Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: SSAP

https://packages.ecosyste.ms/registries/pypi.org/packages/SSAP

tonylab
49 versions
Latest release: over 3 years ago

Papers Mentioning SSAP 48

10.1371/journal.pone.0100018
Transcriptome Profiling Reveals Higher Vertebrate Orthologous of Intra-Cytoplasmic Pattern Recognition Receptors in Grey Bamboo Shark
Cited by: 18
Author(s): Tirumurugaan Krishnaswamy Gopalan, Pradheepa Gururaj, Ravi P. Gupta, Gopal Dhinakar Raj, Preeti Rajesh, Balachandran Chidambaram, Aravindan Kalyanasundaram, R. Amri
Software Mentions: 4
Published: over 10 years ago
10.1186/1471-2105-13-105
Multiple structure alignment with msTALI
Cited by: 26
Author(s): Paul Shealy, Homayoun Valafar
Software Mentions: 3
Published: over 12 years ago
10.1186/1472-6807-8-18
A multi-template combination algorithm for protein comparative modeling
Cited by: 86
Author(s): Jianlin Cheng
Software Mentions: 3
Published: almost 17 years ago
10.1186/1471-2105-11-138
An optimized TOPS+ comparison method for enhanced TOPS models
Cited by: 2
Author(s): Mallika Veeramalai, David Gilbert, Gabriel Valiente
Software Mentions: 3
Published: over 14 years ago
10.1186/1471-2121-8-S1-S6
Surface similarity-based molecular query-retrieval
Cited by: 9
Author(s): Rahul Singh
Software Mentions: 3
Published: over 17 years ago
10.1186/1471-2105-7-510
Connectivity independent protein-structure alignment: a hierarchical approach
Cited by: 53
Author(s): Bjoern Kolbeck, Patrick May, Tobias Schmidt-Goenner, Thomas Steinke, Ernst‐Walter Knapp
Software Mentions: 3
Published: almost 18 years ago
10.3389/fchem.2020.602291
Development of a TSR-Based Method for Protein 3-D Structural Comparison With Its Applications to Protein Classification and Motif Discovery
Cited by: 4
Author(s): Sarika Kondra, Titli Sarkar, Vijay V. Raghavan, Wu Xu
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pcbi.1004926
Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases
Cited by: 25
Author(s): David A. Lee, Sayoni Das, Natalie L. Dawson, Dragana Dobrijevic, John M. Ward, Christine A. Orengo
Software Mentions: 3
Published: over 8 years ago
10.1186/1471-2105-10-S1-S4
SE: an algorithm for deriving sequence alignment from a pair of superimposed structures
Cited by: 7
Author(s): Chin‐Hsien Tai, James J. Vincent, Changhoon Kim, Byung Kook Lee
Software Mentions: 3
Published: almost 16 years ago
10.1186/1471-2105-9-352
Alignment of protein structures in the presence of domain motions
Cited by: 48
Author(s): Roberto Mosca, Barbara Brannetti, Thomas R. Schneider
Software Mentions: 3
Published: about 16 years ago
10.1186/1471-2105-11-155
Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity
Cited by: 13
Author(s): Zong Hong Zhang, Hwee Kuan Lee, Ivana Mihalek
Software Mentions: 3
Published: over 14 years ago
10.1186/1472-6807-7-50
Comparative Analysis of Protein Structure Alignments
Cited by: 85
Author(s): Gabriele Mayr, Francisco S. Domingues, Peter Lackner
Software Mentions: 3
Published: over 17 years ago
10.1186/1471-2105-15-S8-S4
Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space
Cited by: 11
Author(s): Kevin Molloy, Mien Van, Daniel Barbará, Amarda Shehu
Software Mentions: 2
Published: over 10 years ago
10.1186/1471-2105-8-77
Comparison of protein structures by growing neighborhood alignments
Cited by: 8
Author(s): Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma Chandra
Software Mentions: 2
Published: over 17 years ago
10.1186/1471-2105-7-460
Representing and comparing protein structures as paths in three-dimensional space
Cited by: 14
Author(s): Degui Zhi, S. Sri Krishna, Hongjun Cao, Pavel A. Pevzner, Adam Godzik
Software Mentions: 2
Published: about 18 years ago
10.1186/1471-2105-9-556
The meaning of alignment: lessons from structural diversity
Cited by: 12
Author(s): Walter Pirovano, K. Anton Feenstra, Jaap Heringa
Software Mentions: 2
Published: almost 16 years ago
10.1186/1471-2105-10-129
Improving classification in protein structure databases using text mining
Cited by: 14
Author(s): Antonis Koussounadis, Oliver Redfern, David T. Jones
