-
Notifications
You must be signed in to change notification settings - Fork 15
/
CITING_OSPREY.txt
51 lines (29 loc) · 4.18 KB
/
CITING_OSPREY.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
We ask that users of OSPREY cite the following papers, and also mention the name OSPREY, when presenting results from or extensions to OSPREY in papers, patents, and conference presentations. OSPREY relies on grants for its development, and to get grants it's essential for the impacts of OSPREY to be visible in the scientific literature.
For all work using the version of OSPREY in this repository (OSPREY 3.0), we ask users to mention the name OSPREY and cite the following paper. This is a recently accepted manuscript whose preprint is currently available on BioRxiv, and we will update the citation as it moves through the review process:
Mark A. Hallen, Jeffrey W. Martin, Adegoke Ojewole, Jonathan D. Jou, Anna U. Lowegard, Marcel S. Frenkel, Pablo Gainza, Hunter M. Nisonoff, Aditya Mukund, Siyu Wang, Graham T. Holt, David Zhou, Elizabeth Dowd, Bruce R. Donald. OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features. Journal of Computational Chemistry 2018; 39(30): 2494-2507;
URL: https://onlinelibrary.wiley.com/doi/10.1002/jcc.25522
We also ask users to cite the following papers for specific modules in OSPREY:
iMinDEE:
P. Gainza, K.E. Roberts, and B.R. Donald. Protein Design using Continuous Rotamers. PLoS Computational Biology, (1): e1002335. doi:10.1371/journal.pcbi.1002335, 2012.
Protein:Protein Interactions:
K. Roberts, P. Cushing, P. Boisguerin, D. Madden, and B. R. Donald. Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity. PLoS Computational Biology 2012; 8(4): e1002477. doi:10.1371/journal.pcbi.1002477.
minDEE/K*:
I. Georgiev, R. Lilien, and B. R. Donald. The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. J Comput Chem, 29(10):1527–42, 2008.
To cite the general idea of K*, you can also cite:
R. Lilien, B. Stevens, A. Anderson, and B. R. Donald. A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the Gramicidin Synthetase A phenylalanine adenylation enzyme. J Comp Biol, 12(6–7):740–761, 2005.
CATS:
Mark A. Hallen and Bruce R. Donald. CATS (Coordinates of Atoms by Taylor Series): Protein design with backbone flexibility in all locally feasible directions. Bioinformatics (2017) 33 (14): i5-i12.
BBK*:
A. Ojewole, J. Jou, V. Fowler, and B. R. Donald. BBK* (Branch and Bound over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces. Journal of Computational Biology 2018 (Accepted; in press).
LUTE:
M. A. Hallen, J. D. Jou, and B. R. Donald. LUTE (Local Unpruned Tuple Expansion): Accurate continuously flexible protein design with general energy functions and rigid-rotamer-like efficiency. Journal of Computational Biology 2016 Sep 28;24(6):536. PMID: 27681371
COMETS:
M. A. Hallen and B. R. Donald. COMETS (Constrained Optimization of Multistate Energies by Tree Search): A provable and efficient protein design algorithm to optimize binding affinity and specificity with respect to sequence. Journal of Computational Biology 2016;23(5):311.
BWM*:
J. Jou, S. Jain, I. Georgiev, and B. R. Donald. BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. Journal of Computational Biology 2016;23(6):413.
A* with MPLP and dynamic ordering:
K. E. Roberts, P. Gainza, M. A. Hallen, and B. R. Donald. Fast Gap-Free Enumeration of Conformations and Sequences for Protein Design. Proteins (2015) doi: 10.1002/prot.24870 volume 83 issue 10 pages 1859-1877.
EPIC:
M. Hallen, P. Gainza, and B. R. Donald. A compact representation of continuous energy surfaces for more efficient protein design. Journal of Chemical Theory and Computation. 2015; 11(5):2292-2306.
DEEPer:
M. Hallen, D. Keedy, and B. R. Donald. Dead-End Elimination with Perturbations (`DEEPer'): A provable protein design algorithm with continuous sidechain and backbone flexibility. Proteins 2013; 80(1):18-39. DOI: 10.1002/prot.24150.