pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.15252/msb.20177902

A unified approach for quantifying and interpreting <scp>DNA</scp> shape readout by transcription factors
Cited by: 31
Author(s): H. Tomas Rube, Chaitanya Rastogi, Judith F. Kribelbauer, Harmen J. Bussemaker
Software Mentions: 2
Published: almost 8 years ago

10.18632/oncotarget.21652

Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab
Cited by: 54
Author(s): Fei Zhang, Xiaoqiang Qi, Xiaoxiao Wang, Diyang Wei, Jiawei Wu, Lingling Feng, Haiyan Cai, Yugang Wang, Naiyan Zeng, Ting Xu, Aiwu Zhou, Ying Zheng
Software Mentions: 2
Published: about 8 years ago

10.1038/srep38137

Engineering of a thermostable esterase Est816 to improve its quorum-quenching activity and the underlying structural basis
Cited by: 11
Author(s): Xiwen Liu, Liping Cao, Xiaoran Fan, Yuhuan Liu, Wei Xie
Software Mentions: 2
Published: almost 9 years ago

10.3389/fimmu.2020.01529

The Effects of Framework Mutations at the Variable Domain Interface on Antibody Affinity Maturation in an HIV-1 Broadly Neutralizing Antibody Lineage
Cited by: 11
Author(s): Jeffrey Zhou, Hussain Zaidi, Therese Ton, Daniela Fera
Software Mentions: 2
Published: over 5 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: about 8 years ago

10.3389/fimmu.2021.621153

Structural Comparison Between MHC Classes I and II; in Evolution, a Class-II-Like Molecule Probably Came First
Cited by: 16
Author(s): Yanan Wu, Nianzhi Zhang, Keiichiro Hashimoto, Chun Xia, Johannes M. Dijkstra
Software Mentions: 2
Published: over 4 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: almost 8 years ago

10.18632/oncotarget.24305

Unbiased compound-protein interface mapping and prediction of chemoresistance loci through forward genetics in haploid stem cells
Cited by: 15
Author(s): Moritz Horn, Virginia Kroef, Kira Allmeroth, Nicole Schuller, Stephan Miethe, Martin Peifer, Josef Penninger, Ulrich Elling, Martin S. Denzel
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13040-016-0083-7

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level
Cited by: 0
Author(s): Florian Heinke, Sebastian Bittrich, Florian Kaiser, Dirk Labudde
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep39024

Comparative Proteomics Reveals that Phosphorylation of β Carbonic Anhydrase 1 Might be Important for Adaptation to Drought Stress in Brassica napus
Cited by: 31
Author(s): Limin Wang, Xiang Jin, Qingbin Li, Xuchu Wang, Zaiyun Li, Xiaoming Wu
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0090915

Crystal Structures of the Novel Cytosolic 5′-Nucleotidase IIIB Explain Its Preference for m7GMP
Cited by: 13
Author(s): Thomas Monecke, Juliane Buschmann, Piotr Neumann, Elmar Wahle, Ralf Ficner
Software Mentions: 2
Published: over 11 years ago

10.15252/msb.20188371

Deep scanning lysine metabolism in Escherichia coli
Cited by: 31
Author(s): Marcelo C. Bassalo, Andrew D. Garst, Alaksh Choudhury, William C Grau, Eun‐Suok Oh, Eileen Spindler, Tanya Warnecke Lipscomb, Ryan T. Gill
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0256141

Genomics-guided identification of potential modulators of SARS-CoV-2 entry proteases, TMPRSS2 and Cathepsins B/L
Cited by: 12
Author(s): Kartikay Prasad, Suliman Yousef Alomar, Eman Abdullah Almuqri, Hassan Ahmed Rudayni, Vijay Kumar
Software Mentions: 2
Published: over 4 years ago

10.1038/srep40254

Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode
Cited by: 5
Author(s): Tianle Qian, Jing Wo, Yan Zhang, Quanwei Song, Guoqiang Feng, Ray Luo, Shuangjin Lin, Geng Wu, Haifeng Chen
Software Mentions: 2
Published: almost 9 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: over 12 years ago

