Swati Jain
Zitiert von
Zitiert von
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
D Liebschner, PV Afonine, ML Baker, G Bunkóczi, VB Chen, TI Croll, ...
Acta Crystallographica Section D: Structural Biology 75 (10), 861-877, 2019
MolProbity: More and better reference data for improved all‐atom structure validation
CJ Williams, JJ Headd, NW Moriarty, MG Prisant, LL Videau, LN Deis, ...
Protein Science 27 (1), 293-315, 2018
The Phenix software for automated determination of macromolecular structures
PD Adams, PV Afonine, G Bunkóczi, VB Chen, N Echols, JJ Headd, ...
Methods 55 (1), 94-106, 2011
Generating Uniform Incremental Grids on SO(3) Using the Hopf Fibration
A Yershova, S Jain, SM Lavalle, JC Mitchell
The International journal of robotics research 29 (7), 801-812, 2010
Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element
T Schlick, Q Zhu, S Jain, S Yan
Biophysical journal 120 (6), 1040-1053, 2021
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage
GJ Kapral, S Jain, J Noeske, JA Doudna, DC Richardson, JS Richardson
Nucleic acids research 42 (20), 12833-12846, 2014
To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element
T Schlick, Q Zhu, A Dey, S Jain, S Yan, A Larderach
J. Am. Chem. Soc 143 (30), 11404–11422, 2021
Computational methods for RNA structure validation and improvement
S Jain, DC Richardson, JS Richardson
Methods in enzymology 558, 181-212, 2015
F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly
S Jain, T Schlick
Journal of molecular biology 429 (23), 3587-3605, 2017
Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression
S Yan, Q Zhu, S Jain, T Schlick
Research Square, 2022
BWM*: A novel, provable, ensemble-based dynamic programming algorithm for sparse approximations of computational protein design
JD Jou, S Jain, IS Georgiev, BR Donald
Journal of Computational Biology 23 (6), 413-424, 2016
A pipeline for computational design of novel RNA-like topologies
S Jain, A Laederach, SBV Ramos, T Schlick
Nucleic acids research 46 (14), 7040-7051, 2018
Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies
S Jain, Y Tao, T Schlick
Journal of structural biology 209 (3), 107438, 2020
An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures
S Jain, S Saju, L Petingi, T Schlick
Methods 162, 74-84, 2019
Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs
S Jain, C Bayrak, L Petingi, T Schlick
Genes 9 (8), 371, 2018
RAG-Web: RNA structure prediction/design using RNA-As-Graphs
G Meng, M Tariq, S Jain, S Elmetwaly, T Schlick
Bioinformatics 36 (2), 647-648, 2020
BWM*: a novel, provable, ensemble-based dynamic programming algorithm for sparse approximations of computational protein design
JD Jou, S Jain, I Georgiev, BR Donald
International Conference on Research in Computational Molecular Biology, 154-166, 2015
Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library
S Jain, Q Zhu, ASP Paz, T Schlick
Biochimica et Biophysica Acta (BBA)-General Subjects 1864 (6), 129534, 2020
A critical analysis of computational protein design with sparse residue interaction graphs
S Jain, JD Jou, IS Georgiev, BR Donald
PLOS Computational Biology 13 (3), e1005346, 2017
RNA 3D Structure Analysis and Validation, and Design Algorithms for Proteins and RNA
S Jain
Duke University, 2015
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