pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.1128/AAC.00564-19

Molecular Basis of Class A β-Lactamase Inhibition by Relebactam
Cited by: 41
Author(s): C.L. Tooke, P. Hinchliffe, Pauline A. Lang, Adrian J. Mulholland, Jürgen Brem, Christopher J. Schofield, James Spencer
Software Mentions: 1
Published: almost 7 years ago

10.1128/AAC.00582-20

Discovery and Preclinical Development of Antigiardiasis Fumagillol Derivatives
Cited by: 5
Author(s): Janak Padia, Liudmila Kulakova, Andrey Galkin, Osnat Herzberg
Software Mentions: 1
Published: almost 6 years ago

10.1128/AAC.00126-18

Characterization of the Anti-Hepatitis C Virus Activity of New Nonpeptidic Small-Molecule Cyclophilin Inhibitors with the Potential for Broad Anti-Flaviviridae Activity
Cited by: 11
Author(s): Quentin Nevers, Isaac Ruiz, Nazim Ahnou, Flora Donati, Rozenn Brillet, Laurent Softic, Maxime Chazal, Nolwenn Jouvenet, Slim Fourati, Camille Baudesson, Patrice Bruscella, Muriel Gelin, Jean-François Guichou, Jean‐Michel Pawlotsky, Abdelhakim Ahmed–Belkacem
Software Mentions: 1
Published: about 8 years ago

10.1128/AAC.01963-19

VNRX-5133 (Taniborbactam), a Broad-Spectrum Inhibitor of Serine- and Metallo-β-Lactamases, Restores Activity of Cefepime in Enterobacterales and Pseudomonas aeruginosa
Cited by: 105
Author(s): Jodie Hamrick, Jean Denis Docquier, Tsuyoshi Uehara, Cullen L. Myers, David A. Six, Cassandra L Chatwin, Kaitlyn John, Salvador Vernacchio, Susan M Cusick, Robert E. Lee Trout, Cecilia Pozzi, Filomena De Luca, Manuela Benvenuti, Stefano Mangani, Bin Liu, Randy W. Jackson, Greg Moeck, L Xerri, Christopher J. Burns, Daniel C. Pevear, Denis M. Daigle
Software Mentions: 1
Published: over 6 years ago

10.1128/AAC.00357-16

Staphylococcus aureus Alpha-Toxin Is Conserved among Diverse Hospital Respiratory Isolates Collected from a Global Surveillance Study and Is Neutralized by Monoclonal Antibody MEDI4893
Cited by: 42
Author(s): David E. Tabor, Li Yu, Hoyin Mok, Christine Tkaczyk, Bret R. Sellman, Yuling Wu, Vaheh Oganesyan, Tim Slidel, Hasan S. Jafri, Michael McCarthy, Patricia A. Bradford, Mark T. Esser
Software Mentions: 1
Published: almost 10 years ago

10.1128/AAC.00201-18

Selection and Characterization of Rupintrivir-Resistant Norwalk Virus Replicon Cells In Vitro
Cited by: 19
Author(s): Mitsutaka Kitano, Myra Hosmillo, Edward Emmott, Lianshun Jia, Ian Goodfellow
Software Mentions: 1
Published: about 8 years ago

10.3390/antiox10091339

Anti-Wrinkle Effect of Isatis indigotica Leaf Extract: Evaluation of Antioxidant, Anti-Inflammation, and Clinical Activity
Cited by: 9
Author(s): Jihun Kim, Gao Da, Won Seok Jeong, Cheong Taek Kim, Chong Woon Cho, Hyung Min Kim, Jong Seong Kang
Software Mentions: 1
Published: almost 5 years ago

10.3390/antiox9080655

Hybrid Heme Peroxidases from Rice Blast Fungus Magnaporthe oryzae Involved in Defence against Oxidative Stress
Cited by: 8
Author(s): Marcel Zámocký, Anna Kamlárová, Daniel Maresch, Katarína Chovanová, Jana Harichová, Paul G. Furtmüller
Software Mentions: 1
Published: almost 6 years ago