10.1155/2017/4342789

Identification, Characterization, and Structure of Tm16 fromTrichuris muris
Cited by: 10
Author(s): Zhuyun Liu, Alan Kelleher, Shanii Tabb, Junfei Wei, Jeroen Pollet, Peter J. Hotez, María Elena Bottazzi, Bin Zhan, Oluwatoyin A. Asojo
Software Mentions: 2
Published: almost 9 years ago

10.1021/acs.jpcb.1c03639

Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody
Cited by: 24
Author(s): Hung Van Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O’Brien, Mai Suan Li
Software Mentions: 2
Published: over 4 years ago

10.1038/srep41487

Identification of a novel selective PPARγ ligand with a unique binding mode and improved therapeutic profile in vitro
Cited by: 15
Author(s): Wei Yi, Jingjing Shi, Guanguan Zhao, Xuemei Zhou, Kelly Suino-Powell, Karsten Melcher, H. Eric Xu
Software Mentions: 2
Published: almost 9 years ago

10.1113/JP277079

ORAI1 channel gating and selectivity is differentially altered by natural mutations in the first or third transmembrane domain
Cited by: 36
Author(s): Monica Bulla, Gergely Gyimesi, Jihee Kim, Rajesh Bhardwaj, Matthias A. Hediger, Maud Frieden, Nicolas Demaurex
Software Mentions: 2
Published: almost 7 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: almost 8 years ago

10.1038/srep41212

Two strategies to engineer flexible loops for improved enzyme thermostability
Cited by: 111
Author(s): Haoran Yu, Yihan Yan, Cheng Zhang, Paul A. Dalby
Software Mentions: 2
Published: almost 9 years ago

10.4172/jpb.1000419

A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning
Cited by: 9
Author(s): Haiou Li
Software Mentions: 2
Published: almost 10 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 11 years ago

10.1016/j.bbrep.2016.03.004

Molecular docking, a tool to determine interaction of CuO and TiO 2 nanoparticles with human serum albumin
Cited by: 18
Author(s): Sandesh Chibber, Irshad Ahmad
Software Mentions: 2
Published: over 9 years ago

10.1098/rsob.120142

Structure and function of cytidine monophosphate kinase from Yersinia pseudotuberculosis , essential for virulence but not for survival
Cited by: 11
Author(s): Nicola Walker, Elizabeth A. Clark, Donna C. Ford, Helen L. Bullifent, Erin V. McAlister, Melanie Duffield, K. Ravi Acharya, Petra C. F. Oyston
Software Mentions: 2
Published: almost 13 years ago

10.1186/1472-6807-13-6

Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach
Cited by: 37
Author(s): Rajaram Gana, Shruti Rao, Hongzhan Huang, Cathy H. Wu, Sona Vasudevan
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0248394

Anti-asthmatic effect of nitric oxide metallo-donor FOR811A [cis-[Ru(bpy)2(2-MIM)(NO)](PF6)3] in the respiratory mechanics of Swiss mice
Cited by: 6
Author(s): Paula Priscila Correia Costa, Stefanie Bressan Waller, Gilvan Ribeiro dos Santos, Fladimir de Lima Gondim, Daniel Silveira Serra, Francisco Sales Ávila Cavalcante, Florêncio Sousa Gouveia Júnior, Valdir Ferreira de Paula Júnior, Eduardo Henrique Silva Sousa, Luiz Gonzaga de França Lopes, Wesley Lyeverton Correia Ribeiro, Helena Serra Azul Monteiro
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0115409

Characterization of M. tuberculosis SerB2, an Essential HAD-Family Phosphatase, Reveals Novel Properties
Cited by: 12
Author(s): Gaya P. Yadav, Sonal Shree, Ruchi Maurya, Niyati Rai, Diwakar Singh, Kirti Srivastava, Ravishankar Ramachandran
Software Mentions: 2
Published: almost 11 years ago

10.1042/BSR20170001

Crystal structure of thermostable alkylsulfatase SdsAP from Pseudomonas sp. S9
Cited by: 3
Author(s): Lifang Sun, Pu Chen, Su Y, Zhixiong Cai, Lingwei Ruan, Xun Xu, Yunkun Wu
Software Mentions: 2
Published: over 8 years ago

