cran: DOPE | Projects | Ecosyste.ms: Papers

10.3389/fpls.2017.00819

Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach
Cited by: 37
Author(s): Mohd Aamir, Vinay Kumar Singh, Mukesh Meena, Ram Sanmukh Upadhyay, Vijai Kumar Gupta, Surendra Singh
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms20030606

Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields
Cited by: 41
Author(s): Maciej Pawel Ciemny, Aleksandra E. Badaczewska-Dawid, Monika Pikuzinska, Andrzej Koliński, Sebastian Kmiecik
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1007219

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
Cited by: 11
Author(s): Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini, Alessandro Paiardini
Software Mentions: 4
Published: almost 5 years ago

10.1186/1472-6807-9-71

Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations
Cited by: 9
Author(s): Patrick Aloy, Baldo Oliva
Software Mentions: 4
Published: almost 16 years ago

10.1186/1472-6807-8-46

A knowledge-based structure-discriminating function that requires only main-chain atom coordinates
Cited by: 10
Author(s): Yoshihide Makino, Nobuhide Itoh
Software Mentions: 4
Published: almost 17 years ago

10.1128/mSphere.00298-16

Human Norovirus Aptamer Exhibits High Degree of Target Conformation-Dependent Binding Similar to That of Receptors and Discriminates Particle Functionality
Cited by: 18
Author(s): Matthew D. Moore, Benjamin G. Bobay, Brittany S. Mertens, Lee‐Ann Jaykus
Software Mentions: 4
Published: almost 8 years ago

10.3390/ijms21155248

Drug Discovery Targeting the Disorder-To-Order Transition Regions through the Conformational Diversity Mimicking and Statistical Analysis
Cited by: 5
Author(s): Insung Na, Sungwoo Choi, Sang Jun Son, Vladimir N. Uversky, Chul Geun Kim
Software Mentions: 3
Published: over 4 years ago

10.1016/j.str.2020.01.013

Structure of Microtubule-Trapped Human Kinesin-5 and Its Mechanism of Inhibition Revealed Using Cryoelectron Microscopy
Cited by: 20
Author(s): Alejandro Peña, Aaron Sweeney, Alexander D. Cook, Julia Locke, Maya Topf, Carolyn A. Moores
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-10-611

Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure
Cited by: 15
Author(s): Luciane V. Mello, Helen O’Meara, Daniel J. Rigden, Steve Paterson
Software Mentions: 3
Published: almost 16 years ago

10.3389/fmolb.2020.00040

Computational Investigation of Voltage-Gated Sodium Channel β3 Subunit Dynamics
Cited by: 4
Author(s): William G. Glass, Anna L. Duncan, Philip C. Biggin
Software Mentions: 3
Published: over 4 years ago

10.1016/j.csbj.2017.01.010

Antibody H3 Structure Prediction
Cited by: 45
Author(s): Claire Marks, Charlotte M. Deane
Software Mentions: 3
Published: almost 8 years ago

10.3390/ijms21082764

Structural Characterization of Carbonic Anhydrase VIII and Effects of Missense Single Nucleotide Variations to Protein Structure and Function
Cited by: 11
Author(s): Taremekedzwa Allan Sanyanga, Özlem Tastan Bishop
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0221331

Identification of lead molecules against potential drug target protein MAPK4 from L. donovani: An in-silico approach using docking, molecular dynamics and binding free energy calculation
Cited by: 35
Author(s): Shweta Raj, Santanu Sasidharan, Vikash Kumar Dubey, Prakash Saudagar
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0054178

Evolutionary, Structural and Functional Interplay of the IκB Family Members
Cited by: 22
Author(s): Shaherin Basith, Balachandran Manavalan, Vijayakumar Gosu, Sangdun Choi
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0050200

eThread: A Highly Optimized Machine Learning-Based Approach to Meta-Threading and the Modeling of Protein Tertiary Structures
Cited by: 32
Author(s): Michał Bryliński, Daswanth Lingam
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0229085