10.3390/antiox9010022

Consumption of Terpenoids-Rich Padina pavonia Extract Attenuates Hyperglycemia, Insulin Resistance and Oxidative Stress, and Upregulates PPARγ in a Rat Model of Type 2 Diabetes
Cited by: 19
Author(s): Mousa O. Germoush, Hassan A. Elgebaly, Sherif Hassan, Emadeldin M. Kamel, May Bin-Jumah, Ayman M. Mahmoud
Software Mentions: 1
Published: over 6 years ago

10.3390/antiox9080768

Cotinine and 6-Hydroxy-L-Nicotine Reverses Memory Deficits and Reduces Oxidative Stress in Aβ25-35-Induced Rat Model of Alzheimer’s Disease
Cited by: 14
Author(s): Răzvan Ştefan Boiangiu, Marius Mihăşan, Dragoș Lucian Gorgan, Bogdan Alexandru Stache, Brînduşa Alina Petre, Lucian Hrițcu
Software Mentions: 1
Published: almost 6 years ago

10.3390/antiox10071032

Effects of Serine or Threonine in the Active Site of Typical 2-Cys Prx on Hyperoxidation Susceptibility and on Chaperone Activity
Cited by: 4
Author(s): Carlos A. Tairum, M. C. dos Santos, Carlos Alexandre Breyer, Ana Oliveira, Vitoria Isabela Montanhero Cabrera, Guilherme Toledo-Silva, Gustavo Maruyama Mori, Marcos H. Toyama, Luís Eduardo Soares Netto, Marcos Antônio de Oliveira
Software Mentions: 1
Published: about 5 years ago

10.3390/antiox7110152

Towards Initial Indications for a Thiol-Based Redox Control of Arabidopsis 5-Aminolevulinic Acid Dehydratase
Cited by: 8
Author(s): Daniel Wittmann, Sigri Kløve, Peng Wang, Bernhard Grimm
Software Mentions: 1
Published: over 7 years ago

10.3390/antiox10060946

Specificity of Human Sulfiredoxin for Reductant and Peroxiredoxin Oligomeric State
Cited by: 12
Author(s): Tom E. Forshaw, Julie A. Reisz, Kimberly Nelson, R. Gumpena, J. Reed Lawson, Thomas J. Jönsson, Hanzhi Wu, Jill E. Clodfelter, Lynnette C. Johnson, Cristina M. Furdui, W. Todd Lowther
Software Mentions: 1
Published: about 5 years ago

10.1007/s12010-014-1130-9

Crystal Structure of Talaromyces cellulolyticus (Formerly Known as Acremonium cellulolyticus) GH Family 11 Xylanase
Cited by: 17
Author(s): Mikio Kataoka, Fusamichi Akita, Yuka Maeno, Benchaporn Inoue, Hiroyuki Inoue, Kazuhiko Ishikawa
Software Mentions: 1
Published: almost 12 years ago

10.1128/AEM.00778-20

Ancestral Resurrection and Directed Evolution of Fungal Mesozoic Laccases
Cited by: 14
Author(s): Bernardo J. Gómez-Fernández, Valeria A. Risso, Andrés M. Rueda, José M. Sanchez-Ruiz, Miguel Alcalde
Software Mentions: 1
Published: about 6 years ago

10.1128/AEM.02535-18

Identification of a Novel Elastin-Degrading Enzyme from the Fish Pathogen Flavobacterium psychrophilum
Cited by: 17
Author(s): Tatiana Rochat, David Pérez-Pascual, Hanne Nilsen, Marie-Christine Carpentier, Sébastien Bridel, Jean‐François Bernardet, Éric Duchaud
Software Mentions: 1
Published: over 7 years ago

10.1128/AEM.00842-20

Screening and Evaluation of New Hydroxymethylfurfural Oxidases for Furandicarboxylic Acid Production
Cited by: 17
Author(s): Mario Viñambres, Marta Espada, Ángel T. Martínez, Ana Serrano
Software Mentions: 1
Published: almost 6 years ago

10.1128/AEM.02131-20

Expanding the Enzyme Repertoire for Sugar Nucleotide Epimerization: the CDP-Tyvelose 2-Epimerase from Thermodesulfatator atlanticus for Glucose/Mannose Interconversion
Cited by: 4
Author(s): Christian Rapp, Stevie Van Overtveldt, Koen Beerens, Hansjörg Weber, Tom Desmet, Bernd Nidetzky
Software Mentions: 1
Published: over 5 years ago