10.1098/rsob.130021

Structure of a bacterial putative acetyltransferase defines the fold of the human O -GlcNAcase C-terminal domain
Cited by: 43
Author(s): Francesco Rao, Alexander W. Schüttelkopf, Helge C. Dorfmueller, Andrew T. Ferenbach, Iva Navrátilová, Daan M. F. van Aalten
Software Mentions: 2
Published: about 12 years ago

10.3389/fmolb.2020.00029

Molecular Simulation of Oncostatin M and Receptor (OSM–OSMR) Interaction as a Potential Therapeutic Target for Inflammatory Bowel Disease
Cited by: 19
Author(s): Qingqing Du, Qian Yan, Weiwei Xue
Software Mentions: 2
Published: over 5 years ago

10.1038/srep42711

Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage ΦAB6 tailspike protein
Cited by: 37
Author(s): I‐Ming Lee, I-Fan Tu, Yang Fu, Tzu‐Ping Ko, Jiahn-Haur Liao, Ning Lin, Chung‐Yi Wu, Chien‐Tai Ren, Andrew H.‐J. Wang, Ching-Ming Chang, Kai‐Fa Huang, Shih‐Hsiung Wu
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmolb.2017.00068

Structure and Interactions of the TPR Domain of Sgt2 with Yeast Chaperones and Ybr137wp
Cited by: 18
Author(s): E. Krysztofinska, N.J. Evans, Arjun Thapaliya, James W. Murray, Rhodri M. L. Morgan, Santiago Martínez-Lumbreras, Rivka L. Isaacson
Software Mentions: 2
Published: about 8 years ago

10.1098/rsob.150005

Three-dimensional topology of the SMC2/SMC4 subcomplex from chicken condensin I revealed by cross-linking and molecular modelling
Cited by: 46
Author(s): Helena Barysz, Ji Hun Kim, Zhuo A. Chen, Damien F. Hudson, Juri Rappsilber, Dietlind L. Gerloff, William C. Earnshaw
Software Mentions: 2
Published: almost 11 years ago

10.1098/rsob.150128

Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA
Cited by: 22
Author(s): Akihisa Osakabe, Fumiya Adachi, Yasuhiro Arimura, Kazuhira Maehara, Yasuyuki Ohkawa, Hitoshi Kurumizaka
Software Mentions: 2
Published: about 10 years ago

10.1098/rsob.160090

Structural and biochemical analyses of monoubiquitinated human histones H2B and H4
Cited by: 32
Author(s): Shuichi Machida, Satoshi Sekine, Yuka Nishiyama, Naoki Horikoshi, Hitoshi Kurumizaka
Software Mentions: 2
Published: over 9 years ago

10.1098/rsob.160127

Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A
Cited by: 24
Author(s): Naoki Horikoshi, Yasuhiro Arimura, Hiroyuki Taguchi, Hitoshi Kurumizaka
Software Mentions: 2
Published: over 9 years ago

10.1098/rsob.160157

Exploring the active site of the Streptococcus pneumoniae topoisomerase IV–DNA cleavage complex with novel 7,8-bridged fluoroquinolones
Cited by: 18
Author(s): Ivan Laponogov, Xiao Su Pan, D. A. Veselkov, Ryan T. Cirz, Allan S. Wagman, Heinz Moser, L. Mark Fisher, Mark Sanderson
Software Mentions: 2
Published: about 9 years ago

10.1098/rsob.160327

Structural and functional analysis of Oceanobacillus iheyensis macrodomain reveals a network of waters involved in substrate binding and catalysis
Cited by: 15
Author(s): Rubén Zapata-Pérez, F. Gil-Ortiz, Ana Belén Martínez-Moñino, Antonio Ginés García-Saura, Judith Juanhuix, Álvaro Sánchez‐Ferrer
Software Mentions: 2
Published: over 8 years ago

10.1098/rsob.170135

Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus
Cited by: 6
Author(s): Grace M. Loxley, Jennifer Unsworth, Michael J. Turton, Alexandra Jebb, Kathryn S. Lilley, Deborah M. Simpson, Daniel J. Rigden, Jane L. Hurst, Robert J. Beynon
Software Mentions: 2
Published: about 8 years ago

