cran: SSM | Projects | Ecosyste.ms: Papers

10.1186/s12870-019-1685-2

Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors
Cited by: 15
Author(s): Konstantin Kozlov, A. K. Singh, Jens Berger, Eric J. B. von Wettberg, Abdullah Kahraman, Abdulkadir Aydoğan, Douglas R. Cook, Sergey V. Nuzhdin, Maria Samsonova
Software Mentions: 5
Published: over 5 years ago

10.1107/S2059798318003455

Recent developments inMrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment
Cited by: 34
Author(s): Ronan Keegan, Stuart McNicholas, Jens M. H. Thomas, Adam J Simpkin, Felix Šimkovic, Ville Uski, Charles Ballard, Martyn Winn, K.S. Wilson, Daniel J. Rigden
Software Mentions: 5
Published: over 6 years ago

10.1107/S0907444911007281

Presenting your structures: theCCP4mgmolecular-graphics software
Cited by: 1,079
Author(s): Stuart McNicholas, E. A. Potterton, K.S. Wilson, M.E.M. Noble
Software Mentions: 5
Published: over 13 years ago

10.1186/1471-2105-5-197

Cited by: 43
Author(s): Sara Cheek, Yuan Qi, S. Sri Krishna, Lisa N. Kinch, Nick V. Grishin
Software Mentions: 4
Published: almost 21 years ago

10.1107/S2059798318001353

Gyreandgimble: a maximum-likelihood replacement for Patterson correlation refinement
Cited by: 13
Author(s): Airlie J. McCoy, Robert D. Oeffner, Claudia Millán, Massimo Sammito, Isabel Usón, Randy J. Read
Software Mentions: 4
Published: over 6 years ago

10.3390/s21041344

DSSM: Distributed Streaming Data Sharing Manager
Cited by: 0
Author(s): Hiroaki Fukuda, Ryota Gunji, Tadahiro Hasegawa, Paul Leger, Ismael Figueroa
Software Mentions: 4
Published: over 3 years ago

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

10.1016/j.str.2011.03.023

Insights into the Evolution of a Complex Virus from the Crystal Structure of Vaccinia Virus D13
Cited by: 79
Author(s): Mohammad W. Bahar, Stephen C. Graham, David I. Stuart, Jonathan M. Grimes
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.ppat.1005165

Structure Elucidation of Coxsackievirus A16 in Complex with GPP3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses
Cited by: 19
Author(s): Luigi De Colibus, Xiangxi Wang, Aloys Tijsma, Johan Neyts, John A. B. Spyrou, Jingshan Ren, Jonathan M. Grimes, Gerhard Puerstinger, Pieter Leyssen, Elizabeth E. Fry, Zihe Rao, David I. Stuart
Software Mentions: 3
Published: about 9 years ago

10.1093/molbev/msaa100

Structural Phylogenetics with Confidence
Cited by: 5
Author(s): Ashar J Malik, Anthony M. Poole, Jane R. Allison
Software Mentions: 3
Published: over 4 years ago

10.1107/S0907444911035943

High-resolution structure of a retroviral protease folded as a monomer
Cited by: 22
Author(s): Mirosław Gilski, Maciej Kazmierczyk, Szymon Krzywda, Helena Zábranská, Seth Cooper, Zoran Popović, Firas Khatib, Frank DiMaio, James Thompson, David Baker, Iva Pichová, Mariusz Jaskólski
Software Mentions: 3
Published: about 13 years ago

10.1186/1472-6807-8-45

Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites
Cited by: 66
Author(s): T.A. Binkowski, Andrzej Joachimiak
Software Mentions: 3
Published: almost 17 years ago

10.1186/1471-2105-11-446

Fast and accurate protein substructure searching with simulated annealing and GPUs
Cited by: 44
Author(s): Alex Stivala, Peter J. Stuckey, Anthony Wirth
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0174248

Inter-nesting movements and habitat-use of adult female Kemp’s ridley turtles in the Gulf of Mexico
Cited by: 15
Author(s): Donna J. Shaver, Kristen M. Hart, Ikuko Fujisaki, David N. Bucklin, Autumn R. Iverson, Cynthia Rubio, Thomas F. Backof, Patrick M. Burchfield, Raul de Jesus Gonzales Diaz Miron, Peter H. Dutton, Amy Frey, Jaime Peña, Daniel Gomez Gamez, H. Martínez, Jaime Ortíz
Software Mentions: 3
Published: over 7 years ago

