from Trichoderma: Structural considerations and transcriptional modulation during mycoparasitic association with Fusarium solani olive trees
Cited by: 10
Author(s): Maroua Ben Amira, Robin Mom, David Lopez, Hatem Chaar, Ali Khouaja, Valérie Pujade-Renaud, Boris Fumanal, Aurélie Gousset-Dupont, Gisèle Bronner, Philippe Label, Jean-Louis Julien, Mohamed Ali Triki, Daniel Auguin, Jean-Stéphane Venisse
Software Mentions: 2
Published: over 6 years ago

10.1107/S1399004714019725

Structural characterization of the virulence factor nuclease A from<i>Streptococcus agalactiae</i>
Cited by: 7
Author(s): A.F. Moon, Philippe Gaudu, Lars C. Pedersen
Software Mentions: 2
Published: about 10 years ago

10.1107/S2053230X20006172

Enhanced X-ray diffraction of <i>in vivo</i>-grown μNS crystals by viscous jets at XFELs
Cited by: 5
Author(s): Nirupa Nagaratnam, Yanyang Tang, Sabine Botha, Justin M. Saul, Chufeng Li, Hao Hu, Sahba Zaare, Mark S. Hunter, David Lowry, Uwe Weierstall, Nadia A. Zatsepin, John C. H. Spence, Ji Qiu, Joshua LaBaer, Petra Fromme, José M. Martín-García
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0216427

Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain
Cited by: 22
Author(s): Md. Imran Khan, Deepu Dowarha, Revansiddha Katte, Ruey Hwang Chou, Anna Filipek, Chin Yu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12906-015-0588-5

Molecular docking studies of (4Z, 12Z)-cyclopentadeca-4, 12-dienone from Grewia hirsuta with some targets related to type 2 diabetes
Cited by: 36
Author(s): Abirami Natarajan, Shanmugam Shobana, B. Sivakumar, Natarajan Balasubramanyan
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0152049

On the Applicability of Elastic Network Models for the Study of RNA CUG Trinucleotide Repeat Overexpansion
Cited by: 8
Author(s): Àlex L. González, Jordi Teixidó, José I. Borrell, Roger Estrada‐Tejedor
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0255736

Network pharmacology and molecular docking reveal the effective substances and active mechanisms of Dalbergia Odoriferain protecting against ischemic stroke
Cited by: 3
Author(s): Kedi Liu, Xingru Tao, Jing Su, Fĕi Li, Fei Mu, S. J. Zhao, Xinming Lu, Jing Li, Sha Chen, Taiwei Dong, Jialin Duan, Peifeng Wei, Miaomiao Xi
Software Mentions: 2
Published: about 3 years ago

10.1186/s12862-021-01819-4

Searching for signatures of positive selection in cytochrome b gene associated with subterranean lifestyle in fast-evolving arvicolines (Arvicolinae, Cricetidae, Rodentia)
Cited by: 5
Author(s): Olga Bondareva, Nadezhda A. Potapova, Kirill A. Konovalov, Tatyana V. Petrova, Natalia I. Abramson
Software Mentions: 2
Published: over 3 years ago

10.1107/S205979832001253X

Structure of a GH51 α-<scp>L</scp>-arabinofuranosidase from <i>Meripilus giganteus</i>: conserved substrate recognition from bacteria to fungi
Cited by: 7
Author(s): N.G.S. McGregor, J.P. Turkenburg, Kristian B. R. M. Krogh, Jens Erik Nielsen, Marta Artola, Keith A. Stubbs, Herman S. Overkleeft, G.J. Davies
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0139137

Engineering Streptavidin and a Streptavidin-Binding Peptide with Infinite Binding Affinity and Reversible Binding Capability: Purification of a Tagged Recombinant Protein to High Purity via Affinity-Driven Thiol Coupling
Cited by: 10
Author(s): Dawson Fogen, Sau‐Ching Wu, Kenneth Ng, Sui‐Lam Wong
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0210842

Potent, multi-target serine protease inhibition achieved by a simplified β-sheet motif
Cited by: 7
Author(s): Xingchen Chen, Blake T. Riley, Simon J. de Veer, David E. Hoke, Jessica Van Haeften, Darren Leahy, Joakim E. Swedberg, Maria Brattsand, Perry J. Hartfield, Ashley M. Buckle, Jonathan M. Harris
Software Mentions: 2
Published: almost 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: over 13 years ago

10.1107/S2053230X1501657X

High-resolution structures of<i>Lactobacillus salivarius</i>transketolase in the presence and absence of thiamine pyrophosphate
Cited by: 1
Author(s): P. Lukacik, C.M.C. Lobley, Mario Bumann, Victoria Arena De Souza, Raymond J. Owens, Paul W. O’Toole, Martin A. Walsh
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0076803

Elucidation of Substrate Specificity in Aspergillus nidulans UDP-Galactose-4-Epimerase
Cited by: 7
Author(s): Sean A. Dalrymple, Jennifer S. Ko, I. S. Sheoran, Susan G. W. Kaminskyj, D.A.R. Sanders
Software Mentions: 2
Published: about 11 years ago

10.1107/S2053230X14003793

1.55 Å resolution X-ray crystal structure of Rv3902c fromMycobacterium tuberculosis
Cited by: 1
Author(s): Bharat Reddy, Derek Moates, Heung-Bok Kim, Todd Green, Chang-Yub Kim, Thomas C. Terwilliger, Lawrence J. DeLucas
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0097519

Differential Effects of CSF-1R D802V and KIT D816V Homologous Mutations on Receptor Tertiary Structure and Allosteric Communication
Cited by: 11
Author(s): Priscila da Silva Figueiredo Celestino Gomes, Nicolas Panel, Élodie Laine, Pedro Geraldo Pascutti, Éric Solary, Luba Tchertanov
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0158702

Membrane Mediated Antimicrobial and Antitumor Activity of Cathelicidin 6: Structural Insights from Molecular Dynamics Simulation on Multi-Microsecond Scale
Cited by: 13
Author(s): Bikash R. Sahoo, Toshimichi Fujiwara
Software Mentions: 2
Published: over 8 years ago

10.1107/S2053230X18012992

Crystal structures and kinetics of<i>N</i>-acetylneuraminate lyase from<i>Fusobacterium nucleatum</i>
Cited by: 5
Author(s): J. Kumar, Harshvardhan Rao, Vinod Nayak, S. Ramaswamy
Software Mentions: 2
Published: about 6 years ago