Inter-species variation in monovalent anion substrate selectivity and inhibitor sensitivity in the sodium iodide symporter (NIS)
Cited by: 12
Author(s): Susanna C. Concilio, Hristina R. Zhekova, Sergei Y. Noskov, Stephen J. Russell
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pcbi.1004981

Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation
Cited by: 28
Author(s): Dario Corrada, Anatoly A. Soshilov, Michael S. Denison, Laura Bonati
Software Mentions: 3
Published: over 8 years ago

10.1098/rsob.170135

Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, <i>Myodes glareolus</i>
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 7 years ago

10.1186/1471-2105-11-535

Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots
Cited by: 9
Author(s): Jérôme Gracy, Laurent Chiche
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2105-13-S4-S2

PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL
Cited by: 130
Author(s): Emanuele Bramucci, Alessandro Paiardini, Francesco Bossa, Stefano Pascarella
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-12-48

A quality metric for homology modeling: the H-factor
Cited by: 18
Author(s): Eric di Luccio, Patrice Koehl
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2105-9-437

OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology
Cited by: 5
Author(s): Kieran O’Neill, Alexander García, Anita Schwegmann, Rafael C. Jiménez, Dan Jacobson, Henning Hermjakob
Software Mentions: 2
Published: about 16 years ago

10.1186/1472-6750-11-85

Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)
Cited by: 36
Author(s): Gustavo R. Oliveira, Maria C. M. Silva, Wagner Alexandre Lucena, Erich Yukio Tempel Nakasu, Alexandre Augusto Pereira Firmino, Magda Aparecida Beneventi, Djair S.L. Souza, José Erick Galindo Gomes, José Dijair Antonino, Daniel J. Rigden, H. B. Ramos, Carlos Ricardo Soccol, Maria Fátima Grossi‐de‐Sá
Software Mentions: 2
Published: about 13 years ago

10.1186/1472-6807-11-28

A model for the Escherichia coli FtsB/FtsL/FtsQ cell division complex
Cited by: 42
Author(s): Felipe Villanelo, Alexis Órdenes, Juan E. Brunet, Rosalba Lagos, Octavio Monasterio
Software Mentions: 2
Published: over 13 years ago

10.1186/s13062-021-00291-w

Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites
Cited by: 9
Author(s): Birgit Eisenhaber, Swati Sinha, Chaitanya K. Jadalanki, Vladimir A. Shitov, Qiao Wen Tan, Fernanda L. Sirota, Frank Eisenhaber
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0247050

Patterns and risk factors of opioid-suspected EMS overdose in Houston metropolitan area, 2015-2019: A Bayesian spatiotemporal analysis
Cited by: 3
Author(s): Cici Bauer, Tiffany Champagne‐Langabeer, Christine Bakos-Block, Kehe Zhang, David Persse, James R. Langabeer
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0052642

Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases
Cited by: 6
Author(s): Cédric Grauffel, Angèle Abboud, Glen Liszczak, Ronen Marmorstein, Thomas Arnesen, Nathalie Reuter
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0029406

Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII
Cited by: 21
Author(s): Melanie I. Stefan, David P. Marshall, Nicolas Le Novère
Software Mentions: 2
Published: almost 13 years ago

10.3390/cells8060566

Cardiac Rhythm and Molecular Docking Studies of Ion Channel Ligands with Cardiotoxicity in Zebrafish
Cited by: 10
Author(s): Bonifasius Putera Sampurna, Fiorency Santoso, Jia-Hau Lee, Wenhao Yu, Chin Chung Wu, Gilbert Audira, Stevhen Juniardi, Jung–Ren Chen, Ying‐Ting Lin, Chung-Der Hsiao
Software Mentions: 2
Published: over 5 years ago

10.1093/database/bav026

CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis
Cited by: 23
Author(s): Bernardo Ochoa‐Montaño, Nishita Mohan, Tom L. Blundell
Software Mentions: 2
Published: almost 10 years ago

