pypi: SSAP | Projects | Ecosyste.ms: Papers

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: about 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: over 16 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: about 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: over 3 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: about 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: over 15 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: about 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: about 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: almost 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: over 19 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: about 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: over 11 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: almost 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: about 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: over 13 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: about 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: almost 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: over 15 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: over 13 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: over 14 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: over 14 years ago

10.1128/mBio.00226-20

Structural Basis of Ca 2+ -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 Alex-1 in the Genus Coffea 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: almost 13 years ago

10.3390/biom10020193

Exploring Protein Fold Space
Cited by: 7
Author(s): William R. Taylor
Software Mentions: 1
Published: over 4 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

Projects: pypi: SSAP

Papers Mentioning SSAP 48