pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1006900

Rapid interpretation of small-angle X-ray scattering data
Cited by: 20
Author(s): Marie Weiel, Ines Reinartz, Alexander Schug
Software Mentions: 2
Published: over 7 years ago

Peptide probes derived from pertuzumab by molecular dynamics modeling for HER2 positive tumor imaging
Cited by: 14
Author(s): Xiaoliang Yang, Zihua Wang, Zhichu Xiang, Dan Li, Zhiyuan Hu, Wei Cui, Li Geng, Qiaojun Fang
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pcbi.1000357

Amyloidogenesis Abolished by Proline Substitutions but Enhanced by Lipid Binding
Cited by: 39
Author(s): Ping Jiang, Wei Xu, Yuguang Mu
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pcbi.1000918

An Introduction to Biomolecular Graphics
Cited by: 40
Author(s): Cameron Mura, Colin M. McCrimmon, Jason Vertrees, M.R. Sawaya
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pcbi.1003995

Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation
Cited by: 8
Author(s): Michael Graf, Zhihua Lin, Urban Bren, Dietmar Haltrich, W. F. van Gunsteren, Chris Oostenbrink
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pcbi.1005897

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules
Cited by: 24
Author(s): Albert Solernou, Benjamin S. Hanson, Robin A. Richardson, Robert C. Welch, Daniel J. Read, Oliver G. Harlen, Sarah A. Harris
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pcbi.1003007

Cleavage Entropy as Quantitative Measure of Protease Specificity
Cited by: 50
Author(s): Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Michael A. Margreiter, Gudrun M. Spitzer, Hannes G. Wallnoefer, Klaus R. Liedl
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pcbi.1003379

Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70
Cited by: 29
Author(s): Adrien Nicolaı̈, Patrice Delarue, Patrick Senet
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pcbi.1008060

REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution
Cited by: 8
Author(s): Casey A. Cole, Nourhan S. Daigham, Gaohua Liu, Gaetano T. Montelione, Homayoun Valafar
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1003022

Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure
Cited by: 11
Author(s): Xin Wan, Yue Ma, Christopher L. McClendon, Lily Huang, Niu Huang
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pcbi.1004398

An Integrated Framework Advancing Membrane Protein Modeling and Design
Cited by: 140
Author(s): Rebecca F. Alford, Julia Koehler Leman, Brian D. Weitzner, Amanda Duran, Drew C. Tilley, Assaf Elazar, Jeffrey J. Gray
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pcbi.1006959

Ten quick tips for using a Raspberry Pi
Cited by: 10
Author(s): Anthony C. Fletcher, Cameron Mura
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pcbi.1004620

NMR Methods to Study Dynamic Allostery
Cited by: 58
Author(s): Sarina Grutsch, Sven Brüschweiler, Martin Tollinger
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pcbi.1000306

Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis
Cited by: 66
Author(s): Wolfram Stacklies, M. Cristina Vega, Matthias Wilmanns, Frauke Gräter
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pcbi.1007749

Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel
Cited by: 4
Author(s): Luca Ponzoni, Nga H. Nguyen, İvet Bahar, Jeffrey L. Brodsky
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1002170

Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity
Cited by: 58
Author(s): Nir London, Corissa L. Lamphear, James L. Hougland, Carol A. Fierke, Ora Schueler‐Furman
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pcbi.1004130

Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts
Cited by: 62
Author(s): Juan Manuel Palacios‐Moreno, Lauren Foltz, Ailan Guo, Matthew P. Stokes, Emily D. Kuehn, Lynn George, Michael J. Comb, Mark L. Grimes
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pcbi.1002326

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding
Cited by: 59
Author(s): Tianyun Liu, Russ B. Altman
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pcbi.1002404

Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex
Cited by: 54
Author(s): Cyril Reboul, Grischa R. Meyer, Benjamin T. Porebski, Natalie A. Borg, Ashley M. Buckle
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pcbi.1000923

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions
Cited by: 52
Author(s): Andreas Kowarsch, Angelika Fuchs, Dmitrij Frishman, Philipp Pagel
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pgen.1008099

LF4/MOK and a CDK-related kinase regulate the number and length of cilia in Tetrahymena
Cited by: 24
Author(s): Yu-Yang Jiang, Wolfgang Maier, Ralf Baumeister, Gregory Minevich, Ewa Joachimiak, Dorota Włoga, Zheng Ruan, Natarajan Kannan, Stephen Bocarro, Anoosh Bahraini, Krishna Kumar Vasudevan, Karl‐Ferdinand Lechtreck, Eduardo Orias, Jacek Gaertig
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1004533