10.1186/s12913-020-05929-5

Change and improvement 50 years in the making: a scoping review of the use of soft systems methodology in healthcare
Cited by: 9
Author(s): Hanna Augustsson, Kate Churruca, Jeffrey Braithwaite
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-018-21667-5

Structure based function-annotation of hypothetical protein MGG_01005 from Magnaporthe oryzae reveals it is the dynein light chain orthologue of dynlt1/3
Cited by: 2
Author(s): Guorui Li, Jinguang Huang, Jun Yang, Dan He, Chao Wang, Xiaoxuan Qi, Ian A. Taylor, Junfeng Liu, You-Liang Peng
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-33193-5

Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas
Cited by: 10
Author(s): Hong‐Hsiang Guan, Yin-Cheng Hsieh, Po‐Chun Lin, Yen‐Chieh Huang, Masato Yoshimura, Liying Chen, Shao-Kang Chen, Phimonphan Chuankhayan, Chien-Chih Lin, Nai-Chi Chen, Atsushi Nakagawa, Sunney I. Chan, Chun‐Jung Chen
Software Mentions: 3
Published: about 6 years ago

10.7717/peerj.4728

Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from Mycobacterium tuberculosis
Cited by: 5
Author(s): Mingjing Yu, Chao Dou, Yijun Gu, Wei Cheng
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pcbi.1009211

A mechanistic and data-driven reconstruction of the time-varying reproduction number: Application to the COVID-19 epidemic
Cited by: 8
Author(s): Bernard Cazelles, Clara Champagne, Benjamin Nguyen-Van-Yen, Catherine Comiskey, Elisabeta Vergu, Benjamín Roche
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0245642

Quantifying non-communicable diseases’ burden in Egypt using State-Space model
Cited by: 1
Author(s): Somaya El‐Saadani, Mohamed Saleh, Sarah Assem Ibrahim
Software Mentions: 3
Published: about 3 years ago

10.1186/1471-2105-10-153

Tableau-based protein substructure search using quadratic programming
Cited by: 11
Author(s): Alex Stivala, Anthony Wirth, Peter J. Stuckey
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pcbi.1006650

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Cited by: 2,164
Author(s): Remco R. Bouckaert, Timothy G. Vaughan, Joëlle Barido‐Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David A. Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Donghua Xie, Chi Zhang, Tanja Stadler, Alexei J. Drummond
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-12-365

Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns
Cited by: 2
Author(s): Jérémy Gruel, Michel LeBorgne, Nolwenn Le Meur, Nathalie Théret
Software Mentions: 3
Published: about 13 years ago

10.1128/JB.00115-20

A Novel Growth-Based Selection Strategy Identifies New Constitutively Active Variants of the Major Virulence Regulator PrfA in Listeria monocytogenes
Cited by: 4
Author(s): S. Hansen, Michael Hall, C. Grundström, Kristoffer Brännström, A. Elisabeth Sauer‐Eriksson, Jörgen Johansson
Software Mentions: 3
Published: over 4 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

10.1186/1472-6807-7-50

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

10.1186/1471-2105-9-352

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

10.1186/1471-2164-10-611

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

10.7554/eLife.19874

Structure in the variability of the basic reproductive number (R0) for Zika epidemics in the Pacific islands
Cited by: 34
Author(s): Clara Champagne, David Georges Salthouse, Paul Rácz, Van-Mai Cao-Lormeau, Benjamín Roche, Bernard Cazelles
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.41741

Crystal structure of a natural light-gated anion channelrhodopsin
Cited by: 30
Author(s): Hai Li, Chia‐Ying Huang, Elena G. Govorunova, Christopher T. Schafer, Oleg A. Sineshchekov, Meitian Wang, Lei Zheng, John L. Spudich
Software Mentions: 3
Published: almost 6 years ago

10.1042/BSR20140088

Apo, Zn2+-bound and Mn2+-bound structures reveal ligand-binding properties of SitA from the pathogen Staphylococcus pseudintermedius
Cited by: 29
Author(s): Francesca Abate, E. Malito, Roberta Cozzi, Paola Lo Surdo, Domenico Maione, Matthew J. Bottomley
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.ppat.1000128

