pypi: PyMOL | Projects | Ecosyste.ms: Papers

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

10.1371/journal.pone.0109354

BioGPS Descriptors for Rational Engineering of Enzyme Promiscuity and Structure Based Bioinformatic Analysis
Cited by: 17
Author(s): Virgilio F. Ferrario, Lydia Siragusa, Cynthia Ebert, Massimo Baroni, Marco Foscato, Gabriele Cruciani, Lucia Gardossi
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0017055

Histidine Hydrogen-Deuterium Exchange Mass Spectrometry for Probing the Microenvironment of Histidine Residues in Dihydrofolate Reductase
Cited by: 28
Author(s): Masaru Miyagi, Qun Wan, Md. Faiz Ahmad, Giridharan Gokulrangan, Sara E. Tomechko, Brad C. Bennett, Chris Dealwis
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0113294

Design and Development of a Novel Vaccine for Protection against Lyme Borreliosis
Cited by: 45
Author(s): Pär Comstedt, Markus Hanner, Wolfgang Schüler, Andreas Meinke, Urban Lundberg
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0018300

Biochemical and Structural Properties of Cyanases from Arabidopsis thaliana and Oryza sativa
Cited by: 27
Author(s): Dawei Qian, Lin Jiang, Lu Lu, Chunhong Wei, Li Yi
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0043788

Atomistic Mechanism of MicroRNA Translation Upregulation via Molecular Dynamics Simulations
Cited by: 14
Author(s): Yaguang Wei, Fang Qin, Jian Zhang, Ray Luo, Haifeng Chen
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0075582

Putative Bioactive Motif of Tritrpticin Revealed by an Antibody with Biological Receptor-Like Properties
Cited by: 8
Author(s): Raghava Sharma, Suvendu Lomash, Dinakar M. Salunke
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0108946

Structural Insights into RNA Polymerase Recognition and Essential Function of Myxococcus xanthus CdnL
Cited by: 18
Author(s): Aránzazu Gallego-García, Yasmina Mirassou, Diana García‐Moreno, Montserrat Elı́as-Arnanz, María Ángeles Sánchez Jiménez, S. Padmanabhan
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0241728

PharmaNet: Pharmaceutical discovery with deep recurrent neural networks
Cited by: 5
Author(s): Paola Ruiz Puentes, Natalia Valderrama, Cristina González, Laura Daza, Carolina Muñoz-Camargo, Juan C. Cruz, Pablo Arbeláez
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0020872

Anchored Design of Protein-Protein Interfaces
Cited by: 59
Author(s): Steven M. Lewis, Brian Kuhlman
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0119608

Glycans Flanking the Hypervariable Connecting Peptide between the A and B Strands of the V1/V2 Domain of HIV-1 gp120 Confer Resistance to Antibodies That Neutralize CRF01_AE Viruses
Cited by: 14
Author(s): Sara M. O’Rourke, Ruengpung Sutthent, Pham Phung, Kathryn A. Mesa, Normand L. Frigon, Briana To, Navin Horthongkham, Kay Limoli, Terri Wrin, Phillip W. Berman
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0223773

Engineering a single-chain antibody against Trypanosoma cruzi metacyclic trypomastigotes to block cell invasion
Cited by: 4
Author(s): Lara Maria Kalempa Demeu, Rodrigo Jahn Soares, Juliana Severo Miranda, Lisandro Pacheco-Lugo, Kelin Gonçalves de Oliveira, Cristian Andrés Cortez Plaza, Philippe Billiald, Juliana de Moura, Nobuko Yoshida, Larissa M. Alvarenga, Wanderson D. DaRocha
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0096536

The Tertiary Origin of the Allosteric Activation of E. coli Glucosamine-6-Phosphate Deaminase Studied by Sol-Gel Nanoencapsulation of Its T Conformer
Cited by: 4
Author(s): Sergio Zonszein, Laura I. Álvarez‐Añorve, Roberto J. Vázquez-Núñez, Mario L. Calcagno
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0201922

Structures of NHBA elucidate a broadly conserved epitope identified by a vaccine induced antibody
Cited by: 5
Author(s): Martina Maritan, Daniele Veggi, Roberta Cozzi, Lucia Dello Iacono, Erika Bartolini, Paola Lo Surdo, Giulietta Maruggi, Glen Spraggon, Matthew J. Bottomley, E. Malito
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0024766

Modulation of Catalytic Activity in Multi-Domain Protein Tyrosine Phosphatases
Cited by: 12
Author(s): L.L. Madan, Shivamurthy Veeranna, Khader Shameer, Chilamakuri Chandra Sekhar Reddy, Ramanathan Sowdhamini, B. Gopal
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0025118

Comparative Analysis of Species-Specific Ligand Recognition in Toll-Like Receptor 8 Signaling: A Hypothesis
Cited by: 47
Author(s): Rajiv Gandhi Govindaraj, Balachandran Manavalan, Shaherin Basith, Sangdun Choi
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0082020

