pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0008672

Critical Structural and Functional Roles for the N-Terminal Insertion Sequence in Surfactant Protein B Analogs
Cited by: 49
Author(s): Frans J. Walther, Alan J. Waring, José M. Hernández-Juviel, Larry M. Gordon, Zhengdong Wang, Chun‐Ling Jung, Piotr Ruchala, Andrew P. Clark, Wesley M. Smith, Sanjai Sharma, Robert H. Notter
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0151806

Involvement of Endoplasmic Reticulum Stress in TULP1 Induced Retinal Degeneration
Cited by: 23
Author(s): Glenn P. Lobo, Adrian Au, Philip D. Kiser, Stephanie A. Hagstrom
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0010104

Protein Evolution via Amino Acid and Codon Elimination
Cited by: 9
Author(s): Lise Goltermann, Marie Sofie Yoo Larsen, Rajat Banerjee, A.C. Joerger, Michael Ibba, Thomas Bentin
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0021875

Structural and Sequence Analysis of Imelysin-Like Proteins Implicated in Bacterial Iron Uptake
Cited by: 18
Author(s): Qingping Xu, Neil D. Rawlings, Carol L. Farr, Hsiu‐Ju Chiu, Joanna C Grant, Lukasz Jaroszewski, Heath E. Klock, Mark W. Knuth, Mitchell D. Miller, Dana Weekes, Marc‐André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0083958

Functional Consequences of the Macrophage Stimulating Protein 689C Inflammatory Bowel Disease Risk Allele
Cited by: 16
Author(s): Steven E. Kauder, Lydia Santell, Elaine Mai, Lilyan Wright, Elizabeth Luis, Elsa N N'Diaye, Jeff Lutman, Navneet Ratti, M. Susan, Henry R. Maun, Eric Stefanich, Lino C. Gonzalez, Robert Graham, Lauri Diehl, William A. Faubion, Mary E. Keir, Judy Young, Amitabha Chaudhuri, Robert A. Lazarus, Jackson G. Egen
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0173582

Identification of small molecule inhibitors for influenza a virus using in silico and in vitro approaches
Cited by: 24
Author(s): Juliann Nzembi Makau, Ken Watanabe, Takeshi Ishikawa, Satoshi Mizuta, Takashi Hamada, Nobuyuki Kobayashi, Naoshi Nishida
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0124377

Molecular Dynamics Simulation Reveals Insights into the Mechanism of Unfolding by the A130T/V Mutations within the MID1 Zinc-Binding Bbox1 Domain
Cited by: 46
Author(s): Yunjie Zhao, Chen Zeng, Michael A. Massiah
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0049849

A Computational Methodology to Screen Activities of Enzyme Variants
Cited by: 16
Author(s): Martin R. Hediger, Luca De Vico, Allan Svendsen, Werner Besenmatter, Jan H. Jensen
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0044317

Sub-Domains of Ricin’s B Subunit as Targets of Toxin Neutralizing and Non-Neutralizing Monoclonal Antibodies
Cited by: 31
Author(s): Anastasiya Yermakova, David J. Vance, Nicholas J. Mantis
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0027228

Profiling of Substrate Specificities of 3C-Like Proteases from Group 1, 2a, 2b, and 3 Coronaviruses
Cited by: 69
Author(s): Chi-Pang Chuck, Hak‐Fun Chow, David Chi Cheong Wan, Kam‐Bo Wong
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0193667

Crystal structure and insights into the oligomeric state of UDP-glucose pyrophosphorylase from sugarcane
Cited by: 11
Author(s): Camila A. Cotrim, José Sérgio Soares, Boštjan Kobe, Marcelo Menossi
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0053840

Crystallographic Observation of pH-Induced Conformational Changes in the Amyelois transitella Pheromone-Binding Protein AtraPBP1
Cited by: 35
Author(s): Eric di Luccio, Yuko Ishida, Walter S. Leal, D. Keith Wilson
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0028833