Vaccinia Virus Proteins A52 and B14 Share a Bcl-2–Like Fold but Have Evolved to Inhibit NF-κB rather than Apoptosis
Cited by: 145
Author(s): Stephen C. Graham, Mohammad W. Bahar, Samantha Cooray, Ron A.-J. Chen, Daniel M. Whalen, Nicola G. A. Abrescia, David Alderton, Raymond J. Owens, David I. Stuart, Geoffrey L. Smith, Jonathan M. Grimes
Software Mentions: 3
Published: about 16 years ago

10.1107/S2053273316010731

Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm
Cited by: 9
Author(s): Hongxing He, Hengrui Fang, Mitchell D. Miller, George N. Phillips, W. P. Su
Software Mentions: 3
Published: over 8 years ago

10.1107/S2059798320001679

ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation
Cited by: 15
Author(s): Ana María Medina, Josep Triviño, Rafael J. Borges, Claudia Millán, Isabel Usón, Massimo Sammito
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.ppat.1000251

Rhabdovirus Matrix Protein Structures Reveal a Novel Mode of Self-Association
Cited by: 66
Author(s): Stephen C. Graham, René Assenberg, Olivier Delmas, Anil Kumar Verma, Alireza Gholami, Chiraz Talbi, Raymond J. Owens, David I. Stuart, Jonathan M. Grimes, Hervé Bourhy
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.ppat.1002085

The N-Terminus of the RNA Polymerase from Infectious Pancreatic Necrosis Virus Is the Determinant of Genome Attachment
Cited by: 34
Author(s): Stephen C. Graham, L. Peter Sarin, Mohammad W. Bahar, Robert A. Myers, David I. Stuart, Dennis H. Bamford, Jonathan M. Grimes
Software Mentions: 3
Published: over 13 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

10.1186/1471-2105-7-510

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

10.1186/1471-2105-13-105

Multiple structure alignment with msTALI
Cited by: 26
Author(s): Paul Shealy, Homayoun Valafar
Software Mentions: 3
Published: over 12 years ago

10.3389/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

10.3390/s21103366

In Vitro and In Vivo Multispectral Photoacoustic Imaging for the Evaluation of Chromophore Concentration
Cited by: 5
Author(s): Aneline Dolet, Rita Ammanouil, Virginie Pétrilli, Cédric Richard, Piero Tortoli, Didier Vray, François Varray
Software Mentions: 2
Published: over 3 years ago

10.1016/j.str.2012.02.011

Structure of the Discoidin Domain Receptor 1 Extracellular Region Bound to an Inhibitory Fab Fragment Reveals Features Important for Signaling
Cited by: 78
Author(s): Federico Carafoli, Marie Cathrin Mayer, Kazushige Shiraishi, Mira Anguelova Pecheva, Lai Yi Chan, Ruodan Nan, Birgit Leitinger, Erhard Hohenester
Software Mentions: 2
Published: over 12 years ago

10.1107/S0907444912001862

High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase
Cited by: 36
Author(s): T. Nagae, Takashi Kawamura, Leonard M. G. Chavas, Ken Niwa, Masashi Hasegawa, Chiaki Kato, Nobuhisa Watanabe
Software Mentions: 2
Published: over 12 years ago

10.1128/mBio.02249-20

Biophysical and Biochemical Characterization of TP0037, a <scp>d</scp> -Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum
Cited by: 4
Author(s): Ranjit K. Deka, Wei Z. Liu, Michael V. Norgard, Chad A. Brautigam
Software Mentions: 2
Published: about 4 years ago

10.1107/S1744309109050416

Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction
Cited by: 7
Author(s): Gye Won Han, Constantina Bakolitsa, Mitchell D. Miller, Abhinav Kumar, Dennis Carlton, Rafaël Najmanovich, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Connie Chen, Hsiu Ju Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Dustin C. Ernst, Julie Feuerhelm, Joanna C Grant, Anna Grzechnik, Lukasz Jaroszewski, Kevin K. Jin, Hope A. Johnson, Heath E. Klock, Mark W. Knuth, Piotr Koźbiał, Sanjeev Krishna, David Marciano, Daniel McMullan, Andrew Morse, Edward Nigoghossian, Linda Okach, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J Tien, Christine B Trame, H. van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Marc‐André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson
Software Mentions: 2
Published: over 14 years ago