10.3390/nu11010067

Structural Insights into Phylloquinone (Vitamin K1), Menaquinone (MK4, MK7), and Menadione (Vitamin K3) Binding to VKORC1
Cited by: 16
Author(s): Nolan Chatron, Abdessalem Hammed, Etienne Benoît, Virginie Lattard
Software Mentions: 2
Published: almost 7 years ago

10.3390/vaccines6010001

Structural Analysis and Epitope Prediction of MHC Class-1-Chain Related Protein-A for Cancer Vaccine Development
Cited by: 16
Author(s): Tayo Alex Adekiya, Raphael Taiwo Aruleba, Sbonelo Khanyile, Priscilla Masamba, Babatunji Emmanuel Oyinloye, Abidemi Paul Kappo
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmolb.2021.716466

SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking
Cited by: 17
Author(s): Samuel Murail, Sjoerd J. de Vries, Julien Rey, Gautier Moroy, Pierre Tufféry
Software Mentions: 2
Published: about 4 years ago

10.1038/srep43318

ACCORD: an assessment tool to determine the orientation of homodimeric coiled-coils
Cited by: 6
Author(s): Byeong Won Kim, Yang Ouk Jung, Min Kyung Kim, Do Hoon Kwon, Si Hoon Park, Jun Hoe Kim, Yong Boo Kuk, Sun Joo Oh, Leehyeon Kim, Bong Heon Kim, Woo Seok Yang, Hyun Kyu Song
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0191610

Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii
Cited by: 1
Author(s): Bhumika S. Shah, Heather E. Ashwood, S.J. Harrop, Daniel N. Farrugia, Ian T. Paulsen, Bridget C. Mabbutt
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep44341

Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability
Cited by: 36
Author(s): Marcin Wolny, Matthew Batchelor, Gail J. Bartlett, Emily G. Baker, Marta Kurzawa, Peter J. Knight, Lorna Dougan, Derek N. Woolfson, Emanuele Paci, Michelle Peckham
Software Mentions: 2
Published: over 8 years ago

10.1093/molbev/msab017

Bridging Themes: Short Protein Segments Found in Different Architectures
Cited by: 30
Author(s): Rachel Kolodny, Sergey Nepomnyachiy, Dan S. Tawfik, Nir Ben‐Tal
Software Mentions: 2
Published: almost 5 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 7 years ago

10.1038/srep45224

Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics
Cited by: 10
Author(s): Hannah A. Davies, Daniel J. Rigden, Marie M. Phelan, Jillian Madine
Software Mentions: 2
Published: over 8 years ago

10.3389/fmolb.2015.00056

A script to highlight hydrophobicity and charge on protein surfaces
Cited by: 83
Author(s): Dominique Hagemans, Ianthe A. E. M. van Belzen, Tania Morán Luengo, Stefan Rüdiger
Software Mentions: 2
Published: about 10 years ago

10.3390/vaccines8020288

Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach
Cited by: 50
Author(s): Muhammad Tahir ul Qamar, Zeeshan Shokat, Iqra Muneer, Usman Ali Ashfaq, Hamna Javed, Farooq Anwar, Amna Bari, Barira Zahid, Nazamid Saari
Software Mentions: 2
Published: over 5 years ago

10.1016/j.bbrep.2021.100982

Repurposing of approved drugs with potential to interact with SARS-CoV-2 receptor
Cited by: 5
Author(s): Tamim Ahsan, Abu Ashfaqur Sajib
Software Mentions: 2
Published: over 4 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: over 5 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: 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: almost 9 years ago

10.1186/1472-6807-10-16

Structural definition and substrate specificity of the S28 protease family: the crystal structure of human prolylcarboxypeptidase
Cited by: 48
Author(s): S.M. Soisson, Sangita Patel, Pravien Abeywickrema, Noel Byrne, Ronald E. Diehl, Dawn L. Hall, Rachael E. Ford, John C. Reid, Keith Rickert, Jennifer M. Shipman, Sujata Sharma, Kevin J. Lumb
Software Mentions: 2
Published: almost 16 years ago

