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Results: 17

1.

Computational models of protein kinematics and dynamics: beyond simulation.

Gipson B, Hsu D, Kavraki LE, Latombe JC.

Annu Rev Anal Chem (Palo Alto Calif). 2012;5:273-91. doi: 10.1146/annurev-anchem-062011-143024. Epub 2012 Apr 9. Review.

PMID:
22524225
[PubMed - indexed for MEDLINE]
2.

Sampling-based exploration of folded state of a protein under kinematic and geometric constraints.

Yao P, Zhang L, Latombe JC.

Proteins. 2012 Jan;80(1):25-43. doi: 10.1002/prot.23134. Epub 2011 Oct 4.

PMID:
21971749
[PubMed - indexed for MEDLINE]
3.

Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories.

Chikalov I, Yao P, Moshkov M, Latombe JC.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S34. doi: 10.1186/1471-2105-12-S1-S34.

PMID:
21342565
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Markov dynamic models for long-timescale protein motion.

Chiang TH, Hsu D, Latombe JC.

Bioinformatics. 2010 Jun 15;26(12):i269-77. doi: 10.1093/bioinformatics/btq177.

PMID:
20529916
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers.

van den Bedem H, Dhanik A, Latombe JC, Deacon AM.

Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1107-17. doi: 10.1107/S0907444909030613. Epub 2009 Sep 16.

PMID:
19770508
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Efficient algorithms to explore conformation spaces of flexible protein loops.

Yao P, Dhanik A, Marz N, Propper R, Kou C, Liu G, van den Bedem H, Latombe JC, Halperin-Landsberg I, Altman RB.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Oct-Dec;5(4):534-45. doi: 10.1109/TCBB.2008.96.

PMID:
18989041
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Using stochastic roadmap simulation to predict experimental quantities in protein folding kinetics: folding rates and phi-values.

Chiang TH, Apaydin MS, Brutlag DL, Hsu D, Latombe JC.

J Comput Biol. 2007 Jun;14(5):578-93.

PMID:
17683262
[PubMed - indexed for MEDLINE]
8.

On the structure of the inverse kinematics map of a fragment of protein backbone.

Milgram RJ, Liu G, Latombe JC.

J Comput Chem. 2008 Jan 15;29(1):50-68.

PMID:
17542001
[PubMed - indexed for MEDLINE]
9.

Algorithm and data structures for efficient energy maintenance during Monte Carlo simulation of proteins.

Lotan I, Schwarzer F, Halperin D, Latombe JC.

J Comput Biol. 2004;11(5):902-32.

PMID:
15700409
[PubMed - indexed for MEDLINE]
10.

Real-space protein-model completion: an inverse-kinematics approach.

van den Bedem H, Lotan I, Latombe JC, Deacon AM.

Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):2-13. Epub 2004 Dec 17.

PMID:
15608370
[PubMed - indexed for MEDLINE]
11.

Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion.

Apaydin MS, Brutlag DL, Guestrin C, Hsu D, Latombe JC, Varma C.

J Comput Biol. 2003;10(3-4):257-81.

PMID:
12935328
[PubMed - indexed for MEDLINE]
12.

Using robotics to fold proteins and dock ligands.

Brutlag D, Apaydin S, Guestrin C, Hsu D, Varma C, Singh A, Latombe JC.

Bioinformatics. 2002;18 Suppl 2:S74.

PMID:
12385986
[PubMed - indexed for MEDLINE]
Free Article
13.

Stochastic roadmap simulation for the study of ligand-protein interactions.

Apaydin MS, Guestrin CE, Varma C, Brutlag DL, Latombe JC.

Bioinformatics. 2002;18 Suppl 2:S18-26.

PMID:
12385979
[PubMed - indexed for MEDLINE]
Free Article
14.

Algorithmic tools for real-time microsurgery simulation.

Brown J, Sorkin S, Latombe JC, Montgomery K, Stephanides M.

Med Image Anal. 2002 Sep;6(3):289-300.

PMID:
12270233
[PubMed - indexed for MEDLINE]
15.

Simulated learning environments in anatomy and surgery delivered via the next generation internet.

Dev P, Heinrichs WL, Srivastava S, Montgomery KN, Senger S, Temkin B, Hasser C, Latombe JC, Heegaard J, Youngblood P, Friedman CP, Waldron K.

Stud Health Technol Inform. 2001;84(Pt 2):1014-8.

PMID:
11604884
[PubMed - indexed for MEDLINE]
16.

A motion planning approach to flexible ligand binding.

Singh AP, Latombe JC, Brutlag DL.

Proc Int Conf Intell Syst Mol Biol. 1999:252-61.

PMID:
10786308
[PubMed - indexed for MEDLINE]
17.

CARABEAMER: a treatment planner for a robotic radiosurgical system with general kinematics.

Tombropoulos RZ, Adler JR, Latombe JC.

Med Image Anal. 1999 Sep;3(3):237-64.

PMID:
10710294
[PubMed - indexed for MEDLINE]

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