Conformational Polymorphism of m7GTP in Crystal Structure of the PB2 Middle Domain from Human Influenza A Virus
Cited by: 8
Author(s): Toshiharu Tsurumura, Hao Qiu, Toru Yoshida, Yayoi Tsumori, Dai Hatakeyama, Takashi Kuzuhara, Hideaki Tsuge
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0065045

Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging
Cited by: 100
Author(s): Chung-ke Chang, Chia Min Michael Chen, Ming Hui Chiang, Yen Lan Hsu, Tai Huang Huang
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0043863

Crystal Structures of Archaemetzincin Reveal a Moldable Substrate-Binding Site
Cited by: 4
Author(s): Christine Graef, M. Schacherl, S. Waltersperger, Ulrich Baumann
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0025317

Obesity Risk Gene TMEM18 Encodes a Sequence-Specific DNA-Binding Protein
Cited by: 28
Author(s): Jaana Jurvansuu, Adrian Goldman
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0009990

Detection and Architecture of Small Heat Shock Protein Monomers
Cited by: 76
Author(s): Pierre Poulain, Jean‐Christophe Gelly, Delphine Flatters
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0173767

Streptococcus suis sortase A is Ca2+ independent and is inhibited by acteoside, isoquercitrin and baicalin
Cited by: 8
Author(s): Fuguang Chen, Fang Xie, Baoxue Yang, Yuming Wang, Siguo Liu, Yueling Zhang
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0237181

Comprehensive genome based analysis of Vibrio parahaemolyticus for identifying novel drug and vaccine molecules: Subtractive proteomics and vaccinomics approach
Cited by: 14
Author(s): Mahmudul Hasan, Kazi Faizul Azim, Abdus Shukur Imran, Ishtiak Malique Chowdhury, Shah Rucksana Akhter Urme, Sorwer Alam Parvez, Md. Bashir Uddin, Syed Sayeem Uddin Ahmed
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0043437

Random Mutagenesis Reveals Residues of JAK2 Critical in Evading Inhibition by a Tyrosine Kinase Inhibitor
Cited by: 23
Author(s): Michael R. Marit, Manprit Chohan, Natasha Matthew, Kai Huang, D.A. Kuntz, David R. Rose, Dwayne L. Barber
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0052732

Prime-Boost Immunization of Rabbits with HIV-1 gp120 Elicits Potent Neutralization Activity against a Primary Viral Isolate
Cited by: 16
Author(s): Kristin Narayan, Nitish Agrawal, Sean X. Du, Janelle Muranaka, Katherine W. Bauer, Daniel P. Leaman, Pham Phung, Kay Limoli, Helen Chen, Rebecca I. Boenig, Terri Wrin, Michael B. Zwick, Robert G. Whalen
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0123567

Crystal Structure of Plasmodium knowlesi Apical Membrane Antigen 1 and Its Complex with an Invasion-Inhibitory Monoclonal Antibody
Cited by: 15
Author(s): B. Vulliez-Le Normand, Bart W. Faber, F.A. Saul, Marjolein van der Eijk, Alan W. Thomas, Balbir Singh, Clemens H. M. Kocken, G.A. Bentley
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0089116

Structural Analysis of Viral Infectivity Factor of HIV Type 1 and Its Interaction with A3G, EloC and EloB
Cited by: 16
Author(s): Kauȇ Santana da Costa, Élcio Leal, Alberto Monteiro dos Santos, Anderson Henrique Lima e Lima, Cláudio Nahum Alves, Jerônimo Lameira
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0149903

Structure of the Response Regulator NsrR from Streptococcus agalactiae, Which Is Involved in Lantibiotic Resistance
Cited by: 12
Author(s): Sakshi Khosa, A. Hoeppner, Holger Gohlke, Lutz Schmitt, Sander H. J. Smits
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0100797

QSAR and Docking Studies on Capsazepine Derivatives for Immunomodulatory and Anti-Inflammatory Activity
Cited by: 30
Author(s): Aparna Shukla, Pooja Sharma, Om Prakash, Mohinder Singh, Komal Kalani, Feroz Khan, Dnyaneshwar Umrao Bawankule, Suaib Luqman, Santosh K. Srivastava
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0223387

Structural mechanism for regulation of DNA binding of BpsR, a Bordetella regulator of biofilm formation, by 6-hydroxynicotinic acid
Cited by: 5
Author(s): William T. Booth, Ryan R. Davis, Rajendar Deora, Thomas Hollis
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0047665

The Metagenome-Derived Enzymes LipS and LipT Increase the Diversity of Known Lipases
Cited by: 73
Author(s): Jennifer Chow, Filip Kovačić, Yuliya Dall Antonia, Ulrich Krauß, Francesco Fersini, Christel Schmeisser, Benjamin Lauinger, Patrick Bongen, Jörg Pietruszka, Marlen Schmidt, Ina Menyes, Uwe T. Bornscheuer, Marrit Eckstein, Oliver Thum, Andreas Liese, Jochen Mueller‐Dieckmann, Karl‐Erich Jaeger, Wolfgang R. Streit
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0080393

