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Items: 1 to 50 of 56

1.

Can One Trust Kinetic and Thermodynamic Observables from Biased Metadynamics Simulations?: Detailed Quantitative Benchmarks on Millimolar Drug Fragment Dissociation.

Pramanik D, Smith Z, Kells A, Tiwary P.

J Phys Chem B. 2019 May 2;123(17):3672-3678. doi: 10.1021/acs.jpcb.9b01813. Epub 2019 Apr 22.

PMID:
30974941
2.

Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization.

Smith Z, Pramanik D, Tsai ST, Tiwary P.

J Chem Phys. 2018 Dec 21;149(23):234105. doi: 10.1063/1.5064856.

PMID:
30579304
3.

Kinetics of Ligand-Protein Dissociation from All-Atom Simulations: Are We There Yet?

Ribeiro JML, Tsai ST, Pramanik D, Wang Y, Tiwary P.

Biochemistry. 2019 Jan 22;58(3):156-165. doi: 10.1021/acs.biochem.8b00977. Epub 2018 Dec 28.

PMID:
30547565
4.

Colored dots on trichoscopy-beware of artifacts.

Sonthalia S, Tiwary P.

J Am Acad Dermatol. 2019 Jun;80(6):e143-e144. doi: 10.1016/j.jaad.2018.11.052. Epub 2018 Dec 6. No abstract available.

PMID:
30529542
5.

Toward Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE.

Lamim Ribeiro JM, Tiwary P.

J Chem Theory Comput. 2019 Jan 8;15(1):708-719. doi: 10.1021/acs.jctc.8b00869. Epub 2018 Dec 24.

PMID:
30525598
6.

Frequency adaptive metadynamics for the calculation of rare-event kinetics.

Wang Y, Valsson O, Tiwary P, Parrinello M, Lindorff-Larsen K.

J Chem Phys. 2018 Aug 21;149(7):072309. doi: 10.1063/1.5024679.

PMID:
30134721
7.

Reweighted autoencoded variational Bayes for enhanced sampling (RAVE).

Ribeiro JML, Bravo P, Wang Y, Tiwary P.

J Chem Phys. 2018 Aug 21;149(7):072301. doi: 10.1063/1.5025487.

PMID:
30134694
8.

A Comparison of Intrathecal Dexmedetomidine and Neostigmine as Adjuvant to Ropivacaine for Lower Limb Surgeries: A Double-blind Randomized Controlled Study.

Singh AK, Kumar A, Kumar A, Prasad BK, Tiwary PK, Kumar R.

Anesth Essays Res. 2017 Oct-Dec;11(4):987-992. doi: 10.4103/aer.AER_62_17.

9.

Identification and Functional Validation of a Biomarker for the Diagnosis of Miltefosine Relapse during Visceral Leishmaniasis.

Tiwary P, Kumar D, Sundar S.

Am J Trop Med Hyg. 2018 Feb;98(2):492-496. doi: 10.4269/ajtmh.16-0983. Epub 2017 Dec 21.

10.

Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin-Streptavidin.

Tiwary P.

J Phys Chem B. 2017 Dec 7;121(48):10841-10849. doi: 10.1021/acs.jpcb.7b09510. Epub 2017 Nov 21.

PMID:
29117680
11.

Predicting reaction coordinates in energy landscapes with diffusion anisotropy.

Tiwary P, Berne BJ.

J Chem Phys. 2017 Oct 21;147(15):152701. doi: 10.1063/1.4983727.

12.

Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations.

Salvalaglio M, Tiwary P, Maggioni GM, Mazzotti M, Parrinello M.

J Chem Phys. 2016 Dec 7;145(21):211925. doi: 10.1063/1.4966265.

PMID:
28799374
13.

Effect of Agonist and Antagonist on the In Vitro Contractility of Inflamed Vermiform Appendix.

Singh PB, Tiwary P, Singh SK, Pandey R, Roy A, Kar AG, Basu S, Tiwari AK.

J Clin Diagn Res. 2017 Jun;11(6):CC25-CC30. doi: 10.7860/JCDR/2017/28804.10124. Epub 2017 Jun 1.

14.

Styloid Process Fracture Associated With Maxillofacial Trauma: Incidence, Distribution, and Management.

Tiwary P, Sahoo N, Thakral A, Ranjan U.

J Oral Maxillofac Surg. 2017 Oct;75(10):2177-2182. doi: 10.1016/j.joms.2017.06.016. Epub 2017 Jun 23.

PMID:
28697349
15.

How and when does an anticancer drug leave its binding site?

Tiwary P, Mondal J, Berne BJ.

Sci Adv. 2017 May 31;3(5):e1700014. doi: 10.1126/sciadv.1700014. eCollection 2017 May.

16.

Establishing, Expanding, and Certifying a Closed Colony of Phlebotomus argentipes (Diptera: Psychodidae) for Xenodiagnostic Studies at the Kala Azar Medical Research Center, Muzaffarpur, Bihar, India.

Tiwary P, Singh SK, Kushwaha AK, Rowton E, Sacks D, Singh OP, Sundar S, Lawyer P.

J Med Entomol. 2017 Sep 1;54(5):1129-1139. doi: 10.1093/jme/tjx099.

17.

Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration.

