pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0082549

CLCN1 Mutations in Czech Patients with Myotonia Congenita, In Silico Analysis of Novel and Known Mutations in the Human Dimeric Skeletal Muscle Chloride Channel
Cited by: 27
Author(s): Daniela Skálová, Jana Zídková, Stanislav Voháňka, Radim Mazanec, Zuzana Mušová, Petr Vondráček, Lenka Mrázová, Josef Kraus, Kamila Réblová, Lenka Fajkusová
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0035305

The GPI Anchor Signal Sequence Dictates the Folding and Functionality of the Als5 Adhesin from Candida albicans
Cited by: 12
Author(s): Mohammad Faiz Ahmad, Bhawna Yadav, Pravin Kumar, Amrita Puri, Mohit Mazumder, Anwar Ali, S. Gourinath, Rohini Muthuswami, Sneha Sudha Komath
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0176255

Thermal stability and kinetic constants for 129 variants of a family 1 glycoside hydrolase reveal that enzyme activity and stability can be separately designed
Cited by: 16
Author(s): Dylan Alexander Carlin, Siena Hapig-Ward, Bill Wayne Chan, Natalie Damrau, Mary Riley, Ryan Caster, Bowen Bethards, Justin B. Siegel
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0100069

Active-State Model of a Dopamine D2 Receptor - Gαi Complex Stabilized by Aripiprazole-Type Partial Agonists
Cited by: 30
Author(s): Ralf C. Kling, Nuška Tschammer, Harald Lanig, Timothy Clark, Peter Gmeiner
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0126360

A Combination of Doxycycline and Ribavirin Alleviated Chikungunya Infection
Cited by: 95
Author(s): Hussin A. Rothan, Hirbod Bahrani, Mohamed Zeriouh, Teow Chong Teoh, Esaki Muthu Shankar, Noorsaadah Abdul Rahman, Rohana Yusof
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0102481

Flexibility of PCNA-Protein Interface Accommodates Differential Binding Partners
Cited by: 18
Author(s): Anthony M. Pedley, Markus A. Lill, V. Jo Davisson
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0186442

Hydrophobic residues are critical for the helix-forming, hemolytic and bactericidal activities of amphipathic antimicrobial peptide TP4
Cited by: 24
Author(s): Ting-Wei Chang, Shu‐Yi Wei, Shih-Han Wang, Hung-Mu Wei, Yu-June Wang, Chiu‐Feng Wang, Chinpan Chen, You‐Di Liao
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0070273

Mechanistic Insights into the Neutralization of Cytotoxic Abrin by the Monoclonal Antibody D6F10
Cited by: 13
Author(s): Shradha Bagaria, Devasena Ponnalagu, S. Bisht, Anjali A. Karande
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0081301

Molecular Features Related to HIV Integrase Inhibition Obtained from Structure- and Ligand-Based Approaches
Cited by: 8
Author(s): Lucas L. Carvalho, Vinícius Gonçalves Maltarollo, Emmanuela Ferreira de Lima, Karen C. Weber, Káthia Maria Honório, Albérico Borges Ferreira da Silva
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0074436

Direct Regulation of Cytochrome c Oxidase by Calcium Ions
Cited by: 31
Author(s): Tatiana V. Vygodina, Anna Kirichenko, Alexander A. Konstantinov
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0103947

Structural Insights into Calcium-Bound S100P and the V Domain of the RAGE Complex
Cited by: 40
Author(s): Srinivasa R. Penumutchu, Ruey Hwang Chou, Chin Yu
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0019094

Multidimensional Scaling Reveals the Main Evolutionary Pathways of Class A G-Protein-Coupled Receptors
Cited by: 31
Author(s): Julien Pelé, Hervé Abdi, Matthieu Moreau, David Thybert, Marie Chabbert
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0040618

Ipomoelin, a Jacalin-Related Lectin with a Compact Tetrameric Association and Versatile Carbohydrate Binding Properties Regulated by Its N Terminus
Cited by: 9
Author(s): Wei-Chieh Chang, Kai-Lun Liu, Fang‐Chi Hsu, Shih‐Tong Jeng, Yi-Sheng Cheng
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0047056

FUS-NLS/Transportin 1 Complex Structure Provides Insights into the Nuclear Targeting Mechanism of FUS and the Implications in ALS
Cited by: 58
Author(s): Chunyan Niu, Jia Yu Zhang, Feng Gao, Liuqing Yang, Minghao Jia, Haining Zhu, Weimin Gong
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0089935

Improvement in Low-Homology Template-Based Modeling by Employing a Model Evaluation Method with Focus on Topology
Cited by: 10
Author(s): Wentao Dai, Tingrui Song, Xuan Wang, Xinchun Jin, Lizong Deng, Aiping Wu, Taijiao Jiang
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0046388

Engineering a Disulfide Bond in the Lid Hinge Region of Rhizopus chinensis Lipase: Increased Thermostability and Altered Acyl Chain Length Specificity
Cited by: 67
Author(s): Yu Xiang, Nian-Jiang Tan, Rong Xiao, Yan Xu
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0106642

Probing the Activity Modification Space of the Cysteine Peptidase Cathepsin K with Novel Allosteric Modifiers
Cited by: 19
Author(s): Marko Novinec, Brigita Lenarčič, Antonio Baici
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0127081

Distinctive Structure of the EphA3/Ephrin-A5 Complex Reveals a Dual Mode of Eph Receptor Interaction for Ephrin-A5
Cited by: 11
Author(s): G. Jason Forse, Maria Uson, Fariborz Nasertorabi, Anand Kolatkar, Ilaria Lamberto, Elena B. Pasquale, Peter Kühn
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0044313