10.1038/srep45505

Global evolutionary history and spatio-temporal dynamics of dengue virus type 2
Cited by: 29
Author(s): Kaifa Wei, Yuhan Li
Software Mentions: 2
Published: over 8 years ago

10.3389/fnmol.2014.00051

In silico, in vitro and cellular analysis with a kinome-wide inhibitor panel correlates cellular LRRK2 dephosphorylation to inhibitor activity on LRRK2
Cited by: 46
Author(s): Renée Vancraenenbroeck, Joren De Raeymaecker, Evy Lobbestael, Fangye Gao, Marc De Maeyer, Arnout Voet, Veerle Baekelandt, Jean-Marc Taymans
Software Mentions: 2
Published: over 11 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: almost 15 years ago

10.1038/srep08560

The catalytic role of the M2 metal ion in PP2Cα
Cited by: 16
Author(s): Chang Pan, Junyi Tang, Yaping Xu, Xiao Peng, Hongda Liu, Hao-an Wang, Wenbo Wang, Fanyue Meng, Xiao Yu, Junying Sun
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-017-00147-2

PRL3 phosphatase active site is required for binding the putative magnesium transporter CNNM3
Cited by: 41
Author(s): Huizhi Zhang, Guennadi Kozlov, Xinlu Li, Howie Wu, Irina Gulerez, Kalle Gehring
Software Mentions: 2
Published: over 8 years ago

10.3389/fnmol.2018.00113

The LILI Motif of M3-S2 Linkers Is a Component of the NMDA Receptor Channel Gate
Cited by: 24
Author(s): Marek Ladislav, Jiří Černý, Jan Krůšek, Martin Hořák, Aleš Balík, Ladislav Vyklicky
Software Mentions: 2
Published: over 7 years ago

10.3389/fnmol.2018.00330

Molecular Details of Retinal Guanylyl Cyclase 1/GCAP-2 Interaction
Cited by: 9
Author(s): Anne Rehkamp, Dirk Tänzler, Claudio Iacobucci, Ralph Golbik, Christian Ihling, Andrea Sinz
Software Mentions: 2
Published: about 7 years ago

10.3390/vaccines8030448

Immunogenicity and Protective Efficacy of Influenza A DNA Vaccines Encoding Artificial Antigens Based on Conservative Hemagglutinin Stem Region and M2 Protein in Mice
Cited by: 7
Author(s): Sergei I. Bazhan, Денис Антонец, Ekaterina V. Starostina, T. N. Ilyicheva, О. Н. Каплина, Vasiliy Y. Marchenko, А. Г. Дурыманов, С. Ф. Орешкова, Larisa I. Karpenko
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-017-01186-5

Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine
Cited by: 12
Author(s): Cha San Koh, Rohini Madireddy, Timothy J. Beane, Phillip D. Zamore, А.A. Коростелев
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-00917-y

A bacterial ABC transporter enables import of mammalian host glycosaminoglycans
Cited by: 21
Author(s): Shigetoshi Oiki, Bunzo Mikami, Yukie Maruyama, Kousaku Murata, Wataru Hashimoto
Software Mentions: 2
Published: over 8 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: about 14 years ago

10.1038/s41598-017-01057-z

Structural investigations on orotate phosphoribosyltransferase from Mycobacterium tuberculosis, a key enzyme of the de novo pyrimidine biosynthesis
Cited by: 22
Author(s): Stefano Donini, Davide M. Ferraris, Riccardo Miggiano, Alberto Massarotti, Menico Rizzi
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-01989-6

Structural studies of the periplasmic portion of the diguanylate cyclase CdgH from Vibrio cholerae
Cited by: 8
Author(s): Min Xu, Yizhi Wang, Xiu‐An Yang, Tao Jiang, Wei Xie
Software Mentions: 2
Published: over 8 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: about 12 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: over 13 years ago

10.1186/s12900-014-0024-y

Structural insights into Escherichia coli polymyxin B resistance protein D with X-ray crystallography and small-angle X-ray scattering
Cited by: 9
Author(s): Hang-Hyun Jo, Eui Young Jeong, Jinseong Jeon, Changill Ban
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12900-018-0096-1