10.1016/j.jmb.2015.10.017

PhyreStorm: A Web Server for Fast Structural Searches Against the PDB
Cited by: 13
Author(s): Stefans Mezulis, Michael J.E. Sternberg, Lawrence A. Kelley
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.jmb.2016.09.021

MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a Ca 2+ Ion Bound at the Constriction Zone
Cited by: 28
Author(s): Luana Ferrara, Gregor D. Wallat, L. Moynié, Naresh Niranjan Dhanasekar, Soumeya Aliouane, Silvia Acosta‐Gutiérrez, Jean‐Marie Pagès, Jean‐Michel Bolla, Mathias Winterhalter, Matteo Ceccarelli, James H. Naismith
Software Mentions: 2
Published: about 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 11 years ago

10.1371/journal.ppat.1005194

Phospho-dependent Regulation of SAMHD1 Oligomerisation Couples Catalysis and Restriction
Cited by: 90
Author(s): Laurence H. Arnold, Harriet C. T. Groom, Simone Kunzelmann, David Schwefel, Sarah J. Caswell, Paula Ordonez, Melanie C. Mann, Sabrina Rueschenbaum, David C. Goldstone, Simon Pennell, Steven Howell, Jonathan P. Stoye, Michelle Webb, Ian A. Taylor, Kate N. Bishop
Software Mentions: 2
Published: about 9 years ago

10.1107/S205979832100632X

Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA
Cited by: 1
Author(s): Prabhat Kumar Pathak, Fei Zhang, Shu‐Lin Peng, Lifang Niu, Juhi Chaturvedi, Justin Elliott, Yan Xiang, Million Tadege, Junpeng Deng
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0130888

Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies
Cited by: 16
Author(s): Shannon E. Hill, Rebecca K. Donegan, Elaine Nguyen, Tanay M. Desai, Raquel L. Lieberman
Software Mentions: 2
Published: over 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 15 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

10.1186/1472-6807-7-34

The NMR structure of the murine DLC2 SAM domain reveals a variant fold that is similar to a four-helix bundle
Cited by: 17
Author(s): Janice Kwan, Logan W. Donaldson
Software Mentions: 2
Published: almost 18 years ago

10.1186/1471-2105-8-116

ASH structure alignment package: Sensitivity and selectivity in domain classification
Cited by: 40
Author(s): Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
Software Mentions: 2
Published: over 17 years ago

10.1186/1472-6807-6-9

Fold-recognition and comparative modeling of human α2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni
Cited by: 8
Author(s): Sujatha, Petety V. Balaji
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pone.0039166

Engineering of Three-Finger Fold Toxins Creates Ligands with Original Pharmacological Profiles for Muscarinic and Adrenergic Receptors
Cited by: 25
Author(s): Carole Fruchart-Gaillard, Gilles Mourier, Guillaume Blanchet, Laura Vera, Nicolas Gilles, R. Ménez, Elodie Marcon, E.A. Stura, Denis Servent
Software Mentions: 2
Published: over 12 years ago

10.1186/1472-6807-7-24

A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding
Cited by: 24
Author(s): Will A. Stanley, Niko V. Pursiainen, Elspeth F. Garman, André H. Juffer, Matthias Wilmanns, Petri Kursula
Software Mentions: 2
Published: over 17 years ago

10.1186/s12964-016-0140-3

A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein
Cited by: 9
Author(s): Ekaterina Smirnova, Janice Kwan, Ryan Siu, Xin Gao, Georg Zoidl, Borries Demeler, V. Saridakis, Logan W. Donaldson
Software Mentions: 2
Published: about 8 years ago

10.1016/j.cels.2017.10.013

Asymmetry between Activation and Deactivation during a Transcriptional Pulse
Cited by: 12
Author(s): Lee Dunham, Hiroshi Momiji, Claire V. Harper, Polly Downton, Kirsty Hey, A. McNamara, Karen Featherstone, David G. Spiller, D.A.J. Rand, Bärbel Finkenstädt, Michael R. H. White, Julian Davis
Software Mentions: 2
Published: almost 7 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

10.3762/bjoc.12.284

Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934
Cited by: 14
Author(s): Veronika Ulrich, Clara Brieke, Max J. Cryle
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-9-17