The TRIM-NHL Protein LIN-41 Controls the Onset of Developmental Plasticity in Caenorhabditis elegans
Cited by: 59
Author(s): Cristina Tocchini, J.J. Keusch, Sarah Miller, Susanne Finger, H. Gut, Michael Stadler, Rafal Ciosk
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pgen.1009791

A lipoprotein allosterically activates the CwlD amidase during Clostridioides difficile spore formation
Cited by: 7
Author(s): Carolina Alves Feliciano, B.E. Eckenroth, Oscar R. Diaz, Sylvie Doublié, Aimee Shen
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pgen.1005569

LINE-1 Mediated Insertion into Poc1a (Protein of Centriole 1 A) Causes Growth Insufficiency and Male Infertility in Mice
Cited by: 20
Author(s): Krista A. Geister, Michelle L. Brinkmeier, Leonard Cheung, Jennifer Wendt, Melissa J. Oatley, Daniel L. Burgess, Kenneth M. Kozloff, James D. Cavalcoli, Sally A. Camper
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1003103

The Principal Genetic Determinants for Nasopharyngeal Carcinoma in China Involve the HLA Class I Antigen Recognition Groove
Cited by: 84
Author(s): Minzhong Tang, James A. Lautenberger, Xiaojiang Gao, Efe Sezgın, Sher L. Hendrickson, Jennifer L. Troyer, Victor A. David, Li Guan, Carl McIntosh, Xiuchan Guo, Yuming Zheng, Jian Liao, Hong Wen Deng, Michael Malasky, Bailey Kessing, Cheryl A. Winkler, Mary Carrington, Yi Zeng, Stephen J. O’Brien
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1005895

Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer
Cited by: 138
Author(s): Liyan Jiang, Jiaqi Huang, Brandon W. Higgs, Zhibin Hu, Xiaowei Zhan, Xin Yao, R. Scott Conley, Haihong Zhong, Zheng Liu, Philip Z. Brohawn, Dong Shen, Song Wu, Xiaoxiao Ge, Yue Jiang, Yupei Zhao, Yu‐Qing Lou, Chris Morehouse, Wei Zhu, Yinong Sebastian, Meggan Czapiga, Vaheh Oganesyan, Haihua Fu, Yiming Niu, Wei Zhang, Katie Streicher, David A. Tice, Heng Zhao, Meng Zhu, Lin Xu, Ronald Herbst, Xinying Su, Yi Gu, Shyoung Li, Lihua Huang, Jianren Gu, Baohui Han, Bahija Jallal, Hongbing Shen, Yihong Yao
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pgen.1004655

The Nuclear Immune Receptor RPS4 Is Required for RRS1SLH1-Dependent Constitutive Defense Activation in Arabidopsis thaliana
Cited by: 95
Author(s): Kee Hoon Sohn, Cécile Segonzac, Ghanasyam Rallapalli, Panagiotis F. Sarris, Joo Yong Woo, Simon J. Williams, Toby E. Newman, Kyung Hee Paek, Boštjan Kobe, Jonathan D. G. Jones
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1005824

Specific Hsp100 Chaperones Determine the Fate of the First Enzyme of the Plastidial Isoprenoid Pathway for Either Refolding or Degradation by the Stromal Clp Protease in Arabidopsis
Cited by: 94
Author(s): Pablo Pulido, Ernesto Llamas, Briardo Llorente, Salvador Ventura, Louwrance P. Wright, Manuel Rodrı́guez-Concepción
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1002484

Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1
Cited by: 22
Author(s): Takehiro Nishimura, Guillaume Molinard, Tom J. Petty, Larissa Broger, Caroline Gabus, Thanos D. Halazonetis, Stéphane Thore, Jerzy Paszkowski
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0235133

Computational and structure-guided design of phosphoinositide substrate specificity into the tyrosine specific LMW-PTP enzyme
Cited by: 1
Author(s): Eyong Egbe, Colin Levy, Lydia Tabernero
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0134084

Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes
Cited by: 12
Author(s): Radhika Ganu, Yasuko Ishida, Markos Koutmos, Sergios‐Orestis Kolokotronis, Alfred L. Roca, Timothy A. Garrow, Lawrence B. Schook
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0075446

A Purine Analog Synergizes with Chloroquine (CQ) by Targeting Plasmodium falciparum Hsp90 (PfHsp90)
Cited by: 23
Author(s): Dea Shahinas, Asongna Folefoc, Tony Taldone, Gabriela Chiosis, Ian Crandall, Dylan R. Pillai
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0234869

Whole-genome sequencing reveals origin and evolution of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018
Cited by: 7
Author(s): Xiaonan Zhao, Han-Ju Zhang, Duo Li, Ji Zhou, Y. Chen, Yanhong Sun, Adeniyi C. Adeola, Xiaoqing Fu, Yong Shao, Meiling Zhang
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0085940

Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site
Cited by: 47
Author(s): Young Do Kwon, Judith M. LaLonde, Yongping Yang, Mark A. Elban, Akihiro Sugawara, Joel R. Courter, David M. Jones, Amos B. Smith, Asim K. Debnath, Peter D. Kwong
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0128310

Structural Studies of the HIV-1 Integrase Protein: Compound Screening and Characterization of a DNA-Binding Inhibitor
Cited by: 15
Author(s): Peter K. Quashie, Ying-Shan Han, Said Hassounah, Thibault Mésplède, Mark A. Wainberg
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0008006

Structure of an Odorant-Binding Protein from the Mosquito Aedes aegypti Suggests a Binding Pocket Covered by a pH-Sensitive “Lid”
Cited by: 103
Author(s): Ney Ribeiro Leite, Renata Krogh, Wei Xü, Yuko Ishida, J. Iulek, Walter S. Leal, Glaucius Oliva
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0195442

An antibody with Fab-constant domains exchanged for a pair of CH3 domains
Cited by: 9
Author(s): Gordana Wozniak‐Knopp, Gerhard Stadlmayr, Jan Walther Perthold, Katharina Stadlbauer, Mathias Gotsmy, Stefan Becker, Florian Rüker
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0184627

Structure-based design, synthesis and crystallization of 2-arylquinazolines as lipid pocket ligands of p38α MAPK
Cited by: 10
Author(s): Mike Bührmann, Bianca Wiedemann, Matthias Müller, Julia Hardick, Mary Ecke, Daniel Rauh
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0174284

Structural insights into the regulation of Bacillus subtilis SigW activity by anti-sigma RsiW
Cited by: 19
Author(s): Shankar Raj Devkota, Eunju Kwon, Soonhoi Ha, Hyeun Wook Chang, Dong Young Kim
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0114373

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

10.1371/journal.pone.0140953

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

10.1371/journal.pone.0143876

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

10.1371/journal.pone.0025376

Putting into Practice Domain-Linear Motif Interaction Predictions for Exploration of Protein Networks
Cited by: 37
Author(s): Katja Luck, Sadek Fournane, Bruno Kieffer, Murielle Masson, Yves Nominé, Gilles Travé
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0248634

Prediction of LncRNA-encoded small peptides in glioma and oligomer channel functional analysis using in silico approaches
Cited by: 6
Author(s): Yipeng Cao, Rui Yang, Imshik Lee, Wenwen Zhang, Jiana Sun, Xiangfei Meng, Wei Wang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0155846

The Crystal Structure of the YknZ Extracellular Domain of ABC Transporter YknWXYZ from Bacillus amyloliquefaciens
Cited by: 9
Author(s): Yongbin Xu, Jianyun Guo, Lulu Wang, Rui Jiang, Xiaoling Jin, Jing Liu, Fan Sheng-di, Chunshan Quan, Nam‐Chul Ha
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0124272

LucY: A Versatile New Fluorescent Reporter Protein
Cited by: 4
Author(s): M.E. Auldridge, Heidi B. Cao, Satyabrata Sen, Laura Franz, C.A. Bingman, Ragothaman M. Yennamalli, George N. Phillips, David A. Mead, Eric J. Steinmetz
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0188267

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

10.1371/journal.pone.0188005

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

10.1371/journal.pone.0063370

Structural Basis for the Oligomerization-State Switch from a Dimer to a Trimer of an Engineered Cortexillin-1 Coiled-Coil Variant
Cited by: 2
Author(s): Saša Bjelić, Mara M. Wieser, Daniel Frey, Christian U. Stirnimann, Mark R. Chance, Rolf Jaussi, Michel O. Steinmetz, Richard A. Kammerer
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0193028

Folic acid derived-P5779 mimetics regulate DAMP-mediated inflammation through disruption of HMGB1:TLR4:MD-2 axes
Cited by: 13
Author(s): Shan Sun, Mingzhu He, Yongjun Wang, Huan Yang, Yousef Al‐Abed
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0091232

Molecular Recognition of the Neurotransmitter Acetylcholine by an Acetylcholine Binding Protein Reveals Determinants of Binding to Nicotinic Acetylcholine Receptors
Cited by: 34
Author(s): Jeppe Olsen, Thomas Balle, Michael Gajhede, Philip K. Ahring, J.S. Kastrup
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0170232