Effect of P to A Mutation of the N-Terminal Residue Adjacent to the Rgd Motif on Rhodostomin: Importance of Dynamics in Integrin Recognition
Cited by: 11
Author(s): Jia Hau Shiu, Chiu Yueh Chen, Yi Chun Chen, Yao Chang, Yung Sheng Chang, Chen‐Hung Huang, Woei Jer Chuang
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0134879

Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization
Cited by: 7
Author(s): Nan Wang, Jiahong Jiang, Xichen Li, Hongwei Tan, Jimin Zheng, Guangju Chen, Zongchao Jia
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0164662

The Biophysical Characterisation and SAXS Analysis of Human NLRP1 Uncover a New Level of Complexity of NLR Proteins
Cited by: 12
Author(s): Luigi Martino, Louise Holland, Evangelos Christodoulou, Simone Kunzelmann, Diego Esposito, Katrin Rittinger
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0177330

Action of tyrosinase on alpha and beta-arbutin: A kinetic study
Cited by: 46
Author(s): Antonio García‐Jiménez, José A. Teruel, José Berná, José Neptuno Rodríguez-López, José Tudela, Francisco Garcı́a-Cánovas
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0221666

Structural analysis of the recognition of the -35 promoter element by SigW from Bacillus subtilis
Cited by: 5
Author(s): Eunju Kwon, Shankar Raj Devkota, Deepak Pathak, Pawan Dahal, Dong Young Kim
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0026939

Structure Analysis of a New Psychrophilic Marine Protease
Cited by: 16
Author(s): Si-Cai Zhang, Ming Sun, Li Tang, Qihai Wang, Jianhua Hao, Yujie Han, Xiaojian Hu, Ming Zhou, Sheng‐Xiang Lin
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0007179

βα-Hairpin Clamps Brace βαβ Modules and Can Make Substantive Contributions to the Stability of TIM Barrel Proteins
Cited by: 18
Author(s): Xiao-Yan Yang, Sagar V. Kathuria, Ramakrishna Vadrevu, C. Robert Matthews
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0079687

High Resolution Crystal Structure of Human β-Glucuronidase Reveals Structural Basis of Lysosome Targeting
Cited by: 50
Author(s): Md. Imtaiyaz Hassan, Abdül Waheed, Jeffery H. Grubb, Herbert E. Klei, Sergey Korolev, William S. Sly
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0120692

On the Role of Protein Disulfide Isomerase in the Retrograde Cell Transport of Secreted Phospholipases A2
Cited by: 9
Author(s): Jernej Oberčkal, Lidija Kovačič, Jernej Šribar, Adrijana Leonardi, Klemen Dolinar, Anja Pucer Janež, Igor Križaj
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0185060

Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms
Cited by: 11
Author(s): Jie Deng, Hua Gao, Zhen Gao, Huaxian Zhao, Ying Yang, Qiaofen Wu, Bo Wu, Chengjian Jiang
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0107457

Small-Angle X-Ray Scattering Reveals Compact Domain-Domain Interactions in the N-Terminal Region of Filamin C
Cited by: 10
Author(s): Ritika Sethi, Jari Ylänne
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0055516

Isolation of a High Affinity Neutralizing Monoclonal Antibody against 2009 Pandemic H1N1 Virus That Binds at the ‘Sa’ Antigenic Site
Cited by: 13
Author(s): Nachiket Shembekar, Vamsee Mallajosyula, Arpita Mishra, Leena Yeolekar, Rajeev M. Dhere, Subhash V. Kapre, Raghavan Varadarajan, Seema Gupta
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0210100

Holistic engineering of Cal-A lipase chain-length selectivity identifies triglyceride binding hot-spot
Cited by: 13
Author(s): Daniela Quaglia, Lorea Alejaldre, Sara Ouadhi, Olivier Rousseau, Joelle N. Pelletier
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0180772

Comparative studies of three cholesteryl ester transfer proteins and their interactions with known inhibitors
Cited by: 3
Author(s): Ziyun Wang, Manabu Niimi, Qiao Ding, Zhenming Liu, Ling Wang, Jifeng Zhang, Jun Xu, Jianglin Fan
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0182382