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
Cited by: 73
Author(s): David M. Kristensen, R. Matthew Ward, Andreas Martin Lisewski, Serkan Erdin, Brian Y. Chen, Viacheslav Y. Fofanov, Marek Kimmel, Lydia E. Kavraki, Olivier Lichtarge
Software Mentions: 2
Published: almost 17 years ago

10.3389/fbioe.2020.00318

A Combined Geometric Morphometric and Discrete Element Modeling Approach for Hip Cartilage Contact Mechanics
Cited by: 15
Author(s): Jan Van Houcke, Emmanuel Audenaert, Penny R. Atkins, Andrew E. Anderson
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2105-11-439

CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation
Cited by: 16
Author(s): Gong‐Hua Li, Jing‐Fei Huang
Software Mentions: 2
Published: about 14 years ago

10.3389/fpsyt.2021.594229

When Depression Breeds Rejection Rather Than Compassion: Disagreeableness, Stigma, and Lack of Empathic Concern Among Support Providers
Cited by: 1
Author(s): Myriam Mongrain, Ariel Shoikhedbrod
Software Mentions: 2
Published: over 3 years ago

10.3390/v9110321

Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction
Cited by: 6
Author(s): Nikéa Pittman, Adam Misseldine, Lorena Geilen, Sujata Halder, J. W. G. Smith, Justin Kurian, Paul R. Chipman, Mandy E.W. Janssen, Robert McKenna, Timothy S. Baker, Anthony D’Abramo, Susan F. Cotmore, Peter Tattersall, Mavis Agbandje‐McKenna
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10040298

Computational Methods for Detection of Differentially Methylated Regions Using Kernel Distance and Scan Statistics
Cited by: 2
Author(s): Faith Dunbar, Hongyan Xu, Dongseok Ryu, Santu Ghosh, Huidong Shi, Varghese George
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1000160

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function
Cited by: 90
Author(s): Marco Punta, Yishai Ofran
Software Mentions: 2
Published: about 16 years ago

10.1107/S0907444912029599

Crystallization, dehydration and experimental phasing of WbdD, a bifunctional kinase and methyltransferase fromEscherichia coliO9a
Cited by: 5
Author(s): Gregor Hagelueken, Hexian Huang, K. Harlos, Bradley R. Clarke, Chris Whitfield, James H. Naismith
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0015969

Crystal Structure of Spy0129, a Streptococcus pyogenes Class B Sortase Involved in Pilus Assembly
Cited by: 46
Author(s): Hae Joo Kang, F. Coulibaly, Thomas Proft, Edward N. Baker
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0096198

Structural Basis for the Site-Specific Incorporation of Lysine Derivatives into Proteins
Cited by: 16
Author(s): Veronika Flügel, Milan Vrábel, Sabine Schneider
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-14-S2-S1

New enumeration algorithm for protein structure comparison and classification
Cited by: 5
Author(s): Cody Ashby, Daniel Johnson, Karl Walker, Iyad A. Kanj, Ge Xia, Xiuzhen Huang
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.ppat.1000147

The Cysteine-Rich Interdomain Region from the Highly Variable Plasmodium falciparum Erythrocyte Membrane Protein-1 Exhibits a Conserved Structure
Cited by: 50
Author(s): Max M. Klein, Apostolos G. Gittis, Hua-Poo Su, Morris O. Makobongo, Jaime M. Moore, Sanjay Singh, Louis H. Miller, David N. Garboczi
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0205628

Minimal medical imaging can accurately reconstruct geometric bone models for musculoskeletal models
Cited by: 19
Author(s): Edin Suwarganda, Laura E. Diamond, David G. Lloyd, Thor F. Besier, Zhang Ju, Bryce A. Killen, Trevor N. Savage, David J. Saxby
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1003376

A Unique Spumavirus Gag N-terminal Domain with Functional Properties of Orthoretroviral Matrix and Capsid
Cited by: 28
Author(s): David C. Goldstone, Thomas G Flower, Neil J. Ball, Marta Sanz-Ramos, Melvyn W. Yap, R.W. Ogrodowicz, Nicole Stanke, Juliane Reh, Dirk Lindemann, Jonathan P. Stoye, Ian A. Taylor
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1003966