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

10.1371/journal.pone.0015199

Tracing the Origin of the Fungal α1 Domain Places Its Ancestor in the HMG-Box Superfamily: Implication for Fungal Mating-Type Evolution
Cited by: 92
Author(s): Tom Martin, Shunwen Lu, Herman van Tilbeurgh, Daniel R. Ripoll, Christina Dixelius, B. Gillian Turgeon, Robert Debuchy
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0040066

The Crystal Structures of Dystrophin and Utrophin Spectrin Repeats: Implications for Domain Boundaries
Cited by: 27
Author(s): M. Muthu, Kylie A. Richardson, Andrew J. Sutherland-Smith
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0216427

Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain
Cited by: 22
Author(s): Md. Imran Khan, Deepu Dowarha, Revansiddha Katte, Ruey Hwang Chou, Anna Filipek, Chin Yu
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0075992

Ligand Pose and Orientational Sampling in Molecular Docking
Cited by: 123
Author(s): Ryan G. Coleman, Michael Carchia, Teague Sterling, John J. Irwin, Brian K. Shoichet
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0242686

Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ
Cited by: 12
Author(s): William C. Scott, Brian Lowrance, Alexander C Anderson, Joel T. Weadge
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0165917

Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes
Cited by: 14
Author(s): Norbert Schormann, Chapelle A. Ayres, Fry Alexandra, Todd Green, Surajit Banerjee, Glen C. Ulett, Debasish Chattopadhyay
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0039993

Analysis of Conformational Variation in Macromolecular Structural Models
Cited by: 6
Author(s): Sandeep Srivastava, S Gayathri, Babu A. Manjasetty, B. Gopal
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0152049

On the Applicability of Elastic Network Models for the Study of RNA CUG Trinucleotide Repeat Overexpansion
Cited by: 8
Author(s): Àlex L. González, Jordi Teixidó, José I. Borrell, Roger Estrada‐Tejedor
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0245822

Sequence and structure comparison of ATP synthase F0 subunits 6 and 8 in notothenioid fish
Cited by: 3
Author(s): Gunjan Katyal, Brad Ebanks, Magnus Lucassen, Chiara Papetti, Lisa Chakrabarti
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0193760

MIP diversity from Trichoderma: Structural considerations and transcriptional modulation during mycoparasitic association with Fusarium solani olive trees
Cited by: 10
Author(s): Maroua Ben Amira, Robin Mom, David Lopez, Hatem Chaar, Ali Khouaja, Valérie Pujade-Renaud, Boris Fumanal, Aurélie Gousset-Dupont, Gisèle Bronner, Philippe Label, Jean-Louis Julien, Mohamed Ali Triki, Daniel Auguin, Jean-Stéphane Venisse
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0045379

BioFET-SIM Web Interface: Implementation and Two Applications
Cited by: 10
Author(s): Martin R. Hediger, Jan H. Jensen, Luca De Vico
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0099408

Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes
Cited by: 16
Author(s): Laura J. Kingsley, Markus A. Lill
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0175758

Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages
Cited by: 8
Author(s): Qi Chen, Michał Vieth, David E. Timm, Christine Humblet, Dina Stroopinsky, Ilan E. Chemmama, Andrej Šali, Wei Zeng, Jirong Lu, Ling Liu
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0044124

Complex Structure of Engineered Modular Domains Defining Molecular Interaction between ICAM-1 and Integrin LFA-1
Cited by: 3
Author(s): Sungkwon Kang, Chae Un Kim, Xiaoling Gu, Róisı́n M. Owens, Sarah J. van Rijn, Vanissra Boonyaleepun, Yuxin Mao, Timothy A. Springer, Moonsoo M. Jin
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0076355

Crystal Structure of the Human Short Coiled Coil Protein and Insights into SCOC-FEZ1 Complex Formation
Cited by: 6
Author(s): Caroline Behrens, Beyenech Binotti, Carla Schmidt, Carol V. Robinson, John Jia En Chua, Karin Kühnel
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0081526

Structural Insights into the Mechanism for Recognizing Substrate of the Cytochrome P450 Enzyme TxtE
Cited by: 18
Author(s): Feng Yu, Minjun Li, Chunyan Xu, Zhijun Wang, Huan Zhou, Min Yang, Yaxing Chen, Lin Tang, Jianhua He
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0039850

Structural Modeling and DNA Binding Autoinhibition Analysis of Ergp55, a Critical Transcription Factor in Prostate Cancer
Cited by: 3
Author(s): S.P. Gangwar, Sharmistha Dey, Ajay K. Saxena
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0086050

Tracking Molecular Recognition at the Atomic Level with a New Protein Scaffold Based on the OB-Fold
Cited by: 18
Author(s): John D. Steemson, Matthias Baake, Jasna Rakonjac, Vickery L. Arcus, Mark T. Liddament
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0026792