Deciphering evolution of immune recognition in antibodies
Cited by: 4
Author(s): Harmeet Kaur, Neetu Sain, Debasisa Mohanty, Dinakar M. Salunke
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-017-02823-9

Efficient Generation of Bispecific Murine Antibodies for Pre-Clinical Investigations in Syngeneic Rodent Models
Cited by: 31
Author(s): Aran F. Labrijn, Joyce Meesters, Matthew W. Bunce, Anthony A. Armstrong, Sandeep Somani, Tom Nesspor, Mark L. Chiu, Işıl Altıntaş, Sandra Verploegen, Janine Schuurman, Paul W.H.I. Parren
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0006820

The Crystal Structure of the Escherichia coli Autoinducer-2 Processing Protein LsrF
Cited by: 17
Author(s): Zamia Diaz, Karina B. Xavier, Stephen T. Miller
Software Mentions: 2
Published: about 16 years ago

10.1038/s41598-017-02805-x

A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases
Cited by: 32
Author(s): Rubén M. Buey, David Fernández‐Justel, Íñigo Marcos‐Alcalde, Graeme Winter, Paulino Gómez‐Puertas, José M. de Pereda, José Luis Revuelta
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-02803-z

Construction of novel repeat proteins with rigid and predictable structures using a shared helix method
Cited by: 22
Author(s): Suk-Jun Youn, Nayoung Kwon, Ji Hyun Lee, Jin Hong Kim, Jin‐Woo Choi, Hayyoung Lee, Jie‐Oh Lee
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-03220-y

Bacterial protease uses distinct thermodynamic signatures for substrate recognition
Cited by: 13
Author(s): G.A. Bezerra, Yuko Ohara‐Nemoto, Irina Cornaciu, Sofiya Fedosyuk, Guillaume Hoffmann, Adam Round, José Antonio Márquez, Takayuki Nemoto, Kristina Djinović-Carugo
Software Mentions: 2
Published: over 8 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: almost 12 years ago

10.3390/vaccines9060658

Integrated Core Proteomics, Subtractive Proteomics, and Immunoinformatics Investigation to Unveil a Potential Multi-Epitope Vaccine against Schistosomiasis
Cited by: 28
Author(s): Abdur Rehman, Sajjad Ahmad, Farah Shahid, Aqel Albutti, Ameen S. S. Alwashmi, Mohammad Aljasir, Naif Alhumeed, Muhammad Qasim, Usman Ali Ashfaq, Muhammad Tahir ul Qamar
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-017-03664-2

Antibacterial and detoxifying activity of NZ17074 analogues with multi-layers of selective antimicrobial actions against Escherichia coli and Salmonella enteritidis
Cited by: 48
Author(s): Na Yang, Xuehui Liu, Da Teng, Zhanzhan Li, Xiumin Wang, Ruoyu Mao, Xiao Wang, Ya Hao, Jianhua Wang
Software Mentions: 2
Published: over 8 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: over 4 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: almost 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 12 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 4 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: about 10 years ago

10.1186/1756-6606-4-28

Impairment of adult hippocampal neural progenitor proliferation by methamphetamine: role for nitrotyrosination
Cited by: 49
Author(s): Arun Venkatesan, Lerna Uzasci, Zhaohui Chen, Labchan Rajbhandari, Carol Anderson, Myoung Hwa Lee, M.A. Bianchet, Robert J. Cotter, Hongjun Song, Avindra Nath
Software Mentions: 2
Published: almost 15 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 4 years ago

10.1186/1472-6807-12-7

Crystal structure of a new benzoic acid inhibitor of influenza neuraminidase bound with a new tilt induced by overpacking subsite C6
Cited by: 10
Author(s): Lalitha Venkatramani, Eric S. Johnson, Gundurao Kolavi, Gillian M. Air, Wayne J. Brouillette, Blaine H. M. Mooers
Software Mentions: 2
Published: over 13 years ago