Crystal structure of mimivirus uracil-DNA glycosylase
Cited by: 5
Author(s): Eunju Kwon, Deepak Pathak, Hyeun Wook Chang, Dong Young Kim
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0029948

Structural and Functional Insights into Endoglin Ligand Recognition and Binding
Cited by: 86
Author(s): Aaron Alt, Laura Miguel-Romero, Jordi Donderis, Mikel Aristorena, Francisco J. Blanco, Adam Round, Vicente Rubio, Carmelo Bernabeu, Alberto Marina
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0087750

CorA Is a Copper Repressible Surface-Associated Copper(I)-Binding Protein Produced in Methylomicrobium album BG8
Cited by: 13
Author(s): Kenneth A. Johnson, Thomas Ve, Øivind Larsen, Rolf B. Pedersen, Johan R. Lillehaug, Harald B. Jensen, Ronny Helland, Odd André Karlsen
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0054899

Potassium and Ionic Strength Effects on the Conformational and Thermal Stability of Two Aldehyde Dehydrogenases Reveal Structural and Functional Roles of K+-Binding Sites
Cited by: 13
Author(s): Georgina Garza‐Ramos, Carlos Mújica-Jiménez, Rosario A. Muñoz‐Clares
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0094978

Identification of a Novel Function of CX-4945 as a Splicing Regulator
Cited by: 70
Author(s): Hyeongki Kim, Kwangman Choi, Hyunju Kang, So-Young Lee, Seung‐Wook Chi, Min‐Sung Lee, Song Jaehyoung, Im Donghwa, Young‐Ho Choi, Sungchan Cho
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0048389

Predicting Turns in Proteins with a Unified Model
Cited by: 6
Author(s): Qi Song, Tonghua Li, Cong Peng, Jiangming Sun, Dapeng Li, Shengnan Tang
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0021327

High-Resolution X-Ray Structure of the Trimeric Scar/WAVE-Complex Precursor Brk1
Cited by: 10
Author(s): Joern Linkner, Gregor Witte, Theresia E. B. Stradal, Ute Curth, Jan Faix
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0004155

Peptides Derived from HIV-1 Integrase that Bind Rev Stimulate Viral Genome Integration
Cited by: 31
Author(s): Aviad Levin, Zvi Hayouka, Markus Helfer, Ruth Brack‐Werner, Assaf Friedler, Abraham Loyter
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0188127

Crystal structure of a tripartite complex between C3dg, C-terminal domains of factor H and OspE of Borrelia burgdorferi
Cited by: 13
Author(s): R. Kolodziejczyk, Kornelia M. Mikula, Tommi Kotila, Vincent L. G. Postis, T. Sakari Jokiranta, Adrian Goldman, Taru Meri
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0180999

Spatial location of neutralizing and non-neutralizing B cell epitopes on domain 1 of ricin toxin’s binding subunit
Cited by: 16
Author(s): Yinghui Rong, Greta Van Slyke, David J. Vance, Jennifer Westfall, Dylan Ehrbar, Nicholas J. Mantis
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0108419

Fine Epitope Mapping of the Central Immunodominant Region of Nucleoprotein from Crimean-Congo Hemorrhagic Fever Virus (CCHFV)
Cited by: 18
Author(s): Dongliang Liu, Li Yang, Jing Zhao, Fei Deng, Duan Xiao-mei, Kou Chun, Ting Wu, Yijie Li, Yongxing Wang, J i, Jianhua Yang, Zhìhóng Hú, Fuchun Zhang, Yújiāng Zhāng, Song Sun
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0133556

Correction: MamA as a Model Protein for Structure-Based Insight into the Evolutionary Origins of Magnetotactic Bacteria
Cited by: 2
Author(s): N. Zeytuni, Samuel Cronin, Christopher T. Lefèvre, Pascal Arnoux, Dror Baran, Zvi Shtein, Geula Davidov, Raz Zarivach
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0183085