Involvement of and Interaction between WNT10A and EDA Mutations in Tooth Agenesis Cases in the Chinese Population
Cited by: 48
Author(s): Huiying He, Dong Han, Hailan Feng, Hong Qu, Seng Song, Baojing Bai, Zhenting Zhang
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0040846

Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms
Cited by: 25
Author(s): Keng‐Chang Tsai, Jhih-Wei Jian, Ei-Wen Yang, Po-Chiang Hsu, Hung-Pin Peng, Ching-Tai Chen, Jun‐Bo Chen, Jeng-Yih Chang, Wen-Lian Hsu, An-Suei Yang
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0033416

Crystal Structure of Diedel, a Marker of the Immune Response of Drosophila melanogaster
Cited by: 17
Author(s): Franck Coste, Cordula Kemp, Vanessa Bobezeau, Charles Hétru, Christine Kellenberger, Jean‐Luc Imler, Alain Roussel
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0055650

Characterization of the N-Terminal Domain of BteA: A Bordetella Type III Secreted Cytotoxic Effector
Cited by: 5
Author(s): Chen Guttman, Geula Davidov, Hadassa Shaked, Sofiya Kolusheva, Ronit Bitton, Atish Ganguly, Jeff F. Miller, Jordan H. Chill, Raz Zarivach
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0022253

Single-Molecule Fluorescence Polarization Study of Conformational Change in Archaeal Group II Chaperonin
Cited by: 7
Author(s): Ryo Iizuka, Taro Ueno, Nobuhiro Morone, Takashi Funatsu
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0000685

Mutations in the UBIAD1 Gene, Encoding a Potential Prenyltransferase, Are Causal for Schnyder Crystalline Corneal Dystrophy
Cited by: 104
Author(s): Andrew Orr, Marie‐Pierre Dubé, Julien L. Marcadier, Haiyan Jiang, Antonio Federico, Stanley George, Christopher Seamone, David Q. Andrews, Paul Dubord, Simon Holland, Sylvie Provost, Vanessa Mongrain, Susan C. Evans, Brent Higgins, Sharen Bowman, Duane L. Guernsey, Mark E. Samuels
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pone.0037645

Protein Sequence Alignment Analysis by Local Covariation: Coevolution Statistics Detect Benchmark Alignment Errors
Cited by: 19
Author(s): Russell J. Dickson, Gregory B. Gloor
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0180241

Metal ion coordination in the E. coli Nudix hydrolase dihydroneopterin triphosphate pyrophosphatase: New clues into catalytic mechanism
Cited by: 4
Author(s): Shannon E. Hill, Elaine Nguyen, Chiamaka U. Ukachukwu, Dana M. Freeman, Stephen Quirk, Raquel L. Lieberman
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0162273

GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism
Cited by: 3
Author(s): Alejandra Young, Uma Dandekar, Calvin Pan, Avery Sader, Jie Zheng, Richard A. Lewis, Débora B. Farber
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0031445

Protein-Protein Interactions in Clathrin Vesicular Assembly: Radial Distribution of Evolutionary Constraints in Interfaces
Cited by: 1
Author(s): Rupali A. Gadkari, Narayanaswamy Srinivasan
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0079544

New Antimalarial Hits from Dacryodes edulis (Burseraceae) - Part I: Isolation, In Vitro Activity, In Silico “drug-likeness” and Pharmacokinetic Profiles
Cited by: 27
Author(s): Denis Zofou, Esther Laure Tematio, Fidele Ntie‐Kang, Mathieu Téné, Moses N. Ngemenya, Pierre Tane, Vincent P. K. Titanji
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0112902

Identification of Functionally Important Residues of the Rat P2X4 Receptor by Alanine Scanning Mutagenesis of the Dorsal Fin and Left Flipper Domains
Cited by: 9
Author(s): Vendula Tvrdoňová, Milos B. Rokic, Stanko S. Stojilković, Hana Zemková
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0240920

A highly active heparinase I from Bacteroides cellulosilyticus: Cloning, high level expression, and molecular characterization
Cited by: 4
Author(s): Liwei Gao, Hongtao Zhu, Caiyun Liu, Zhixiang Lv, Xue‐Gong Fan, Ye-Wang Zhang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0074636

Frequency and Pattern of Heteroplasmy in the Complete Human Mitochondrial Genome
Cited by: 71
Author(s): Ariel Delgado Ramos, Cristina Santos, Ligia Mateiu, María del Mar González, Luis Álvarez, Luı́sa Azevedo, António Amorim, María Pilar Aluja
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0072718

NMR Structure of Temporin-1 Ta in Lipopolysaccharide Micelles: Mechanistic Insight into Inactivation by Outer Membrane
Cited by: 30
Author(s): Rathi Saravanan, M. S. Joshi, Harini Mohanram, Anirban Bhunia, Maria Luisa Mangoni, Surajit Bhattacharjya
Software Mentions: 1
Published: almost 13 years ago

Projects: pypi: PyMOL

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Papers Mentioning PyMOL 8,266