10.3389/fbioe.2020.00073

Push It to the Limit: Identification of Novel Amino Acid Changes on the Acetolactate Synthase Enzyme of Rice That Putatively Confer High Level of Tolerance to Different Imidazolinones
Cited by: 1
Author(s): Giseli Buffon, Thainá Inês Lamb, Mara Cristina Barbosa Lopes, Raul Antônio Sperotto, Luís Fernando Saraiva Macedo Timmers
Software Mentions: 2
Published: almost 5 years ago

10.3389/fpls.2017.01572

Conjecture Regarding Posttranslational Modifications to the Arabidopsis Type I Proton-Pumping Pyrophosphatase (AVP1)
Cited by: 6
Author(s): Gastón A. Pizzio, Kendal D. Hirschi, Roberto A. Gaxiola
Software Mentions: 2
Published: about 7 years ago

10.1186/2043-9113-2-18

The H-factor as a novel quality metric for homology modeling
Cited by: 5
Author(s): Eric di Luccio, Patrice Koehl
Software Mentions: 2
Published: almost 13 years ago

10.3797/scipharm.1106-24

Prediction of the Human EP1 Receptor Binding Site by Homology Modeling and Molecular Dynamics Simulation
Cited by: 6
Author(s): Bijan Zare, Armin Madadkar-Sobhani, Siavoush Dastmalchi, M Mahmoudian
Software Mentions: 2
Published: almost 14 years ago

10.1038/s41598-018-22735-6

Structural insights into positive and negative allosteric regulation of a G protein-coupled receptor through protein-lipid interactions
Cited by: 34
Author(s): Agustín Bruzzese, Carles Gil, James A. R. Dalton, Jesús Giraldo
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-32079-w

DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins
Cited by: 31
Author(s): Yasaman Karami, Frédéric Guyon, Sjoerd de Vries, Pierre Tufféry
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms14011788

Modeling of Anopheles minimus Mosquito NADPH-Cytochrome P450 Oxidoreductase (CYPOR) and Mutagenesis Analysis
Cited by: 8
Author(s): Songklod Sarapusit, Panida Lertkiatmongkol, Panida Duangkaew, Pornpimol Rongnoparut
Software Mentions: 2
Published: almost 12 years ago

10.3390/ijms22010012

MHCII3D—Robust Structure Based Prediction of MHC II Binding Peptides
Cited by: 9
Author(s): Josef Laimer, Peter Lackner
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12575-015-0025-7

Mitogen Activated Protein Kinase (MPK) Interacts With Auxin Influx Carrier (OsAux/LAX1) Involved in Auxin Signaling in Plant
Cited by: 7
Author(s): Tapan Kumar Mohanta, Nibedita Mohanta, Pratap Parida, Hanhong Bae
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-12-368

LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates
Cited by: 6
Author(s): Stewart Moughon, Ram Samudrala
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0166698

PRIMO: An Interactive Homology Modeling Pipeline
Cited by: 45
Author(s): Rowan Hatherley, David K. Brown, Michael Glenister, Özlem Tastan Bishop
Software Mentions: 1
Published: about 8 years ago

10.1186/s13578-016-0072-z

RETRACTED ARTICLE: Universal minicircle sequence binding protein of Leishmania donovani regulates pathogenicity by controlling expression of cytochrome-b
Cited by: 14
Author(s): R. A. Singh, Bidyut Purkait, Kumar Abhishek, Savita Saini, Sushmita Das, Sudha Verma, Abhishek Mandal, Ayan Kr. Ghosh, Yousuf Ansari, Ashish Kumar, Abul Hasan Sardar, Pradeep Parrack, Pradeep Das
Software Mentions: 1
Published: almost 9 years ago

10.3390/toxins13040259

Pharmaceutical Assessment Suggests Locomotion Hyperactivity in Zebrafish Triggered by Arecoline Might Be Associated with Multiple Muscarinic Acetylcholine Receptors Activation
Cited by: 4
Author(s): Petrus Siregar, Gilbert Audira, Ling-Yi Feng, Jia-Hau Lee, Fiorency Santoso, Wenhao Yu, Yu‐Heng Lai, Jih-Heng Li, Ying‐Ting Lin, Jung–Ren Chen, Chung-Der Hsiao
Software Mentions: 1
Published: over 3 years ago