Novel Adiponectin Variants Identified in Type 2 Diabetic Patients Reveal Multimerization and Secretion Defects
Cited by: 13
Author(s): Prapaporn Jungtrakoon, Nattachet Plengvidhya, Watip Tangjittipokin, Sarin Chimnaronk, Wanisa Salaemae, Nalinee Chongjaroen, Kanjana Chanprasert, Jatuporn Sujjitjoon, Chatchawan Srisawat, Pa‐thai Yenchitsomanus
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0056742

Towards Improved Quality of GPCR Models by Usage of Multiple Templates and Profile-Profile Comparison
Cited by: 50
Author(s): Dorota Latek, Paweł Pasznik, Teresa Carlomagno, Sławomir Filipek
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0026251

Structural Analysis of Prolyl Oligopeptidases Using Molecular Docking and Dynamics: Insights into Conformational Changes and Ligand Binding
Cited by: 28
Author(s): Sushmita Kaushik, Ramanathan Sowdhamini
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0123195

An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor β (RARβ, NR1B2) Selective Agonist
Cited by: 12
Author(s): Nadendla EswarKumar, Catherine Teyssier, V. Delfosse, Valérie Vivat, Krishnasamy Gunasekaran, Hinrich Gronemeyer, William Bourguet, Pierre Germain
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0232757

Characterization of a human monoclonal antibody generated from a B-cell specific for a prefusion-stabilized spike protein of Middle East respiratory syndrome coronavirus
Cited by: 10
Author(s): Jang Hoon Choi, Hye Min Woo, Tae Young Lee, So Young Lee, Sang Mu Shim, Woo Jung Park, Jeong Sun Yang, Joo Ae Kim, Mi Ran Yun, Dae Won Kim, Sung Soon Kim, Yi Zhang, Wei Shi, Lingshu Wang, Barney S. Graham, John R. Mascola, Nanshuang Wang, Jason S. McLellan, Joo Yeon Lee, Hansaem Lee
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0026278

A Novel Metagenomic Short-Chain Dehydrogenase/Reductase Attenuates Pseudomonas aeruginosa Biofilm Formation and Virulence on Caenorhabditis elegans
Cited by: 108
Author(s): P. Bijtenhoorn, Hubert Mayerhofer, Jochen Müller-Dieckmann, Christian Utpatel, Christina Schipper, C. Hornung, Matthias Szesny, Stephanie Grond, Andrea Thürmer, Elżbieta Brzuszkiewicz, Rolf Daniel, Katja Dierking, Hinrich Schulenburg, Wolfgang R. Streit
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0074788

The Structural Basis of Erwinia rhapontici Isomaltulose Synthase
Cited by: 17
Author(s): Zheng Xu, Sha Li, Jie Li, Yan Li, Xiaohai Feng, Renxiao Wang, Hong Xu, Jiahai Zhou
Software Mentions: 2
Published: almost 13 years ago

10.3390/cancers13153847

Identification of Cancer Hub Gene Signatures Associated with Immune-Suppressive Tumor Microenvironment and Ovatodiolide as a Potential Cancer Immunotherapeutic Agent
Cited by: 23
Author(s): Jiahong Chen, Alexander T.H. Wu, Bashir Lawal, David T.W. Tzeng, Jih‐Chin Lee, Ching–Liang Ho, Tsu‐Yi Chao
Software Mentions: 2
Published: almost 5 years ago

10.3390/cancers13040909

Role of PFKFB3 and PFKFB4 in Cancer: Genetic Basis, Impact on Disease Development/Progression, and Potential as Therapeutic Targets
Cited by: 53
Author(s): Krzysztof Kotowski, Jakub Rosik, Filip Machaj, Stanisław Supplitt, Daniel Wiczew, Karolina Jabłońska, Emilia Wiecheć, Saeid Ghavami, Piotr Dzięgiel
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers13061244

3D Pharmacophore-Based Discovery of Novel KV10.1 Inhibitors with Antiproliferative Activity
Cited by: 5
Author(s): Žan Toplak, Louise Antonia Hendrickx, Špela Gubič, Štefan Možina, Bojana Žegura, Alja Štern, Matjaž Novak, Xiaoyi Shi, Steve Peigneur, Jan Tytgat, Tihomir Tomašič, Luis A. Pardo, Lucíja Peterlin Mašič
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers13112843

Elevated Expression of the RAGE Variant-V in SCLC Mitigates the Effect of Chemotherapeutic Drugs
Cited by: 4
Author(s): Bindhu K. Madhavan, Zhe Han, B.K. Singh, Nico Bordt, Serap Kaymak, Obul Reddy Bandapalli, Lars Kihm, Khurrum Shahzad, Berend Isermann, Stephan Herzig, Peter P. Nawroth, Vaijayanti A. Kumar
Software Mentions: 2
Published: about 5 years ago