10.3390/vaccines9080818

Towards an Ensemble Vaccine against the Pegivirus Using Computational Modelling Approaches and Its Validation through In Silico Cloning and Immune Simulation
Cited by: 8
Author(s): Bowen Zheng, Muhammad Suleman, Zonara Zafar, Syed Shujait Ali, Syed Nouman Nasir, Namra, Zahid Hussain, Muhammad Waseem, Abbas Khan, Fakhrul Hassan, Yanjing Wang, Dong‐Qing Wei
Software Mentions: 2
Published: over 4 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: over 4 years ago

10.3389/fonc.2021.606820

Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level
Cited by: 3
Author(s): Michael T. Zimmermann, Angela Mathison, Tim Stodola, Douglas B. Evans, Jenica Abrudan, Wendy Demos, Michael Tschannen, Mohammed Aldakkak, Jennifer L. Geurts, Gwen Lomberk, Susan Tsai, Raúl Urrutia
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-017-05234-y

Structural and Biochemical Characterization of Apicomplexan Inorganic Pyrophosphatases
Cited by: 2
Author(s): Abhishek Jamwal, Manickam Yogavel, M. Z. Abdin, Swatantra Kumar Jain, Amit Sharma
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-05509-4

Structure of polyhydroxyalkanoate (PHA) synthase PhaC from Chromobacterium sp. USM2, producing biodegradable plastics
Cited by: 69
Author(s): Min Fey Chek, Sunyong Kim, Tomoyuki Mori, Hasni Arsad, Mohammed Razip Samian, Kumar Sudesh, Toshio Hakoshima
Software Mentions: 2
Published: over 8 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: almost 6 years ago

10.3390/vaccines9091012

New 1,2,3-Triazole Scaffold Schiff Bases as Potential Anti-COVID-19: Design, Synthesis, DFT-Molecular Docking, and Cytotoxicity Aspects
Cited by: 21
Author(s): Musa A. Said, Daoud J O Khan, Fawzia Faleh Al-blewi, Nadia S. Al-Kaff, Adeeb Al-Sheikh Ali, Nadjet Rezki, Mohamed Reda Aouad, Mohamed Hagar
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-017-05657-7

Plasticity in the Oxidative Folding Pathway of the High Affinity Nerita Versicolor Carboxypeptidase Inhibitor (NvCI)
Cited by: 4
Author(s): Sebastián Esperante, Giovanni Covaleda, Sebastián A. Trejo, Sílvia Bronsoms, Francesc X. Aviles, Salvador Ventura
Software Mentions: 2
Published: over 8 years ago

10.3390/vaccines9090986

Multiepitope Proteins for the Differential Detection of IgG Antibodies against RBD of the Spike Protein and Non-RBD Regions of SARS-CoV-2
Cited by: 7
Author(s): Larissa Rodrigues Gomes, Andressa da Matta Durans, Paloma Napoleão-Pêgo, Jessica A. Waterman, Mariana S. Freitas, Nathalia Beatriz Ramos de Sá, Lilian V. Pereira, Jéssica S. Furtado, Romário G. Aquino, Mario C. R. Machado, Natalia Fintelman‐Rodrigues, Thiago Moreno L. Souza, Carlos Médicis Morel, David William Provance, Salvatore Giovanni De-Simone
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-017-05627-z

X-ray crystallographic structure of a bacterial polysialyltransferase provides insight into the biosynthesis of capsular polysialic acid
Cited by: 12
Author(s): Christian Lizak, L.J. Worrall, Lars Baumann, Moritz M. Pfleiderer, Gesa Volkers, Tianjun Sun, Lyann Sim, Warren W. Wakarchuk, Stephen G. Withers, N.C.J. Strynadka
Software Mentions: 2
Published: over 8 years ago

10.3389/fonc.2019.01294

p38α Mitogen-Activated Protein Kinase Is a Druggable Target in Pancreatic Adenocarcinoma
Cited by: 19
Author(s): Ling Yang, Xiaoting Sun, Ying Ye, Yongtian Lu, Jiane Zuo, Wen Li, Adrian H. Elcock, Shun Zhu
Software Mentions: 2
Published: almost 6 years ago

Projects: pypi: PyMOL

Science Score: 90/100

Bonuses:

Penalties:

Papers Mentioning PyMOL 8,266