Cysteine-rich protein 2 accelerates actin filament cluster formation
Cited by: 2
Author(s): Takanori Kihara, Yoshiaki Sugimoto, Satoko Shinohara, Shunpei Takaoka, Jun Miyake
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0031164

Insights into SCP/TAPS Proteins of Liver Flukes Based on Large-Scale Bioinformatic Analyses of Sequence Datasets
Cited by: 24
Author(s): Cinzia Cantacessi, Andreas Hofmann, Neil D. Young, Ursula Broder, Ross S. Hall, Alex Loukas, Robin B. Gasser
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0034627

Identification of Critical Amino Acids in an Immunodominant IgE Epitope of Pen c 13, a Major Allergen from Penicillium citrinum
Cited by: 17
Author(s): Jui-Chieh Chen, Li-Li Chiu, Kuang-Lun Lee, Weining Huang, Jiing-Guang Chuang, Hsin-Kai Liao, Lu-Ping Chow
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0024366

Minimal Antizyme Peptide Fully Functioning in the Binding and Inhibition of Ornithine Decarboxylase and Antizyme Inhibitor
Cited by: 14
Author(s): Ju-Yi Hsieh, Jiawei Yang, Chih‐Li Lin, Guang‐Yaw Liu, Hui‐Chih Hung
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0116990

Photoactive Protochlorophyllide-Enzyme Complexes Reconstituted with PORA, PORB and PORC Proteins of A. thaliana: Fluorescence and Catalytic Properties
Cited by: 31
Author(s): Michał Gabruk, Anna Stecka, Wojciech Strzałka, Jerzy Kruk, Kazimierz Strzałka, Beata Myśliwa-Kurdziel
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0051660

Functional Roles of the Non-Catalytic Calcium-Binding Sites in the N-Terminal Domain of Human Peptidylarginine Deiminase 4
Cited by: 17
Author(s): Yiliang Liu, I-Chen Tsai, Chia-Wei Chang, Yu‐Ming Liao, Guang‐Yaw Liu, Hui‐Chih Hung
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0111802

Towards Novel Amino Acid-Base Contacts in Gene Regulatory Proteins: AraR – A Case Study
Cited by: 1
Author(s): Isabel Lopes Correia, Irina Saraiva Franco, Isabel Sá‐Nogueira
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0166191

The Diversity of Yellow-Related Proteins in Sand Flies (Diptera: Psychodidae)
Cited by: 12
Author(s): Michal Šíma, Marián Novotný, Lukáš Pravda, Petra Sumová, Iva Rohoušová, Petr Volf
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0010353

Structural Allele-Specific Patterns Adopted by Epitopes in the MHC-I Cleft and Reconstruction of MHC:peptide Complexes to Cross-Reactivity Assessment
Cited by: 23
Author(s): Dinler Amaral Antunes, Gustavo Fioravanti Vieira, Maurício Rigo, Samuel Paulo Cibulski, Marialva Sinigaglia, José Artur Bogo Chies
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0024329

Intrinsic Determinants of Aβ12–24 pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies
Cited by: 27
Author(s): Wei Xu, Ce Zhang, Philippe Derreumaux, Astrid Gräslund, Ludmilla A. Morozova‐Roche, Yuguang Mu
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0097274

ATP1A3 Mutations and Genotype-Phenotype Correlation of Alternating Hemiplegia of Childhood in Chinese Patients
Cited by: 57
Author(s): Xiaoling Yang, Hua Gao, Jie Zhang, Xiaojing Xu, Xiaoyan Liu, Xiru Wu, Liping Wei, Yuehua Zhang
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0011516

Modeling-Dependent Protein Characterization of the Rice Aldehyde Dehydrogenase (ALDH) Superfamily Reveals Distinct Functional and Structural Features
Cited by: 46
Author(s): Simeon O. Kotchoni, José Carlos Jiménez-López, Dongying Gao, Vincent M. Edwards, Emma W. Gachomo, Venu M. Margam, Manfredo J. Seufferheld
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0085768