10.3390/cancers11121828

Synergy of Ginkgetin and Resveratrol in Suppressing VEGF-Induced Angiogenesis: A Therapy in Treating Colorectal Cancer
Cited by: 49
Author(s): Weihui Hu, Gallant Kar-Lun Chan, Ran Duan, Huaiyou Wang, Xiangpeng Kong, Tina Tingxia Dong, Karl Wah-Keung Tsim
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers12061412

A H-REV107 Peptide Inhibits Tumor Growth and Interacts Directly with Oncogenic KRAS Mutants
Cited by: 10
Author(s): Chang Woo Han, Mi Suk Jeong, Soonhoi Ha, Se Bok Jang
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers6031464

Phosphorylation of Large T Antigen Regulates Merkel Cell Polyomavirus Replication
Cited by: 19
Author(s): José Ángel Menéndez Díaz, Xin Wang, Sabrina H. Tsang, Jing Jiao, Jianxin You
Software Mentions: 2
Published: about 12 years ago

10.3390/cancers12061523

New Anti-Cancer Strategy to Suppress Colorectal Cancer Growth Through Inhibition of ATG4B and Lysosome Function
Cited by: 13
Author(s): Yuanyuan Fu, Qianqian Gu, Li Luo, Jiangang Xu, Yuping Luo, Fan Xia, Fanghai Han, Hong Liu, Xiao Ming Yin, Zhiying Huang, Min Li
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers12040813

Ensartinib (X-396) Effectively Modulates Pharmacokinetic Resistance Mediated by ABCB1 and ABCG2 Drug Efflux Transporters and CYP3A4 Biotransformation Enzyme
Cited by: 19
Author(s): Dimitrios Vagiannis, Eva Novotná, Adam Skarka, Sarah Kammerer, Jan-Heiner Küpper, Si Chen, Lei Guo, František Štaud, Jakub Hofman
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers12020456

An Epitope on EGFR Loading Catastrophic Internalization Serve as a Novel Oncotarget for Hepatocellular Carcinoma Therapy
Cited by: 0
Author(s): Dianshuai Huang, Qingjie Fan, Zhiyi Liu, Shuqin Zhang, Wei Huang, Hongrui Li, Chaozhao Liang, Fenyong Sun
Software Mentions: 2
Published: over 6 years ago

10.1016/j.cell.2020.01.010

Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody
Cited by: 89
Author(s): Philipp Schommers, Henning Gruell, Morgan E. Abernathy, My-Kim Tran, Adam S. Dingens, Harry B. Gristick, Christopher O. Barnes, Till Schoofs, Maike Schlotz, Kanika Vanshylla, Christoph Kreer, Daniela Weiland, Udo Holtick, Christof Scheid, Markus M. Valter, Marit J. van Gils, Rogier W. Sanders, Jörg Janne Vehreschild, Oliver A. Cornely, Clara Lehmann, Gerd Fätkenheuer, Michael S. Seaman, Jesse D Bloom, Pamela J. Björkman, Florian Klein
Software Mentions: 2
Published: over 6 years ago

10.1016/j.cell.2021.06.020

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum
Cited by: 571
Author(s): C Liu, H. Ginn, Wanwisa Dejnirattisai, Piyada Supasa, Beibei Wang, Aekkachai Tuekprakhon, Rungtiwa Nutalai, Daming Zhou, Alexander J. Mentzer, Yuguang Zhao, Duyvesteyn Hme., César López-Camacho, J Slon-Campos, T S Walter, Donal Skelly, Síle A. Johnson, Thomas G. Ritter, Chris Mason, Sue Ann Costa Clemens, Felipe Gomes Naveca, Valdinete Alves do Nascimento, Fernanda Nascimento, Cristiano Fernandes da Costa, Paola Cristina Resende, Alex Pauvolid‐Corrêa, Marilda Mendonça Siqueira, Christina Dold, Nigel Temperton, Tao Dong, Andrew J. Pollard, Julian C. Knight, Derrick W. Crook, Teresa Lambe, Elizabeth A. Clutterbuck, Sagida Bibi, Amy Flaxman, Mustapha Bittaye, Sandra Belij‐Rammerstorfer, Sarah C. Gilbert, Tariq Malik, Miles W. Carroll, Paul Klenerman, Eleanor Barnes, Susanna Dunachie, Vicky L. Baillie, Natali Serafin, Zanele Ditse, K Da Silva, Neil G. Paterson, Mark A. Williams, David R. Hall, Shabir A. Madhi, Marta C Nunes, Philip Goulder, Elizabeth E. Fry, Juthathip Mongkolsapaya, Jingshan Ren, D.I. Stuart, Gavin Screaton
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.cell.2021.03.055