10.1128/AEM.00622-20

LuxR Solos in the Plant Endophyte Kosakonia sp. Strain KO348
Cited by: 8
Author(s): Susan Mosquito, Xianmin Meng, Giulia Devescovi, Iris Bertani, Alexander Martin Geller, Asaf Levy, Michael P. Myers, Cristina Bez, Sonia Covaceuszach, Vittorio Venturi
Software Mentions: 1
Published: about 6 years ago

10.1128/AEM.02986-19

Aspergillus fumigatus Mitochondrial Acetyl Coenzyme A Acetyltransferase as an Antifungal Target
Cited by: 12
Author(s): Yuanwei Zhang, Wenfan Wei, Jialu Fan, Cheng Jin, Ling Lü, Wenxia Fang
Software Mentions: 1
Published: over 6 years ago

10.1128/AEM.00268-20

Ferric Uptake Regulator Provides a New Strategy for Acidophile Adaptation to Acidic Ecosystems
Cited by: 15
Author(s): Xianke Chen, Xiaoyan Li, Yi-fan Ha, Jianqiang Lin, Xiang‐Mei Liu, Xin Pang, Lin-xu Chen
Software Mentions: 1
Published: about 6 years ago

10.1128/AEM.00719-16

Listeria monocytogenes DNA Glycosylase AdlP Affects Flagellar Motility, Biofilm Formation, Virulence, and Stress Responses
Cited by: 7
Author(s): Ting Zhang, Dongryeoul Bae, Chinling Wang
Software Mentions: 1
Published: almost 10 years ago

10.1007/s00723-012-0314-0

MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL
Cited by: 181
Author(s): Gregor Hagelueken, Roger Ward, James H. Naismith, Olav Schiemann
Software Mentions: 1
Published: over 14 years ago

10.1007/s00253-016-8041-3

Novel insights into biosynthesis and uptake of rhamnolipids and their precursors
Cited by: 82
Author(s): Andreas Wittgens, Filip Kovačić, Markus Müller, Melanie Gerlitzki, Beatrix Santiago‐Schübel, Diana Hofmann, Till Tiso, Lars M. Blank, Marius Henkel, Rudolf Hausmann, Christoph Syldatk, Susanne Wilhelm, Frank Rosenau
Software Mentions: 1
Published: over 9 years ago

10.1007/s00253-021-11511-8

Identification of a specific surface epitope of OmpC for Escherichia coli O157:H7 with protein topology facilitated affinity mass spectrometry
Cited by: 1
Author(s): Wenbin Wang, Xinyue Zhou, Yunong Sang, Xianwei Liang, Jianxin Liu, Saikun Pan, Luxin Wang
Software Mentions: 1
Published: almost 5 years ago

10.1007/s00253-021-11465-x

Novel oleate hydratases and potential biotechnological applications
Cited by: 6
Author(s): Peter‐Leon Hagedoorn, Frank Hollmann, Ulf Hanefeld
Software Mentions: 1
Published: almost 5 years ago

10.1007/s00253-021-11342-7

A broadly cross-reactive monoclonal antibody against hepatitis E virus capsid antigen
Cited by: 8
Author(s): Barbara Kubíčková, Jörg A. Schenk, Franziska Ramm, Kornelija Markuškienė, Jochen Reetz, Paul Dremsek, Paulius Lukas Tamošiūnas, Laima Cepulyte, Hoai Anh Trinh, Johannes Scholz, Henry Memczak, Marc Hovestädt, René Ryll, Rasa Petraitytė-Burneikienė, Victor M. Corman, Anika Andersson, Dietmar Becher, Martin H. Groschup, Stefan Kubick, Frank Sellrie, Reimar Johne, Rainer G. Ulrich
Software Mentions: 1
Published: about 5 years ago