10.1186/s12918-017-0385-5

Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors
Cited by: 12
Author(s): Pavithra K. Balasubramanian, Anand Balupuri, Heeyoung Kang, Seung Joo Cho
Software Mentions: 1
Published: over 7 years ago

10.5936/csbj.201302003

CONFORMATIONAL SAMPLING IN TEMPLATE-FREE PROTEIN LOOP STRUCTURE MODELING: AN OVERVIEW
Cited by: 15
Author(s): Yaohang Li
Software Mentions: 1
Published: almost 12 years ago

10.1016/j.csbj.2020.08.013

An information gain-based approach for evaluating protein structure models
Cited by: 4
Author(s): Guillaume Postic, Nathalie Janel, Pierre Tufféry, Gautier Moroy
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2105-11-16

A pairwise residue contact area-based mean force potential for discrimination of native protein structure
Cited by: 19
Author(s): Seyed Shahriar Arab, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk, Armita Sheari
Software Mentions: 1
Published: almost 15 years ago

10.3390/ijms221910282

Structure-Based Understanding of ABCA3 Variants
Cited by: 5
Author(s): Marion Onnée, Pascale Fanen, Isabelle Callebaut, Alix de Becdelièvre
Software Mentions: 1
Published: about 3 years ago

10.1186/1472-6807-10-22

Improving predicted protein loop structure ranking using a Pareto-optimality consensus method
Cited by: 16
Author(s): Yaohang Li, Ionel Rata, See‐Wing Chiu, Eric Jakobsson
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2105-11-128

New statistical potential for quality assessment of protein models and a survey of energy functions
Cited by: 79
Author(s): Dmitry Rykunov, András Fiser
Software Mentions: 1
Published: over 14 years ago

10.3389/fpls.2020.00573

Mayahuelin, a Type I Ribosome Inactivating Protein: Characterization, Evolution, and Utilization in Phylogenetic Analyses of Agave
Cited by: 6
Author(s): Fernando Lledı́as, Javier Nieto Gutiérrez, Aída Martínez-Hernández, Abisaí García-Mendoza, Eric Sosa, Felipe Hernández-Bermúdez, Tzvetanka D. Dinkova, Sandi Reyes, Gladys I. Cassab, J. Nieto-Sotelo
Software Mentions: 1
Published: over 4 years ago

10.1186/1472-6785-10-24

Cytochrome P450 diversity and induction by gorgonian allelochemicals in the marine gastropod Cyphoma gibbosum
Cited by: 21
Author(s): Kristen E. Whalen, Victoria R. Starczak, David R. Nelson, Jared V. Goldstone, Mark E. Hahn
Software Mentions: 1
Published: almost 14 years ago

10.1534/g3.111.001933

The Yeast Ubr1 Ubiquitin Ligase Participates in a Prominent Pathway That Targets Cytosolic Thermosensitive Mutants for Degradation
Cited by: 33
Author(s): Farzin Khosrow‐Khavar, Nancy N. Fang, Alex H. M. Ng, Jason M. Winget, Sophie A. Comyn, Thibault Mayor
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms21072488

The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage
Cited by: 4
Author(s): Huan Nguyen-Kim, Hélène San Clemente, Josef Laimer, Peter Lackner, Gabriele Gadermaier, Christophe Dunand, Élisabeth Jamet
Software Mentions: 1
Published: over 4 years ago

10.1186/s12859-020-3499-5

A single-model quality assessment method for poor quality protein structure
Cited by: 3
Author(s): Jianquan Ouyang, Ningqiao Huang, Yunqi Jiang
Software Mentions: 1
Published: over 4 years ago

10.1038/srep33509

ProQ3: Improved model quality assessments using Rosetta energy terms
Cited by: 90
Author(s): Karolis Uziela, Nanjiang Shu, Björn Wallner, Arne Elofsson
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-019-3186-6

Identification of native protein structures captured by principal interactions
Cited by: 1
Author(s): Mehdi Mirzaie
Software Mentions: 1
Published: about 5 years ago