Insights into the Initiation of JC Virus DNA Replication Derived from the Crystal Structure of the T-Antigen Origin Binding Domain
Cited by: 12
Author(s): Gretchen Meinke, Paul J. Phelan, Radha L. Kalekar, Jong Shin, Jacques Archambault, Andrew Bohm, Peter A. Bullock
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0013559

Structural Studies of the Tandem Tudor Domains of Fragile X Mental Retardation Related Proteins FXR1 and FXR2
Cited by: 51
Author(s): Melanie A. Adams-Cioaba, Yahong Guo, Chuanbing Bian, M.F. Amaya, Robert Lam, Gregory A. Wasney, Masoud Vedadi, Chao Xu, Jinrong Min
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.ppat.1005362

Structural Based Analyses of the JC Virus T-Antigen F258L Mutant Provides Evidence for DNA Dependent Conformational Changes in the C-Termini of Polyomavirus Origin Binding Domains
Cited by: 6
Author(s): Gretchen Meinke, Paul J. Phelan, Jong Shin, David Gagnon, Jacques Archambault, Andrew Bohm, Peter A. Bullock
Software Mentions: 2
Published: almost 9 years ago

10.1002/prot.24915

The value of protein structure classification information-Surveying the scientific literature
Cited by: 19
Author(s): Naomi Fox, Steven E. Brenner, John-Marc Chandonia
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0002136

De-Orphaning the Structural Proteome through Reciprocal Comparison of Evolutionarily Important Structural Features
Cited by: 21
Author(s): R. Matthew Ward, Serkan Erdin, Tri M. Tran, David M. Kristensen, Andreas Martin Lisewski, Olivier Lichtarge
Software Mentions: 2
Published: over 16 years ago

10.1038/s41598-017-08742-z

Identification and Characterization of a Bacterial Homolog of Chloride Intracellular Channel (CLIC) Protein
Cited by: 18
Author(s): Shubha Gururaja Rao, Devasena Ponnalagu, Sowmya Sukur, Harkewal Singh, Shridhar Sanghvi, Yixiao Mei, Ding Jun Jin, Harpreet Singh
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0248190

Fungal GH25 muramidases: New family members with applications in animal nutrition and a crystal structure at 0.78Å resolution
Cited by: 3
Author(s): Olga V. Moroz, E.V. Blagova, Edward J. Taylor, J.P. Turkenburg, L.K. Skov, Garry P. Gippert, Kirk Schnorr, Ming Li, Ye Liu, Mikkel Klausen, Marianne Thorup Cohn, E. G. Schmidt, Søren Nymand-Grarup, G.J. Davies, K.S. Wilson
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-018-37908-6

OptiPharm: An evolutionary algorithm to compare shape similarity
Cited by: 13
Author(s): Savíns Puertas-Martín, Juana López Redondo, Pilar M. Ortigosa, Horacio Pérez‐Sánchez
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0154089

Bayesian State-Space Modelling of Conventional Acoustic Tracking Provides Accurate Descriptors of Home Range Behavior in a Small-Bodied Coastal Fish Species
Cited by: 26
Author(s): Josep Alós, Miquel Palmer, S. Balle, Robert Arlinghaus
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0021507

New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins
Cited by: 55
Author(s): Daniel J. Rigden, Duncan David Woodhead, Prudence W. H. Wong, Michael Y. Galperin
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0034263

A Glutathione Transferase from Agrobacterium tumefaciens Reveals a Novel Class of Bacterial GST Superfamily
Cited by: 25
Author(s): Katholiki Skopelitou, Prathusha Dhavala, Anastassios C. Papageorgiou, Nikolaos E. Labrou
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0026981

Structural Basis for Broad Neutralization of Hepatitis C Virus Quasispecies
Cited by: 12
Author(s): Pascal Lapierre, Myriam Troesch, Fernando Álvarez, Hugo Soudeyns
Software Mentions: 2
Published: about 13 years ago

10.1038/s41598-021-86567-7

Statistical shape modeling of the talocrural joint using a hybrid multi-articulation joint approach
Cited by: 14
Author(s): Amy L. Lenz, Nicola Krähenbühl, Andrew C. Peterson, Rich J. Lisonbee, Beat Hintermann, Charles L. Saltzman, Alexej Barg, Andrew E. Anderson
Software Mentions: 1
Published: over 3 years ago