10.1007/s00253-014-5871-8

An Aspergillus nidulans β-mannanase with high transglycosylation capacity revealed through comparative studies within glycosidase family 5
Cited by: 41
Author(s): Anna Rosengren, Sumitha K. Reddy, Johan Svantesson Sjöberg, Oskar Aurelius, D.T. Logan, Katarína Kolenová, Henrik Stålbrand
Software Mentions: 1
Published: about 12 years ago

10.1007/s00253-020-10820-8

Engineering of cellobiose phosphorylase for the defined synthesis of cellotriose
Cited by: 13
Author(s): Zorica Ubiparip, David Sáez Moreno, Koen Beerens, Tom Desmet
Software Mentions: 1
Published: almost 6 years ago

10.1007/s00253-021-11239-5

Engineering of a borneol dehydrogenase from P. putida for the enzymatic resolution of camphor
Cited by: 4
Author(s): Michael Höfer, Julia Diener, Benjamin Begander, Robert Kourist, Volker Sieber
Software Mentions: 1
Published: over 5 years ago

10.1007/s00253-015-6592-3

Optimization of synergism of a recombinant auxiliary activity 9 from Chaetomium globosum with cellulase in cellulose hydrolysis
Cited by: 48
Author(s): In Jung Kim, Ki Hyun Nam, Eun Ju Yun, Sooah Kim, Hak Jin Youn, Hee Jin Lee, In Geol Choi, Kyoung Heon Kim
Software Mentions: 1
Published: about 11 years ago

10.1007/s00253-018-9431-5

Identification and characterization of GH11 xylanase and GH43 xylosidase from the chytridiomycetous fungus, Rhizophlyctis rosea
Cited by: 19
Author(s): Yuhong Huang, Xiujue Zheng, Bo Pilgaard, Jesper Holck, Jan Muschiol, Shengying Li, Lene Lange
Software Mentions: 1
Published: over 7 years ago

10.1007/s00253-019-09938-1

Identification of Thermotoga maritima MSB8 GH57 α-amylase AmyC as a glycogen-branching enzyme with high hydrolytic activity
Cited by: 10
Author(s): Xuewen Zhang, Hans Leemhuis, Štefan Janeček, Mária Martinovičová, Tjaard Pijning, Marc J. E. C. van der Maarel
Software Mentions: 1
Published: about 7 years ago

10.1007/s00204-020-02695-5

Cellular levels and molecular dynamics simulations of estragole DNA adducts point at inefficient repair resulting from limited distortion of the double-stranded DNA helix
Cited by: 7
Author(s): Shuo Yang, Matthias Diem, Jakob D. H. Liu, Sebastiaan Wesseling, Jacques Vervoort, Chris Oostenbrink, Ivonne M.C.M. Rietjens
Software Mentions: 1
Published: over 6 years ago

10.1155/2010/960298

Fidelity in Archaeal Information Processing
Cited by: 3
Author(s): Bart de Koning, Fabian Blombach, Stan J. J. Brouns, John van der Oost
Software Mentions: 1
Published: over 16 years ago

10.1155/2017/5395293

Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the Archaeon Thermococcus onnurineus NA1
Cited by: 4
Author(s): Thien-Hoang Ho, Kim-Hung Huynh, Diem Quynh Nguyen, Hyunjae Park, Kyoungho Jung, Bookyo Sur, Yeh Jin Ahn, Sun Shin, Lin Woo Kang
Software Mentions: 1
Published: over 9 years ago

10.1155/2010/842639

Iron-Sulfur World in Aerobic and Hyperthermoacidophilic ArchaeaSulfolobus
Cited by: 23
Author(s): Toshio Iwasaki
Software Mentions: 1
Published: over 16 years ago

10.1155/2015/179196

Sequence, Structure, and Binding Analysis of Cyclodextrinase (TK1770) fromT. kodakarensis(KOD1) Using anIn SilicoApproach
Cited by: 5
Author(s): Ramzan Ali, Muhammad Shafiq
Software Mentions: 1
Published: over 11 years ago

10.1155/2018/7571984

Crystal Structures of the Putative Isocitrate Dehydrogenase fromSulfolobus tokodaiiStrain 7 in the Apo and NADP+-Bound Forms
Cited by: 2
Author(s): H. Kondo, Midori Murakami
Software Mentions: 1
Published: over 7 years ago