10.3390/v12040360

Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins
Cited by: 199
Author(s): Suhas Srinivasan, Hongzhu Cui, Ziyang Gao, Ming Liu, Senbao Lu, Winnie Mkandawire, Oleksandr Narykov, Min Sun, Dmitry Korkin
Software Mentions: 1
Published: over 4 years ago

10.3390/v7112901

Composite Sequence–Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development
Cited by: 6
Author(s): Siriphan Manocheewa, John E. Mittler, Ram Samudrala, James I. Mullins
Software Mentions: 1
Published: about 9 years ago

10.3390/molecules24071196

A Complete Assessment of Dopamine Receptor- Ligand Interactions through Computational Methods
Cited by: 24
Author(s): Beatriz Bueschbell, Carlos Barreto, António Preto, Anke C. Schiedel, Irina S. Moreira
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0016627

Different Binding Properties and Function of CXXC Zinc Finger Domains in Dnmt1 and Tet1
Cited by: 90
Author(s): Carina Frauer, Andrea Rottach, Daniela Meilinger, Sebastian Bultmann, Karin Fellinger, Stefan Hasenöder, Mengxi Wang, Weihua Qin, Johannes Söding, Fabio Spada, Heinrich Leonhardt
Software Mentions: 1
Published: almost 14 years ago

10.1007/s11032-015-0208-6

Differential expression of the HvCslF6 gene late in grain development may explain quantitative differences in (1,3;1,4)-β-glucan concentration in barley
Cited by: 17
Author(s): Sie Chuong Wong, Neil J. Shirley, Alan Little, Kelvin H. P. Khoo, Julian G. Schwerdt, Geoffrey B. Fincher, Rachel A. Burton, D. E. Mather
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0005694

Regulatory Elements within the Prodomain of Falcipain-2, a Cysteine Protease of the Malaria Parasite Plasmodium falciparum
Cited by: 46
Author(s): Kailash C. Pandey, David T. Barkan, Andrej S̆ali, Philip J. Rosenthal
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-020-03770-5

SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions
Cited by: 7
Author(s): Joaquim Aguirre‐Plans, Alberto Meseguer, Rubén Molina-Fernández, Manuel Alejandro Marín-López, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornés, Narcís Fernández-Fuentes, Baldo Oliva
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0135455

Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data
Cited by: 7
Author(s): Amrita Roy Choudhury, Emilia Sikorska, Johannes van den Boom, Peter Bayer, Łukasz Popenda, Kosma Szutkowski, Stefan Jurga, Massimiliano Bonomi, Andrej S̆ali, Igor Zhukov, Sabina Passamonti, Marjana Novič
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0022990

Structural Basis for Species Specific Inhibition of 17β-Hydroxysteroid Dehydrogenase Type 1 (17β-HSD1): Computational Study and Biological Validation
Cited by: 8
Author(s): Tobias Klein, Claudia Henn, Matthias Negri, Martin Frotscher
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0015386

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction
Cited by: 219
Author(s): Zhang Jian, Yang Zhang
Software Mentions: 1
Published: about 14 years ago

10.3390/biology10060501

Characterization of Rheumatoid Arthritis Risk-Associated SNPs and Identification of Novel Therapeutic Sites Using an In-Silico Approach
Cited by: 8
Author(s): Mehran Akhtar, Yasir Ali, Ziaul Islam, Misbah Arshad, Mamoona Rauf, Muhammad Ali, Saleh N. Maodaa, Saleh Alfarraj, Hamed A. El‐Serehy, Fazal Jalil
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-020-61205-w

Neighborhood Preference of Amino Acids in Protein Structures and its Applications in Protein Structure Assessment
Cited by: 4
Author(s): Siyuan Liu, Xilun Xiang, Xiang Gao, Haiguang Liu
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0028637

The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes
Cited by: 148
Author(s): Mario Orsi, Jonathan W. Essex
Software Mentions: 1
Published: almost 13 years ago

Projects: cran: DOPE

Papers Mentioning DOPE 71