Software Mentions: 2
Published: over 15 years ago
10.1186/1472-6807-5-7
Cited by: 2
Author(s): Michael Roßbach, Oliver Daumke, Claudia Klinger, Alfred Wittinghofer, Michael Kaufmann
Software Mentions: 2
Published: almost 20 years ago
10.1016/j.bbapap.2013.02.042
Functional site plasticity in domain superfamilies
Cited by: 29
Author(s): Benoît H. Dessailly, Natalie L. Dawson, Kenji Mizuguchi, Christine A. Orengo
Software Mentions: 2
Published: over 11 years ago
10.3390/biology2041296
Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust
Cited by: 3
Author(s): Allen Holder, Jacqueline C. Simon, Jonathon Strauser, Jonathan Taylor, Yosi Shibberu
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0017826
Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks
Cited by: 7
Author(s): Garima Agarwal, Swapnil Mahajan, Narayanaswamy Srinivasan, Alexandre G. de Brevern
Software Mentions: 2
Published: over 13 years ago
10.1016/j.compbiolchem.2011.04.008
Exploring the limits of fold discrimination by structural alignment: A large scale benchmark using decoys of known fold
Cited by: 7
Author(s): Siv Midtun Hollup, Michael I. Sadowski, Inge Jonassen, William R. Taylor
Software Mentions: 2
Published: over 13 years ago
10.1093/database/bat048
DoSA: Database of Structural Alignments
Cited by: 2
Author(s): Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard Offmann, Alexandre G. de Brevern, Narayanaswamy Srinivasan
Software Mentions: 2
Published: over 11 years ago
10.3389/fmolb.2021.668184
Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds
Cited by: 9
Author(s): Nicola Bordin, Ian Sillitoe, Jonathan G. Lees, Christine A. Orengo
Software Mentions: 2
Published: over 3 years ago
10.1002/prot.25223
The evolution of function within the Nudix homology clan
Cited by: 49
Author(s): John R. Srouji, Anting Xu, Annsea Park, Jack F. Kirsch, Steven E. Brenner
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-10012-x
Structural and Functional View of Polypharmacology
Cited by: 31
Author(s): Aurelio A. Moya‐García, Tolulope Adeyelu, Felix Krüger, Natalie L. Dawson, Jon Lees, John P. Overington, Christine A. Orengo, Juan A. G. Ranea
Software Mentions: 2
Published: about 7 years ago
10.1155/2013/439681
Implementation of a Parallel Protein Structure Alignment Service on Cloud
Cited by: 24
Author(s): Che Lun Hung, Yaw Ling Lin
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pcbi.1000485
FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies
Cited by: 42
Author(s): Oliver Redfern, Benoît H. Dessailly, Timothy J. Dallman, Ian Sillitoe, Christine A. Orengo
Software Mentions: 1
Published: about 15 years ago
10.1186/1471-2105-10-174
Combining specificity determining and conserved residues improves functional site prediction
Cited by: 35
Author(s): Olga V. Kalinina, Mikhail S. Gelfand, Robert B. Russell
Software Mentions: 1
Published: over 15 years ago
10.1371/journal.pgen.1000868
Derepression of the Plant Chromovirus LORE1 Induces Germline Transposition in Regenerated Plants
Cited by: 44
Author(s): Eigo Fukai, Yosuke Umehara, Shusei Sato, Makoto Endo, Hiroshi Kouchi, Makoto Hayashi, Jens Stougaard, Hirohiko Hirochika
Software Mentions: 1
Published: over 14 years ago
10.1371/journal.pone.0055772
Cytosine Methylation Alteration in Natural Populations of Leymus chinensis Induced by Multiple Abiotic Stresses
Cited by: 36
Author(s): Yingjie Yu, Xuejiao Yang, Huaying Wang, Fu-Ming Shi, Ying Liu, Jushan Liu, Linfeng Li, Deli Wang, Liu B
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0050352
Differential Dynamics of Transposable Elements during Long-Term Diploidization of Nicotiana Section Repandae (Solanaceae) Allopolyploid Genomes
Cited by: 29
Author(s): Christian Parisod, Corinne Mhiri, K. Yoong Lim, James J. Clarkson, Mark W. Chase, Andrew R. Leitch, Marie–Angèle Grandbastien
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pone.0108847
Full Text Clustering and Relationship Network Analysis of Biomedical Publications
Cited by: 8
Author(s): Renchu Guan, Chen Yang, Maurizio Marchese, Yanchun Liang, Xiaohu Shi