10.1186/s13075-015-0685-3

Improved serological detection of rheumatoid arthritis: a highly antigenic mimotope of carbonic anhydrase III selected in a murine model by phage display
Cited by: 11
Author(s): Glaucy Rodrigues de Araújo, Emília Rezende Vaz, Patrícia Tiemi Fujimura, João Eurico Fonseca, Lucélia Maria de Lima, Helena Canhão, Gabriela Venturini, Karina Helena Morais Cardozo, Valdemir Melechco Carvalho, Marcelo Henrique Napimoga, Luiz Ricardo Goulart, João Gonçalves, Carlos Ueira-Vieira
Software Mentions: 1
Published: about 11 years ago

10.31557/APJCP.2020.21.12.3517

Discovery and Protein Modeling Studies of Novel Compound Mutations Causing Resistance to Multiple Tyrosine Kinase Inhibitors in Chronic Myeloid Leukemia
Cited by: 0
Author(s): Zafar Iqbal, Muhammad Absar, Amer Mahmood, Aamer Aleem, Mudassar Iqbal, Abid Jameel, Tanveer Akhtar, Sajjad Karim, Mahmood Rasool, Zeenat Mirza, Muhammad Usman Khalid, Afia Muhammad Akram, Muhammad Farooq Sabar, Ahmad Mukhtar Khalid, Khaled Aljarrah, Janhangir Iqbal, Ijaz Hussain Shah, Nawaf Alanazi
Software Mentions: 1
Published: over 5 years ago

10.1155/2016/5472320

GAKG-RGEKG an Epitope That Provokes Immune Cross-Reactivity betweenPrevotellasp. and Human Collagen: Evidence of Molecular Mimicry in Chronic Periodontitis
Cited by: 4
Author(s): Gustavo Alberto Obando-Pereda
Software Mentions: 1
Published: over 10 years ago

10.1186/s12858-015-0050-9

Purification and characterization of a cytochrome c with novel caspase-3 activation activity from the pathogenic fungus Rhizopus arrhizus
Cited by: 6
Author(s): Manoj Saxena, Rohit K. Sharma, Josell Ramírez‐Paz, Arthur D. Tinoco, Kai Griebenow
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2091-14-23

A highly conserved arginine residue of the chitosanase from Streptomyces sp. N174 is involved both in catalysis and substrate binding
Cited by: 15
Author(s): Marie-Ève Lacombe-Harvey, Mélanie Fortin, Takayuki Ohnuma, Tamo Fukamizo, Thomas Letzel, Ryszard Brzeziński
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2091-11-13

Identification and molecular characterization of a novel flavin-free NADPH preferred azoreductase encoded by azoB in Pigmentiphaga kullae K24
Cited by: 46
Author(s): Huizhong Chen, Jinhui Feng, Ohgew Kweon, Hanlin Xu, Carl E. Cerniglia
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2091-9-8

The pyrroloquinoline quinone biosynthesis pathway revisited: A structural approach
Cited by: 78
Author(s): Sandra Puehringer, Moritz Metlitzky, Robert Schwarzenbacher
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2091-8-15

Module structure of interphotoreceptor retinoid-binding protein (IRBP) may provide bases for its complex role in the visual cycle – structure/function study of Xenopus IRBP
Cited by: 20
Author(s): Federico Gonzalez‐Fernandez, Claxton A. Baer, Debashis Ghosh
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2091-10-3

Structural studies of the Enterococcus faecalis SufU [Fe-S] cluster protein
Cited by: 45
Author(s): Gustavo Pelicioli Riboldi, Hugo Verli, Jeverson Frazzon
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2091-10-24

Mapping of protein phosphatase-6 association with its SAPS domain regulatory subunit using a model of helical repeats
Cited by: 19
Author(s): Julien Guergnon, Urszula Derewenda, Jessica R. Edelson, David L. Brautigan
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2091-13-10

Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein
Cited by: 5
Author(s): Esther E. Biswas‐Fiss, Jirayu Kukiratirat, Subhasis B. Biswas
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2091-13-11