Characterization of a Novel Phenol Hydroxylase in Indoles Biotranformation from a Strain Arthrobacter sp. W1
Cited by: 24
Author(s): Yuanyuan Qu, Shengnan Shi, Hao Zhou, Qiao Ma, Xinliang Li, Xuwang Zhang, Jiti Zhou
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0095183

Molecular Characterization of HIV-1 Subtype C gp-120 Regions Potentially Involved in Virus Adaptive Mechanisms
Cited by: 4
Author(s): Alessandra Cenci, Giuseppe D’Avenio, Lara Tavoschi, Michele Chiappi, Simone Becattini, Maria del Pilar Narino, Orietta Picconi, Daniela Bernasconi, Emanuele Fanales-Belasio, Eftyhia Vardas, Hosea Sukati, Alessandra Lo Presti, Massimo Ciccozzi, Paolo Monini, Barbara Ensoli, Mauro Grigioni, Stefano Buttò
Software Mentions: 1
Published: about 12 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: almost 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: about 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: almost 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

10.1371/journal.pone.0006163

Discovery of a Novel Prolactin in Non-Mammalian Vertebrates: Evolutionary Perspectives and Its Involvement in Teleost Retina Development
Cited by: 45
Author(s): Xigui Huang, Michelle Hui, Yun Liu, Don Yuen, Yong Zhang, Wood Yee Chan, Haoran Lin, Shuk Han Cheng, Christopher H. K. Cheng
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0231542

Unveiling functional motions based on point mutations in biased signaling systems: A normal mode study on nerve growth factor bound to TrkA
Cited by: 5
Author(s): Pedro T. Resende-Lara, David Pérahia, Ana Lígia Scott, Antônio Sérgio Kimus Braz
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0154056

New Cysteine-Rich Ice-Binding Protein Secreted from Antarctic Microalga, Chloromonas sp.
Cited by: 17
Author(s): Woo‐Sik Jung, Robert L. Campbell, Yunho Gwak, Jong Im Kim, Peter L. Davies, EonSeon Jin
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0086083

Critical Amino Acids within the Human Immunodeficiency Virus Type 1 Envelope Glycoprotein V4 N- and C-Terminals Contribute to Virus Entry
Cited by: 12
Author(s): Yan Li, Dan Yang, Jiaye Wang, Yuan Yao, Weizhe Zhang, Lu-Jing Wang, De Cheng, Fengkun Yang, Fengmin Zhang, Min Zhuang, Hong Ling
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0033291

Characterization of a Novel Binding Protein for Fortilin/TCTP — Component of a Defense Mechanism against Viral Infection in Penaeus monodon
Cited by: 8
Author(s): Tanate Panrat, Patuma Sinthujaroen, Benjamas Nupan, Warapond Wanna, Martti T. Tammi, Amornrat Phongdara
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0100165

Insulin-Like Growth Factor 2 Silencing Restores Taxol Sensitivity in Drug Resistant Ovarian Cancer
Cited by: 33
Author(s): Jurriaan Brouwer‐Visser, Jiyeon Lee, Kelly Anne McCullagh, M. Cossio, Yanhua Wang, Gloria S. Huang
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0146393

PLGA-Curcumin Attenuates Opioid-Induced Hyperalgesia and Inhibits Spinal CaMKIIα
Cited by: 16
Author(s): Xiaoyu Hu, Fang Huang, Magdalena Szymusiak, Xiaojing Tian, Ying Liu, Zaijie Jim Wang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0156218

Crystal Structure of the FERM-SH2 Module of Human Jak2
Cited by: 30
Author(s): Randall McNally, A.V. Toms, Michael J. Eck
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0135448

Structural Analysis of the Rubisco-Assembly Chaperone RbcX-II from Chlamydomonas reinhardtii
Cited by: 13
Author(s): A. Bracher, Thomas R. Hauser, Cuimin Liu, F. Ulrich Hartl, Manajit Hayer‐Hartl
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0007258

Masitinib (AB1010), a Potent and Selective Tyrosine Kinase Inhibitor Targeting KIT
Cited by: 329
Author(s): Patrice Dubreuil, Sébastien Létard, Marco A. Ciufolini, Laurent Gros, M. Humbert, Nathalie Castéran, Laurence Borge, Bérengère Hajem, Anne Lermet, Wolfgang Sippl, Edwige Voisset, Michel Arock, Christian Auclair, Phillip S. Leventhal, Colin D. Mansfield, Alain Moussy, Olivier Hermine
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0012029

Optimized Hydrophobic Interactions and Hydrogen Bonding at the Target-Ligand Interface Leads the Pathways of Drug-Designing
Cited by: 313
Author(s): R. R. Patil, S. Das, Ashley Stanley, Lumbani Yadav, Akulapalli Sudhakar, Ashok K. Varma
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0060602

Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry
Cited by: 33
Author(s): Casper Steinmann, Dmitri G. Fedorov, Jan H. Jensen
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0179983

Generation of a rabbit single-chain fragment variable (scFv) antibody for specific detection of Bradyrhizobium sp. DOA9 in both free-living and bacteroid forms
Cited by: 8
Author(s): Nguyễn Xuân Vũ, Natcha Pruksametanan, Witsanu Srila, Watcharin Yuttavanichakul, Kamonluck Teamtisong, Neung Teaumroong, Nantakorn Boonkerd, Panlada Tittabutr, Montarop Yamabhai
Software Mentions: 1
Published: about 9 years ago

Projects: pypi: PyMOL

Science Score: 90/100

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Papers Mentioning PyMOL 8,266