Human Variants in the Neuronal Basic Helix-Loop-Helix/Per-Arnt-Sim (bHLH/PAS) Transcription Factor Complex NPAS4/ARNT2 Disrupt Function
Cited by: 21
Author(s): David C. Bersten, John B. Bruning, Daniel J. Peet, Murray L. Whitelaw
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0017396

Evolution of Acetylcholinesterase and Butyrylcholinesterase in the Vertebrates: An Atypical Butyrylcholinesterase from the Medaka Oryzias latipes
Cited by: 34
Author(s): Leo Pezzementi, Florian Nachon, Arnaud Chatonnet
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0141716

Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus
Cited by: 6
Author(s): Andres H. de la Peña, Allison Suarez, Krisna C. Duong‐Ly, Andrew Schoeffield, Mario A. Pizarro-Dupuy, Melissa Zarr, Silvia A. Piñeiro, L. Mario Amzel, Sandra B. Gabelli
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0146907

Chicken scFvs with an Artificial Cysteine for Site-Directed Conjugation
Cited by: 5
Author(s): Aram Yoon, Jung Won Shin, Soohyun Kim, Hyori Kim, Junho Chung
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0137279

To Hit or Not to Hit, That Is the Question – Genome-wide Structure-Based Druggability Predictions for Pseudomonas aeruginosa Proteins
Cited by: 9
Author(s): Aurijit Sarkar, Ruth Brenk
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0075055

Engineering Yeast Hexokinase 2 for Improved Tolerance Toward Xylose-Induced Inactivation
Cited by: 23
Author(s): Basti Bergdahl, Anders Sandström, Celina Borgström, Tarinee Boonyawan, Ed W. J. van Niel, Marie-Françoise Gorwa-Grauslund
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0026760

Differential Sensitivity of ERBB2 Kinase Domain Mutations towards Lapatinib
Cited by: 103
Author(s): Rama Krishna Kancha, Nikolas von Bubnoff, Natalie Bartosch, Christian Peschel, Richard A. Engh, Justus Duyster
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0045930

NMR and Mutational Identification of the Collagen-Binding Site of the Chaperone Hsp47
Cited by: 12
Author(s): Maho Yagi-Utsumi, Y. Sumi, Yoshiki Yamaguchi, Yoshimi Nishi, Eiji Kurimoto, Yoshihito Ishida, Takayuki Homma, Jun Hoseki, Yohei Nishikawa, Takao Koide, Kazuhiro Nagata, Koichi Kato
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0201298

Mechanism by which water and protein electrostatic interactions control proton transfer at the active site of channelrhodopsin
Cited by: 18
Author(s): Suliman Adam, Ana‐Nicoleta Bondar
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0176078

Observation of σ-pore currents in mutant hKv1.2_V370C potassium channels
Cited by: 2
Author(s): Pavel Tyutyaev, Stephan Grissmer
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0197029

Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding
Cited by: 7
Author(s): Allison R. Sirois, Daniela A. Deny, Samantha Rose Baierl, Katia S. George, Sarah Moore
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0032702

Direct Interaction of the N-Terminal Domain of Ribosomal Protein S1 with Protein S2 in Escherichia coli
Cited by: 26
Author(s): Konstantin Byrgazov, Salim Manoharadas, Anna Chao Kaberdina, Oliver Vesper, Isabella Moll
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0244176

Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches
Cited by: 75
Author(s): Muhammad Tahir ul Qamar, Abdur Rehman, Kishver Tusleem, Usman Ali Ashfaq, Muhammad Qasim, Xitong Zhu, Israr Fatima, Farah Shahid, Ling Ling Chen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0059206

Molecular Modeling of Disease Causing Mutations in Domain C1 of cMyBP-C
Cited by: 19
Author(s): Poornima Gajendrarao, Navaneethakrishnan Krishnamoorthy, Heba Sh. Kassem, Sarah Moharem-Elgamal, Fabiola Cecchi, Iacopo Olivotto, Magdi H. Yacoub
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0207205