10.3390/s20226554

Probabilistic Evaluation of 3D Surfaces Using Statistical Shape Models (SSM)
Cited by: 1
Author(s): Javier Sánchez Pérez, Jose-Luis Guardiola, Alberto Pérez, Juan-Carlos Pérez-Cortés
Software Mentions: 1
Published: almost 4 years ago

10.1128/mBio.01263-20

Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens
Cited by: 9
Author(s): Laura M. Carroll
Software Mentions: 1
Published: about 4 years ago

10.1128/mSphere.00226-17

Structural Characterization of Acidic M17 Leucine Aminopeptidases from the TriTryps and Evaluation of Their Role in Nutrient Starvation in Trypanosoma brucei
Cited by: 14
Author(s): Jennifer Timm, María Valente, Daniel García-Caballero, K.S. Wilson, Dolores González-Pacanowska
Software Mentions: 1
Published: about 7 years ago

10.1186/s13047-017-0216-3

Cross-sectional associations between variations in ankle shape by statistical shape modeling, injury history, and race: the Johnston County Osteoarthritis Project
Cited by: 10
Author(s): Amanda Nelson, Yvonne M. Golightly, Shahmeer Lateef, Jordan B. Renner, Joanne M. Jordan, Richard M. Aspden, Howard J. Hillstrom, Jennifer S. Gregory
Software Mentions: 1
Published: over 7 years ago

10.15171/ijhpm.2019.113

A Systems Thinking Approach to Inform Coherent Policy Action for NCD Prevention Comment on "How Neoliberalism Is Shaping the Supply of Unhealthy Commodities and What This Means for NCD Prevention"
Cited by: 2
Author(s): Penelope Milsom, Richard Smith, Helen Walls
Software Mentions: 1
Published: almost 5 years ago

10.1016/j.joca.2017.09.006

DXA-derived hip shape is related to osteoarthritis: findings from in the MrOS cohort
Cited by: 31
Author(s): Benjamin G Faber, Denis Baird, Celia L Gregson, Jennifer S. Gregory, Rebecca Barr, Richard M. Aspden, J.A. Lynch, Michael C. Nevitt, Nancy E Lane, Eric S. Orwoll, Jonathan H Tobias
Software Mentions: 1
Published: almost 7 years ago

10.1107/S090744491004117X

The Protein Data Bank in Europe (PDBe): bringing structure to biology
Cited by: 25
Author(s): Sameer Velankar, Gerard J. Kleywegt
Software Mentions: 1
Published: over 13 years ago

10.1107/S2053230X1401317X

The RpfC (Rv1884) atomic structure shows high structural conservation within the resuscitation-promoting factor catalytic domain
Cited by: 14
Author(s): Francois Xavier Chauviac, Giles Robertson, Doris H.X. Quay, Claire Bagnéris, Christian Dumas, Brian E. Henderson, John M. Ward, Nicholas H. Keep, Martin Cohen‐Gonsaud
Software Mentions: 1
Published: over 10 years ago

10.1107/S1744309111030879

Structure of aldose reductase fromGiardia lamblia
Cited by: 5
Author(s): Micah J. Ferrell, Jan Abendroth, Y. Zhang, Banumathi Sankaran, Thomas E. Edwards, Bart L. Staker, Wesley C. Van Voorhis, Lance Stewart, Peter J. Myler
Software Mentions: 1
Published: about 13 years ago

10.1107/S1744309111010220

BrabA.11339.a: anomalous diffraction and ligand binding guide towards the elucidation of the function of a `putative β-lactamase-like protein' fromBrucella melitensis
Cited by: 4
Author(s): Jan Abendroth, Banumathi Sankaran, Thomas E. Edwards, A.S. Gardberg, Shellie H. Dieterich, Janhavi Bhandari, Alberto J. Napuli, Wesley C. Van Voorhis, Bart L. Staker, Peter J. Myler, Lance Stewart
Software Mentions: 1
Published: about 13 years ago

10.1107/S174430911101493X

Structure of thymidylate kinase fromEhrlichia chaffeensis
Cited by: 2
Author(s): D.J. Leibly, Jan Abendroth, Cassie M. Bryan, Banumathi Sankaran, Angela Kelley, Lynn K. Barrett, Lance Stewart, Wesley C. Van Voorhis
Software Mentions: 1
Published: about 13 years ago

Projects: cran: SSM

Papers Mentioning SSM 183