185 related articles for article (PubMed ID: 23728619)
1. A homology/ab initio hybrid algorithm for sampling near-native protein conformations.
Dhingra P; Jayaram B
J Comput Chem; 2013 Aug; 34(22):1925-36. PubMed ID: 23728619
[TBL] [Abstract][Full Text] [Related]
2. Bhageerath-H: a homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins.
Jayaram B; Dhingra P; Mishra A; Kaushik R; Mukherjee G; Singh A; Shekhar S
BMC Bioinformatics; 2014; 15 Suppl 16(Suppl 16):S7. PubMed ID: 25521245
[TBL] [Abstract][Full Text] [Related]
3. Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins.
Jayaram B; Bhushan K; Shenoy SR; Narang P; Bose S; Agrawal P; Sahu D; Pandey V
Nucleic Acids Res; 2006; 34(21):6195-204. PubMed ID: 17090600
[TBL] [Abstract][Full Text] [Related]
4. LOOPER: a molecular mechanics-based algorithm for protein loop prediction.
Spassov VZ; Flook PK; Yan L
Protein Eng Des Sel; 2008 Feb; 21(2):91-100. PubMed ID: 18194981
[TBL] [Abstract][Full Text] [Related]
5. TOUCHSTONE II: a new approach to ab initio protein structure prediction.
Zhang Y; Kolinski A; Skolnick J
Biophys J; 2003 Aug; 85(2):1145-64. PubMed ID: 12885659
[TBL] [Abstract][Full Text] [Related]
6. Protein structure evaluation using an all-atom energy based empirical scoring function.
Narang P; Bhushan K; Bose S; Jayaram B
J Biomol Struct Dyn; 2006 Feb; 23(4):385-406. PubMed ID: 16363875
[TBL] [Abstract][Full Text] [Related]
7. Fold recognition and ab initio structure predictions using hidden Markov models and beta-strand pair potentials.
Hubbard TJ; Park J
Proteins; 1995 Nov; 23(3):398-402. PubMed ID: 8710832
[TBL] [Abstract][Full Text] [Related]
8. Heuristic-based tabu search algorithm for folding two-dimensional AB off-lattice model proteins.
Liu J; Sun Y; Li G; Song B; Huang W
Comput Biol Chem; 2013 Dec; 47():142-8. PubMed ID: 24077543
[TBL] [Abstract][Full Text] [Related]
9. Benchmarking of TASSER in the ab initio limit.
Borreguero JM; Skolnick J
Proteins; 2007 Jul; 68(1):48-56. PubMed ID: 17444524
[TBL] [Abstract][Full Text] [Related]
10. From Ramachandran Maps to Tertiary Structures of Proteins.
DasGupta D; Kaushik R; Jayaram B
J Phys Chem B; 2015 Aug; 119(34):11136-45. PubMed ID: 26098815
[TBL] [Abstract][Full Text] [Related]
11. A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation.
Kosinski J; Cymerman IA; Feder M; Kurowski MA; Sasin JM; Bujnicki JM
Proteins; 2003; 53 Suppl 6():369-79. PubMed ID: 14579325
[TBL] [Abstract][Full Text] [Related]
12. Probabilistic search and energy guidance for biased decoy sampling in ab initio protein structure prediction.
Molloy K; Saleh S; Shehu A
IEEE/ACM Trans Comput Biol Bioinform; 2013; 10(5):1162-75. PubMed ID: 24384705
[TBL] [Abstract][Full Text] [Related]
13. TOUCHSTONE: a unified approach to protein structure prediction.
Skolnick J; Zhang Y; Arakaki AK; Kolinski A; Boniecki M; Szilágyi A; Kihara D
Proteins; 2003; 53 Suppl 6():469-79. PubMed ID: 14579335
[TBL] [Abstract][Full Text] [Related]
14. 3DRobot: automated generation of diverse and well-packed protein structure decoys.
Deng H; Jia Y; Zhang Y
Bioinformatics; 2016 Feb; 32(3):378-87. PubMed ID: 26471454
[TBL] [Abstract][Full Text] [Related]
15. A Novel Method Using Abstract Convex Underestimation in Ab-Initio Protein Structure Prediction for Guiding Search in Conformational Feature Space.
Hao XH; Zhang GJ; Zhou XG; Yu XF
IEEE/ACM Trans Comput Biol Bioinform; 2016; 13(5):887-900. PubMed ID: 26552093
[TBL] [Abstract][Full Text] [Related]
16. Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction.
Brasil CR; Delbem AC; da Silva FL
J Comput Chem; 2013 Jul; 34(20):1719-34. PubMed ID: 23666867
[TBL] [Abstract][Full Text] [Related]
17. How well can we predict native contacts in proteins based on decoy structures and their energies?
Zhu J; Zhu Q; Shi Y; Liu H
Proteins; 2003 Sep; 52(4):598-608. PubMed ID: 12910459
[TBL] [Abstract][Full Text] [Related]
18. Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding.
Mishra A; Rao S; Mittal A; Jayaram B
Biochim Biophys Acta; 2013 Aug; 1834(8):1520-31. PubMed ID: 23665455
[TBL] [Abstract][Full Text] [Related]
19. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model.
Felts AK; Gallicchio E; Wallqvist A; Levy RM
Proteins; 2002 Aug; 48(2):404-22. PubMed ID: 12112706
[TBL] [Abstract][Full Text] [Related]
20. Contact order and ab initio protein structure prediction.
Bonneau R; Ruczinski I; Tsai J; Baker D
Protein Sci; 2002 Aug; 11(8):1937-44. PubMed ID: 12142448
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