The phosphorylation of sorting nexin 5 at serine 226 regulates retrograde transport and macropinocytosis
Cited by: 13
Author(s): Nao Itai, Tsukasa Shimazu, Takayuki Kimura, Issei Ibe, Ryo Yamashita, Yasushi Kaburagi, Taeko Dohi, Takashi Tonozuka, Toshifumi Takao, Atsushi Nishikawa
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0176694

Small molecule inhibitors of mesotrypsin from a structure-based docking screen
Cited by: 16
Author(s): Olumide Kayode, Zunnan Huang, Alexei S. Soares, Thomas R. Caulfield, Zigang Dong, Ann M. Bode, Evette S. Radisky
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0039093

Dissecting and Circumventing the Requirement for RAM in CSL-Dependent Notch Signaling
Cited by: 6
Author(s): Scott E. Johnson, Doug Barrick
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0047865

Solution Structure of a Phytocystatin from Ananas comosus and Its Molecular Interaction with Papain
Cited by: 17
Author(s): Deli Irene, Tse-Yu Chung, Bo-Jiun Chen, Ting-Hang Liu, Fengyin Li, Jason T. C. Tzen, Cheng‐I Wang, Chia-Lin Chyan
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0138221

A Novel AXIN2 Missense Mutation Is Associated with Non-Syndromic Oligodontia
Cited by: 18
Author(s): Haochen Liu, Tingting Ding, Yuan Zhan, Hailan Feng
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0034734

Insight on an Arginine Synthesis Metabolon from the Tetrameric Structure of Yeast Acetylglutamate Kinase
Cited by: 18
Author(s): Sergio de Cima, F. Gil-Ortiz, Marjolaine Crabeel, Ignacio Fita, Vicente Rubio
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0234152

S100A1 blocks the interaction between p53 and mdm2 and decreases cell proliferation activity
Cited by: 7
Author(s): Deepu Dowarha, Ruey Hwang Chou, Chin Yu
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0239364

Alkaloids of Abuta panurensis Eichler: In silico and in vitro study of acetylcholinesterase inhibition, cytotoxic and immunomodulatory activities
Cited by: 6
Author(s): Rochelly da Silva Mesquita, Andrii Kyrylchuk, Regiane Costa de Oliveira, Ingrity S.C. Sá, Gabriel Coutinho Borges Camargo, Gemilson Soares Pontes, Felipe M. A. da Silva, Rita de Cássia Saraiva Nunomura, Andriy Grafov
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0076687

Directed Evolution of Aminoglycoside Phosphotransferase (3′) Type IIIa Variants That Inactivate Amikacin but Impose Significant Fitness Costs
Cited by: 9
Author(s): Joseph R. Kramer, Ichiro Matsumura
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0000548

Structure and Evolutionary Origin of Ca2+-Dependent Herring Type II Antifreeze Protein
Cited by: 72
Author(s): Yang Liu, Zhengjun Li, Qingsong Lin, Jan Kosiński, J. Seetharaman, Janusz M. Bujnicki, J. Sivaraman, Choy‐Leong Hew
Software Mentions: 1
Published: about 19 years ago

10.1371/journal.pone.0212687

Detection of ON1 and novel genotypes of human respiratory syncytial virus and emergence of palivizumab resistance in Lebanon
Cited by: 23
Author(s): Hadi Abou-El-Hassan, Elie Massaad, Nadia Soudani, Aia Assaf‐Casals, Rouba Shaker, Mireille Lteif Khoury, Soha Ghanem, Maria Karam, Rabih R. Andary, Reiko Saito, Ghassan Dbaibo, Hassan Zaraket
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0146612

Comparative MD Simulations Indicate a Dual Role for Arg1323.50 in Dopamine-Dependent D2R Activation
Cited by: 8
Author(s): Ralf C. Kling, Timothy Clark, Peter Gmeiner
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0203369