Antibody evasion by the P.1 strain of SARS-CoV-2
Cited by: 480
Author(s): Wanwisa Dejnirattisai, Daming Zhou, Piyada Supasa, C Liu, Alexander J. Mentzer, H. Ginn, Yuguang Zhao, Duyvesteyn Hme., Aekkachai Tuekprakhon, Rungtiwa Nutalai, Beibei Wang, César López-Camacho, J Slon-Campos, Thomas S. Walter, Donal Skelly, Sue Ann Costa Clemens, Felipe Gomes Naveca, Valdinete Alves do Nascimento, Felipe Franco Nascimento, Cristiano Fernandes da Costa, Paola Cristina Resende, Alex Pauvolid‐Corrêa, Marilda Mendonça Siqueira, Christina Dold, Robert H. Levin, Tao Dong, Andrew J. Pollard, Julian C. Knight, Derrick W. Crook, Teresa Lambe, Elizabeth A. Clutterbuck, Sagida Bibi, Amy Flaxman, Mustapha Bittaye, Sandra Belij‐Rammerstorfer, Sarah C. Gilbert, Miles W. Carroll, Paul Klenerman, Eleanor Barnes, Susanna Dunachie, Neil G. Paterson, Mark A. Williams, ' Hall, Ruben J.G. Hulswit, Thomas A. Bowden, Elizabeth E. Fry, Juthathip Mongkolsapaya, Jingshan Ren, D.I. Stuart, Gavin Screaton
Software Mentions: 2
Published: about 5 years ago

10.1016/j.cell.2018.10.037

Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design
Cited by: 52
Author(s): Yin Dong, Hua Wang, A.C.W. Pike, Stephen A. Cochrane, Sadra Hamedzadeh, Filip J. Wyszyński, S.R. Bushell, Sylvain Royer, David A. Widdick, Andaleeb Sajid, Helena I. Boshoff, Yumi Park, Ricardo Dantas de Lucas, Weimin Liu, Seung Seo Lee, Takuya Machida, Leanne Minall, Shahid Mehmood, Katsiaryna Belaya, Weiwei Liu, Amy Chu, L. Shrestha, Shubhashish M.M. Mukhopadhyay, Claire Strain-Damerell, R. Chalk, N. Burgess-Brown, Mervyn J. Bibb, Clifton E. Barry, Carol V. Robinson, David Beeson, Benjamin G. Davis, E.P. Carpenter
Software Mentions: 2
Published: over 7 years ago

10.1016/j.cell.2017.06.025

Development of a Novel Lead that Targets M. tuberculosis Polyketide Synthase 13
Cited by: 115
Author(s): Anup Aggarwal, Maloy Kumar Parai, N.D. Shetty, Deeann Wallis, Lisa K. Woolhiser, Courtney Hastings, Noton K. Dutta, Stacy Galaviz, Ramesh Dhakal, Rupesh Shrestha, Shoko Wakabayashi, Chris Walpole, David J. Matthews, David M. Floyd, Paul Scullion, Jennifer Riley, Ola Epemolu, Suzanne Norval, Thomas Snavely, Gregory T. Robertson, Eric J. Rubín, Thomas R. Ioerger, F A Sirgel, Ruben van der Merwe, Paul D. van Helden, Peter M. Keller, Erik C. Böttger, Petros C. Karakousis, Anne J. Lenaerts, James C. Sacchettini
Software Mentions: 2
Published: about 9 years ago

10.1016/j.cell.2021.01.037

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
Cited by: 508
Author(s): Emma C. Thomson, Laura E. Rosen, James G. Shepherd, Roberto Spreafico, Ana da Silva Filipe, Jason A. Wojcechowskyj, Chris Davis, Luca Piccoli, David Pascall, Josh R Dillen, Spyros Lytras, Nadine Czudnochowski, Rajiv Shah, Marcel Meury, Natasha Jesudason, Anna De Marco, Kathy Li, Jessica Bassi, Áine O’Toole, Dora Pinto, Rachel Colquhoun, Katja Culap, Ben Jackson, Fabrizia Zatta, Andrew Rambaut, Stefano Jaconi, Vattipally B Sreenu, Jay C. Nix, Ivy Zhang, Ruth F. Jarrett, William G. Glass, Martina Beltramello, Kyriaki Nomikou, Matteo Samuele Pizzuto, L. Tong, Elisabetta Cameroni, Tristan I. Croll, Natasha Johnson, Julia di Iulio, Arthur Wickenhagen, Alessandro Ceschi, Aoife M Harbison, Daniel Mair, Paolo Ferrari, Katherine Smollett, Federica Sallusto, Stephen Carmichael, Christian Garzoni, Jenna Nichols, Massimo Galli, Joseph Hughes, Agostino Riva, Antonia Ho, Marco Schiuma, Malcolm G Semple, Peter Openshaw, Elisa Fadda, J Kenneth Baillie, John D. Chodera, Suzannah J. Rihn, Samantha Lycett, Herbert W. Virgin, Amalio Telenti, Davide Corti, David L. Robertson, Gyorgy Snell
Software Mentions: 2
Published: over 5 years ago