Software Mentions: 1
Published: about 10 years ago
10.1107/S2059798317008920
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences
Cited by: 43
Author(s): Lam S, Sayoni Das, Ian Sillitoe, Christine A. Orengo
Software Mentions: 1
Published: over 7 years ago
10.1186/1477-5956-9-S1-S20
SProt: sphere-based protein structure similarity algorithm
Cited by: 13
Author(s): Jakub Galgonek, David Hoksza, Tomáš Skopal
Software Mentions: 1
Published: almost 14 years ago
10.3897/CompCytogen.v9i4.5120
(GAA)n microsatellite as an indicator of the A genome reorganization during wheat evolution and domestication
Cited by: 18
Author(s): И. Г. Адонина, Н. П. Гончаров, Е. Д. Бадаева, E. M. Sergeeva, N. V. Petrash, Е. А. Салина
Software Mentions: 1
Published: about 9 years ago
10.3390/ijms22136783
Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley
Cited by: 5
Author(s): Renata Orłowska, Katarzyna A. Pachota, Wioletta M. Dynkowska, Agnieszka Niedziela, Piotr Tomasz Bednarek
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-020-71936-5
SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals
Cited by: 87
Author(s): Su Datt Lam, Nicola Bordin, Vaishali P. Waman, Harry M. Scholes, Paul Ashford, Neeladri Sen, Lucy van Dorp, Clemens Rauer, Natalie L. Dawson, Camilla S.M. Pang, Mahnaz Abbasian, Ian Sillitoe, Sarah Edwards, Franca Fraternali, Jon Lees, Joanne M. Santini, Christine A. Orengo
Software Mentions: 1
Published: about 4 years ago
10.1186/1471-2148-9-232
Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth
Cited by: 19
Author(s): Alfred L. Roca, Yasuko Ishida, Nikolas Nikolaidis, Sergios‐Orestis Kolokotronis, Stephen Fratpietro, Kristin Stewardson, Shannon M. Hensley, Michele Tisdale, Г. Г. Боескоров, Alex D. Greenwood
Software Mentions: 1
Published: almost 16 years ago
10.1186/1471-2105-7-S5-S5
Projections for fast protein structure retrieval
Cited by: 10
Author(s): Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma Chandra
Software Mentions: 1
Published: almost 18 years ago
10.1186/1472-6807-11-2
1,000 structures and more from the MCSG
Cited by: 13
Author(s): David Lee, Tjaart de Beer, Roman A. Laskowski, Janet M. Thornton, Christine A. Orengo
Software Mentions: 1
Published: almost 14 years ago
10.1186/1471-2105-11-S1-S46
A fast indexing approach for protein structure comparison
Cited by: 13
Author(s): Lei Zhang, James E. Bailey, Arun S. Konagurthu, Kotagiri Ramamohanarao
Software Mentions: 1
Published: almost 15 years ago
10.1186/1748-7188-5-12
FlexSnap: Flexible Non-sequential Protein Structure Alignment
Cited by: 36
Author(s): Saeed Salem, Mohammed J. Zaki, Christopher Bystroff
Software Mentions: 1
Published: almost 15 years ago
10.1128/mBio.00226-20
Structural Basis of Ca <sup>2+</sup> -Dependent Self-Processing Activity of Repeat-in-Toxin Proteins
Cited by: 4
Author(s): Vojtěch Kubáň, Pavel Macek, Jozef Hritz, Kateřina Nechvátalová, Kateřína Nedbalcová, Martin Faldyna, Peter Šebo, Lukáš Žı́dek, Ladislav Bumba
Software Mentions: 1
Published: over 4 years ago
10.1016/j.biochi.2015.08.004
The history of the CATH structural classification of protein domains
Cited by: 34
Author(s): Ian Sillitoe, Natalie L. Dawson, Janet M. Thornton, Christine A. Orengo
Software Mentions: 1
Published: almost 9 years ago
10.4061/2011/358412
Site-Specific Insertion Polymorphism of the MITE <i>Alex-1</i> in the Genus <i>Coffea</i> Suggests Interspecific Gene Flow
Cited by: 3
Author(s): Christine Tranchant‐Dubreuil, Romain Guyot, Amira Guellim, Caroline Duret, Marion de la Mare, Norosoa J. Razafinarivo, Valérie Poncet, Serge Hamon, Perla Hamon, Alexandre de Kochko
Software Mentions: 1
Published: about 13 years ago
10.3390/biom10020193
Exploring Protein Fold Space
Cited by: 7
Author(s): William R. Taylor
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pcbi.0030232
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures
Cited by: 92
Author(s): Oliver Redfern, Andrew Harrison, Timothy J. Dallman, Frances M. G. Pearl, Christine A. Orengo
Software Mentions: 1
Published: almost 17 years ago