The intrinsic GTPase activity of the Gtr1 protein from Saccharomyces cerevisiae
Cited by: 4
Author(s): Palanivelu Sengottaiyan, Cornelia Spetea, Jens O. Lagerstedt, Dieter R. Samyn, Michael R. Andersson, Lorena Ruiz-Pávon, Bengt L. Persson
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2091-13-20

Structure-function analysis indicates that sumoylation modulates DNA-binding activity of STAT1
Cited by: 21
Author(s): Juha Grönholm, Sari Vanhatupa, Daniela Ungureanu, Jouni Väliaho, Tuomo Laitinen, Jarkko Valjakka, Olli Silvennoinen
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12858-017-0084-2

Structural similarities and functional differences clarify evolutionary relationships between tRNA healing enzymes and the myelin enzyme CNPase
Cited by: 1
Author(s): Gopinath Muruganandam, Arne Raasakka, Matti Myllykoski, Inari Kursula, Petri Kursula
Software Mentions: 1
Published: about 9 years ago

10.1186/s12858-019-0104-5

Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins
Cited by: 4
Author(s): Emily N. Kennedy, Skyler D. Hebdon, Smita Menon, Clay A. Foster, D.M. Copeland, Qingping Xu, Fabiola Janiak‐Spens, Ann H. West
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2091-13-3

Enzymatic activity and immunoreactivity of Aca s 4, an alpha-amylase allergen from the storage mite Acarus siro
Cited by: 13
Author(s): Jana Pytelková, Martin Lepšı́k, Miloslav Šanda, Pavel Talacko, Lucie Marešová, Michael Mareš
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-6-240

Sequence variation in ligand binding sites in proteins
Cited by: 74
Author(s): Thomas J. Magliery, Lynne Regan
Software Mentions: 1
Published: almost 21 years ago

10.1186/1471-2105-12-264

MAVENs: Motion analysis and visualization of elastic networks and structural ensembles
Cited by: 37
Author(s): Michael T. Zimmermann, Andrzej Kloczkowski, Robert L. Jernigan
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2105-12-S1-S30

Hsp90/Cdc37 Chaperone/co-chaperone complex, a novel junction anticancer target elucidated by the mode of action of herbal drug Withaferin A
Cited by: 66
Author(s): Abhinav Grover, Ashutosh Shandilya, Vibhuti Agrawal, Piyush Pratik, Divya Bhasme, Virendra S. Bisaria, Durai Sundar
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-019-3254-y

HKPocket: human kinase pocket database for drug design
Cited by: 18
Author(s): Huiwen Wang, Jiadi Qiu, Haoquan Liu, Ying Xu, Ya Jia, Yunjie Zhao
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-10-S12-S15

Extraction, integration and analysis of alternative splicing and protein structure distributed information
Cited by: 0
Author(s): Matteo D’Antonio, Marco Masseroli
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2105-10-207

Ensemble approach to predict specificity determinants: benchmarking and validation
Cited by: 24
Author(s): Saikat Chakrabarti, Anna R. Panchenko
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-12-414

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
Cited by: 158
Author(s): Mathieu Rousseau, James S. Fraser, Maria Ferraiuolo, Josée Dostie, Mathieu Blanchette
Software Mentions: 1
Published: over 14 years ago

10.1186/s12859-017-1867-6

LCS-TA to identify similar fragments in RNA 3D structures
Cited by: 16
Author(s): Jakub Wiedemann, Tomasz Żok, Maciej Miłostan, Marta Szachniuk
Software Mentions: 1
Published: over 8 years ago

10.1186/s12859-016-1339-4

Homology modeling and molecular dynamics provide structural insights into tospovirus nucleoprotein
Cited by: 10
Author(s): Rayane Nunes Lima, Muhammad Faheem, J.A.R.G. Barbosa, Marcelo Depólo Polêto, Hugo Verli, Fernando Lucas Melo, Renato O. Resende
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-10-S6-S13

A chemogenomics view on protein-ligand spaces
Cited by: 30
Author(s): Helena Strömbergsson, Gerard J. Kleywegt
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-15-196

Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase
Cited by: 8
Author(s): Daniel J. Rigden, Ruth Y Eberhardt, Harry J. Gilbert, Qingping Xu, Yuanyuan Chang, Adam Godzik
Software Mentions: 1
Published: about 12 years ago