10.1016/j.cell.2021.02.032

The antigenic anatomy of SARS-CoV-2 receptor binding domain
Cited by: 294
Author(s): Wanwisa Dejnirattisai, Daming Zhou, H. Ginn, Duyvesteyn Hme., Piyada Supasa, William James, Yuguang Zhao, Thomas S. Walter, Alexander J. Mentzer, Chang Liu, Beibei Wang, Guido C. Paesen, J Slon-Campos, César López-Camacho, Natasha M. Kafai, Adam L. Bailey, Rita E. Chen, Ying Bai, Craig Thompson, Jai S Bolton, Alex Fyfe, Sunetra Gupta, Tiong Kit Tan, Javier Gilbert‐Jaramillo, Michael Knight, Miles W. Carroll, Donal Skelly, Christina Dold, Yanchun Peng, Robert H. Levin, Tao Dong, Andrew J. Pollard, Julian C. Knight, Paul Klenerman, Nigel Temperton, David R. Hall, Mark A. Williams, Neil G. Paterson, Felicity K.R. Bertram, C. Alistair Siebert, Daniel K. Clare, Andrew Howe, Julika Radecke, Yun Song, Alain Townsend, Kuan Ying A. Huang, Elizabeth E. Fry, Juthathip Mongkolsapaya, Michael S. Diamond, Jingshan Ren, D.I. Stuart, Gavin Screaton
Software Mentions: 2
Published: over 5 years ago

10.1016/j.cell.2010.05.037

A Comprehensive Comparison of Transmembrane Domains Reveals Organelle-Specific Properties
Cited by: 467
Author(s): Hayley J. Sharpe, Tim J. Stevens, Sean Munro
Software Mentions: 2
Published: about 16 years ago

10.1016/j.cell.2019.12.006

In Situ Structure of an Intact Lipopolysaccharide-Bound Bacterial Surface Layer
Cited by: 73
Author(s): Andriko von Kügelgen, Haiping Tang, Gail G. Hardy, Danguole Kureisaite-Ciziene, Yves V. Brun, Phillip J. Stansfeld, Carol V. Robinson, Tanmay A. M. Bharat
Software Mentions: 2
Published: over 6 years ago

10.1007/s10565-018-9427-z

Developing novel methods to image and visualize 3D genomes
Cited by: 23
Author(s): Tszshan Ma, Long Chen, Maoxiang Shi, Jing Niu, Xu Zhang, Xusan Yang, Karl Zhanghao, Miaoyan Wang, Peng Xi, Dayong Jin, Michael Zhang, Juntao Gao
Software Mentions: 2
Published: over 8 years ago

10.1186/s13578-021-00564-x

Ginkgolic acid and anacardic acid are specific covalent inhibitors of SARS-CoV-2 cysteine proteases
Cited by: 42
Author(s): Zinuo Chen, Qinghua Cui, Laura Cooper, Zhang Pin, Hyun Lee, Zhaoyu Chen, Yanyan Wang, Xiaoyun Liu, Lijun Rong, Ruikun Du
Software Mentions: 2
Published: over 5 years ago

10.1016/j.chembiol.2019.11.007

Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases
Cited by: 15
Author(s): Yi-Chun Isabella Tsai, Henrik Johansson, David P. Dixon, Stephen R. Martin, Chun‐wa Chung, Jane Clarkson, David House, Katrin Rittinger
Software Mentions: 2
Published: over 6 years ago

10.1038/s41419-020-02902-2

Homoharringtonine suppresses tumor proliferation and migration by regulating EphB4-mediated β-catenin loss in hepatocellular carcinoma
Cited by: 21
Author(s): Man Zhu, Zhengyan Gong, Qing Wu, Qi Su, Tianfeng Yang, Runze Yu, Rui Xu, Yanmin Zhang
Software Mentions: 2
Published: almost 6 years ago

Projects: pypi: PyMOL

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Papers Mentioning PyMOL 8,266