Insights on a putative aminoacyl-tRNA-protein transferase of Leishmania major
Cited by: 0
Author(s): Rohit Sharma, Monica Terrao, Felipe Freitas-Castro, Reinhard Breitling, Vítor Marcel Faça, Eduardo B. Oliveira, Ângela K. Cruz
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0154198

SRPK1 and Akt Protein Kinases Phosphorylate the RS Domain of Lamin B Receptor with Distinct Specificity: A Combined Biochemical and In Silico Approach
Cited by: 15
Author(s): Nikolaos Voukkalis, Maria Koutroumani, Christoforos Zarkadas, Eleni Nikolakaki, Metaxia Vlassi, Thomas Giannakouŕos
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0190545

S100B as an antagonist to block the interaction between S100A1 and the RAGE V domain
Cited by: 16
Author(s): Md. Imran Khan, Yu-Kai Su, Jinhao Zou, Lee‐Wei Yang, Ruey Hwang Chou, Chin Yu
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0085349

Identification of a New Epitope in uPAR as a Target for the Cancer Therapeutic Monoclonal Antibody ATN-658, a Structural Homolog of the uPAR Binding Integrin CD11b (αM)
Cited by: 30
Author(s): Xiang Xu, Cai Yuan, Ying Wei, Fernando Doñate, Jose Juarez, Graham Parry, Liqing Chen, Edward J. Meehan, Richard W. Ahn, Andrey Ugolkov, Oleksii Dubrovskyi, Thomas V. O’Halloran, Mingdong Huang, Andrew P. Mazar
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0018142

A Computational Model of the LGI1 Protein Suggests a Common Binding Site for ADAM Proteins
Cited by: 33
Author(s): Emanuela Leonardi, Simonetta Andreazza, Stefano Vanin, Giorgia Busolin, Carlo Nobile, Silvio C. E. Tosatto
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0044282

Insights into Phosphate Cooperativity and Influence of Substrate Modifications on Binding and Catalysis of Hexameric Purine Nucleoside Phosphorylases
Cited by: 10
Author(s): P.O. Giuseppe, N.H. Martins, A.N. Meza, C.R. Santos, H.M. Pereira, Mário Tyago Murakami
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0007072

Prodepth: Predict Residue Depth by Support Vector Regression Approach from Protein Sequences Only
Cited by: 39
Author(s): Jiangning Song, Hao Tan, Khalid Mahmood, Ruby H. P. Law, Ashley M. Buckle, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0081068

Inhibition of Nutlin-Resistant HDM2 Mutants by Stapled Peptides
Cited by: 26
Author(s): Siau Jia Wei, Thomas L. Joseph, Sharon Chee, Ling Li, Larisa Yurlova, Kourosh Zolghadr, Christopher J. Brown, David P. Lane, Chandra Verma, Farid J. Ghadessy
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0085763

Disruption of TgPHIL1 Alters Specific Parameters of Toxoplasma gondii Motility Measured in a Quantitative, Three-Dimensional Live Motility Assay
Cited by: 64
Author(s): Jacqueline M. Leung, Mark A. Rould, Christoph Konradt, Christopher A. Hunter, Gary E. Ward
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0021532

Evolutionary Analysis of Novel Serine Proteases in the Venom Gland Transcriptome of Bitis gabonica rhinoceros
Cited by: 30
Author(s): Sakthivel Vaiyapuri, Simon C. Wagstaff, Robert A. Harrison, Jonathan M. Gibbins, E. Gail Hutchinson
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0196797

A flavin-dependent halogenase from metagenomic analysis prefers bromination over chlorination
Cited by: 55
Author(s): Pia R. Neubauer, Christiane Widmann, Daniel Wibberg, Lea Schröder, Marcel Frese, Tilman Kottke, Jörn Kalinowski, Hartmut H. Niemann, Norbert Sewald
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0048750