10.1186/s12859-014-0416-9

Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum
Cited by: 14
Author(s): Soshichiro Nagano, Ting‐Yu Lin, Jyotheeswara R. Edula, Jonathan G. Heddle
Software Mentions: 1
Published: over 11 years ago

10.1186/s12859-014-0427-6

WEBnm@ v2.0: Web server and services for comparing protein flexibility
Cited by: 88
Author(s): Sandhya Tiwari, Edvin Fuglebakk, Siv Midtun Hollup, Lars Skjærven, Tristan Cragnolini, Svenn Helge Grindhaug, Kidane Tekle, Nathalie Reuter
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-10-29

Using least median of squares for structural superposition of flexible proteins
Cited by: 15
Author(s): Yu Shen Liu, Yi Fang, Karthik Ramani
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-13-S4-I1

Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics
Cited by: 2
Author(s): Paolo Romano, Manuela Helmer-Citterich
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-10-351

A structure filter for the Eukaryotic Linear Motif Resource
Cited by: 41
Author(s): Allegra Via, Cathryn M. Gould, Christine Gemünd, Toby J. Gibson, Manuela Helmer-Citterich
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-11-S7-S16

Identification of a better Homo sapiens Class II HDAC inhibitor through binding energy calculations and descriptor analysis
Cited by: 20
Author(s): Usman Sumo Friend Tambunan, Evi Kristin Wulandari
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-12-160

FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins
Cited by: 63
Author(s): Daniel B. Roche, Stuart J. Tetchner, Liam J. McGuffin
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2105-15-95

A local average distance descriptor for flexible protein structure comparison
Cited by: 7
Author(s): Hsin-Wei Wang, Chia-Han Chu, Wen-Ching Wang, Tun‐Wen Pai
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-15-S8-S2

Computational prediction of hinge axes in proteins
Cited by: 3
Author(s): Rittika Shamsuddin, Milka Doktorova, Sheila S. Jaswal, Audrey Lee-St. John, Kathryn A. McMenimen
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-12-S1-S31

Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses
Cited by: 32
Author(s): Jhang Wei Huang, Jinn-Moon Yang
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-018-2346-4

An integrated strategy for identifying new targets and inferring the mechanism of action: taking rhein as an example
Cited by: 9
Author(s): Hao Sun, Yiting Shen, Guangwen Luo, Yuepiao Cai, Zheng Xiang
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-15-112

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase
Cited by: 12
Author(s): Anna Sheydina, Ruth Y Eberhardt, Daniel J. Rigden, Yuanyuan Chang, Zhanwen Li, Christian C Zmasek, Herbert L. Axelrod, Adam Godzik
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-11-426

TOPSAN: a collaborative annotation environment for structural genomics
Cited by: 13
Author(s): Dana Weekes, S. Sri Krishna, Constantina Bakolitsa, Ian A. Wilson, Adam Godzik, John Wooley
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12859-015-0545-9

CHEXVIS: a tool for molecular channel extraction and visualization
Cited by: 67
Author(s): Talha Bin Masood, Sankaran Sandhya, Nagasuma Chandra, Vijay Natarajan
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-14-265

Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila
Cited by: 3
Author(s): Penelope Coggill, Ruth Y Eberhardt, Alex Bateman, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L. Axelrod, L. Aravind, Alexey G. Murzin, Alex Bateman
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2105-11-424

Computing H/D-Exchange rates of single residues from data of proteolytic fragments
Cited by: 43
Author(s): Ernst Althaus, Stefan Canzar, Carsten Ehrler, Mark R. Emmett, Andreas Karrenbauer, Alan G. Marshall, Anke Meyer-Bäse, Jeremiah D. Tipton, Hui Min Zhang
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-16-S1-S7

On the packing density of the unbound protein-protein interaction interface and its implications in dynamics
Cited by: 2
Author(s): Jau-Ji Lin, Zih Shin Lin, Jiann Yang Hwang, Tsun-Tsao Huang
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-12-S13-S22

Non-nucleosidic inhibition of Herpes simplex virus DNA polymerase: mechanistic insights into the anti-herpetic mode of action of herbal drug withaferin A
Cited by: 45
Author(s): Abhinav Grover, Vibhuti Agrawal, Ashutosh Shandilya, Virendra S. Bisaria, Durai Sundar
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-10-S1-S41

Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses
Cited by: 40
Author(s): Jhang Wei Huang, Chwan-Chuen King, Jinn-Moon Yang
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-10-32

VASCo: computation and visualization of annotated protein surface contacts
Cited by: 70
Author(s): Georg Steinkellner, Robert Rader, Gerhard G. Thallinger, Christoph Kratky, Karl Gruber
Software Mentions: 1
Published: over 17 years ago

10.1186/s12859-018-2317-9

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures
Cited by: 11
Author(s): Maciej Antczak, Tomasz Żok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak, Marta Szachniuk
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-12-S13-S23

In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC)
Cited by: 26
Author(s): Usman Sumo Friend Tambunan, N. Bramantya, Arli Aditya Parikesit
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-11-306

Beyond rotamers: a generative, probabilistic model of side chains in proteins
Cited by: 45
Author(s): Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E. Johansson, Thomas Hamelryck
Software Mentions: 1
Published: about 16 years ago

10.1186/s12859-016-1371-4

SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides
Cited by: 11
Author(s): Tamara Vasylenko, Yi Fan Liou, Po Chin Chiou, Hsiao Wei Chu, Yung Sung Lai, Yu Ling Chou, Hui Ling Huang, Shinn-Ying Ho
Software Mentions: 1
Published: over 9 years ago

10.1186/s12859-014-0370-6

PyTMs: a useful PyMOL plugin for modeling common post-translational modifications
Cited by: 77
Author(s): Andreas Warnecke, Tatyana Sandalova, Adnane Achour, Robert A. Harris
Software Mentions: 1
Published: over 11 years ago

10.1186/s12859-016-1033-6

Evolutionary relationships between heme-binding ferredoxin α + β barrels
Cited by: 8
Author(s): Giriraj Acharya, Gurmeet Kaur, S. Subramanian
Software Mentions: 1
Published: over 10 years ago

10.1186/s12859-016-1124-4

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server
Cited by: 18
Author(s): Luciano A. Abriata, Christophe Bovigny, Matteo Dal Peraro
Software Mentions: 1
Published: about 10 years ago

10.1186/s12859-015-0724-8

Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method
Cited by: 16
Author(s): Andrés H. Gutiérrez, William Martin, Chris Bailey‐Kellogg, Frances Terry, Leonard Moise, Anne S. De Groot
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2105-6-202

PALSSE: A program to delineate linear secondary structural elements from protein structures
Cited by: 59
Author(s): Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin
Software Mentions: 1
Published: almost 21 years ago

10.1186/1741-7007-10-62

Crystal structure of the conserved domain of the DC lysosomal associated membrane protein: implications for the lysosomal glycocalyx
Cited by: 80
Author(s): Sonja Wilke, J. Krausze, Konrad Büssow
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12915-020-00885-2

Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes
Cited by: 4
Author(s): Ryan T. Bell, Yuri I. Wolf, Eugene V. Koonin
Software Mentions: 1
Published: over 5 years ago

10.1186/s12915-020-00936-8

Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity
Cited by: 28
Author(s): Kristýna Pluháčková, Andreas Hörner
Software Mentions: 1
Published: over 5 years ago

10.1186/s12915-016-0313-y

Oligomeric interface modulation causes misregulation of purine 5´-nucleotidase in relapsed leukemia
Cited by: 9
Author(s): Aleš Hnı́zda, Jana Škerlová, Milan Fábry, Petr Pachl, Martina Šinalová, Lukáš Vrzal, Petr Man, Petr Novák, P. Řezáčová, Václav Veverka
Software Mentions: 1
Published: over 9 years ago

10.1186/s12915-017-0464-5

Outer membrane protein folding from an energy landscape perspective
Cited by: 55
Author(s): Bob Schiffrin, David J. Brockwell, Sheena E. Radford
Software Mentions: 1
Published: over 8 years ago

Projects: pypi: PyMOL

Science Score: 90/100

Bonuses:

Penalties:

Papers Mentioning PyMOL 8,266