Immunization with a Hemagglutinin-Derived Synthetic Peptide Formulated with a CpG-DNA-Liposome Complex Induced Protection against Lethal Influenza Virus Infection in Mice
Cited by: 28
Author(s): Jae Won Rhee, Dongbum Kim, Byung Kwon Park, Sang-Hoon Kwon, Sunhee Cho, Ilseob Lee, Man Seong Park, Jae Nam Seo, Yong Sun Kim, Hong Seok Choi, Younghee Lee
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0109705

Computational Insights into the Inhibitory Mechanism of Human AKT1 by an Orally Active Inhibitor, MK-2206
Cited by: 41
Author(s): Mohd Rehan, M.A. Beg, Shadma Parveen, Ghazi A. Damanhouri, Galila Zaher
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0060072

Structural Analysis of a Novel Cyclohexylamine Oxidase from Brevibacterium oxydans IH-35A
Cited by: 22
Author(s): I.A. Mirza, David L. Burk, Bing Xiong, Hiroaki Iwaki, Yoshie Hasegawa, Stephan Große, Peter C. K. Lau, Albert M. Berghuis
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0090445

Fine-Mapping of Immunodominant Linear B-Cell Epitopes of the Staphylococcus Aureus SEB Antigen Using Short Overlapping Peptides
Cited by: 8
Author(s): Zhuo Zhao, Bin Li, Hongling Sun, Jinyong Zhang, Yilin Wang, Li Chen, Jian Hu, Yang He, Hao Zeng, Quanming Zou, Chao Wu
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0088809

Model of a DNA-Protein Complex of the Architectural Monomeric Protein MC1 from Euryarchaea
Cited by: 7
Author(s): Françoise Paquet, Olivier Delalande, S. Goffinont, Françoise Culard, Karine Loth, Ulysse Asseline, B. Castaing, C. Landon
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0063452

Substrate Specificity Provides Insights into the Sugar Donor Recognition Mechanism of O-GlcNAc Transferase (OGT)
Cited by: 28
Author(s): Xiaofeng Ma, Li Pi, Hui Yan, Hong Sun, Xiaoyan Liu, Feng Zheng, Lei Li, Yi Chen, Musleh M. Muthana, Xi Chen, Peng George Wang, Lianwen Zhang
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0201734

Designing bacterial signaling interactions with coevolutionary landscapes
Cited by: 8
Author(s): Ryan R. Cheng, Ellinor Haglund, Nicholas S. Tiee, Faruck Morcos, Herbert Levine, Joseph A. Adams, Patricia A. Jennings, José N. Onuchic
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0025560

Computational Prediction of Heme-Binding Residues by Exploiting Residue Interaction Network
Cited by: 39
Author(s): Rong Liu, Jianjun Hu
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0143107

Negative Feedbacks by Isoprenoids on a Mevalonate Kinase Expressed in the Corpora Allata of Mosquitoes
Cited by: 12
Author(s): Pratik Nyati, Crisalejandra Rivera-Pérez, Fernando G. Noriega
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0020445

Identification of antifreeze proteins and their functional residues by support vector machine and genetic algorithms based on n-peptide compositions.
Cited by: 31
Author(s): Chao Yu, Chih-Hao Lu
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0136239

Structure of the Glycosyltransferase Ktr4p from Saccharomyces cerevisiae
Cited by: 7
Author(s): D.D.D. Possner, Magnus Claesson, Jodie E. Guy
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0066889

SERPINA2 Is a Novel Gene with a Divergent Function from SERPINA1
Cited by: 6
Author(s): Patrícia Marques, Zélia Ferreira, Manuella Martins, Joana Figueiredo, Diana Isabel Silva, Patrícia Castro, Ramiro Morales‐Hojas, Joana Simões‐Correia, Susana Seixas
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0134056

N-Terminal Coiled-Coil Structure of ATPase Subunits of 26S Proteasome Is Crucial for Proteasome Function
Cited by: 8
Author(s): Tomonao Inobe, Reiko Genmei
Software Mentions: 1
Published: almost 11 years ago

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Papers Mentioning PyMOL 8,266