Kannan M, Li J, Fritz SE, Husarek KE, Sanford JC, Sullivan TL, Tiwary PK, An W, Boeke JD, Symer DE.

Mob DNA. 2017 May 10;8:8. doi: 10.1186/s13100-017-0091-2. eCollection 2017.

18.

Kinetics of Ligand Binding Through Advanced Computational Approaches: A Review.

Dickson A, Tiwary P, Vashisth H.

Curr Top Med Chem. 2017;17(23):2626-2641. doi: 10.2174/1568026617666170414142908. Review.

PMID:
28413946
19.

A Dermoscopic Diagnosis and Activity Evaluation of Frontal Fibrosing Alopecia in an Indian Lady.

Sonthalia S, Jha AK, Tiwary PK.

Indian Dermatol Online J. 2017 Mar-Apr;8(2):162-163. doi: 10.4103/idoj.IDOJ_307_16. No abstract available.

20.

Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations.

Casasnovas R, Limongelli V, Tiwary P, Carloni P, Parrinello M.

J Am Chem Soc. 2017 Apr 5;139(13):4780-4788. doi: 10.1021/jacs.6b12950. Epub 2017 Mar 24.

PMID:
28290199
21.

How wet should be the reaction coordinate for ligand unbinding?

Tiwary P, Berne BJ.

J Chem Phys. 2016 Aug 7;145(5):054113. doi: 10.1063/1.4959969.

22.

Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations.

Clark AJ, Tiwary P, Borrelli K, Feng S, Miller EB, Abel R, Friesner RA, Berne BJ.

J Chem Theory Comput. 2016 Jun 14;12(6):2990-8. doi: 10.1021/acs.jctc.6b00201. Epub 2016 May 13.

PMID:
27145262
23.

Kramers turnover: From energy diffusion to spatial diffusion using metadynamics.

Tiwary P, Berne BJ.

J Chem Phys. 2016 Apr 7;144(13):134103. doi: 10.1063/1.4944577.

24.

Pacemaker lead Candida endocarditis: Is medical treatment possible?

Bandyopadhyay S, Tiwary PK, Mondal S, Puthran S.

Indian Heart J. 2015 Dec;67 Suppl 3:S100-2. doi: 10.1016/j.ihj.2015.11.025. Epub 2015 Dec 23. No abstract available.

25.

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint.

Valsson O, Tiwary P, Parrinello M.

Annu Rev Phys Chem. 2016 May 27;67:159-84. doi: 10.1146/annurev-physchem-040215-112229. Epub 2016 Mar 10.

PMID:
26980304
26.

How a Kinase Inhibitor Withstands Gatekeeper Residue Mutations.

Mondal J, Tiwary P, Berne BJ.

J Am Chem Soc. 2016 Apr 6;138(13):4608-15. doi: 10.1021/jacs.6b01232. Epub 2016 Mar 22.

PMID:
26954686
27.

Spectral gap optimization of order parameters for sampling complex molecular systems.

Tiwary P, Berne BJ.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):2839-44. doi: 10.1073/pnas.1600917113. Epub 2016 Feb 29.

28.

A perturbative solution to metadynamics ordinary differential equation.

Tiwary P, Dama JF, Parrinello M.

J Chem Phys. 2015 Dec 21;143(23):234112. doi: 10.1063/1.4937945.

PMID:
26696051
29.

New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations.

Fleming KL, Tiwary P, Pfaendtner J.

J Phys Chem A. 2016 Jan 21;120(2):299-305. doi: 10.1021/acs.jpca.5b10667. Epub 2016 Jan 7.

PMID:
26690335
30.

Path Integral Metadynamics.

Quhe R, Nava M, Tiwary P, Parrinello M.

J Chem Theory Comput. 2015 Apr 14;11(4):1383-8. doi: 10.1021/ct501002a. Epub 2015 Mar 6.

PMID:
26574350
31.

de Broglie Swapping Metadynamics for Quantum and Classical Sampling.

Nava M, Quhe R, Palazzesi F, Tiwary P, Parrinello M.

J Chem Theory Comput. 2015 Nov 10;11(11):5114-9. doi: 10.1021/acs.jctc.5b00818. Epub 2015 Oct 23.

PMID:
26574309
32.

Role of water and steric constraints in the kinetics of cavity-ligand unbinding.

Tiwary P, Mondal J, Morrone JA, Berne BJ.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):12015-9. doi: 10.1073/pnas.1516652112. Epub 2015 Sep 14.

33.

Variationally Optimized Free-Energy Flooding for Rate Calculation.

McCarty J, Valsson O, Tiwary P, Parrinello M.

Phys Rev Lett. 2015 Aug 14;115(7):070601. Epub 2015 Aug 10.

PMID:
26317704
34.

Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps.

Tiwary P, Limongelli V, Salvalaglio M, Parrinello M.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):E386-91. doi: 10.1073/pnas.1424461112. Epub 2015 Jan 20.

35.

Association of interleukin-18 gene polymorphism with susceptibility to visceral leishmaniasis in endemic area of Bihar, an Indian population.

Kumar D, Tiwary P, Chakravarty J, Sundar S.

ScientificWorldJournal. 2014;2014:852104. doi: 10.1155/2014/852104. Epub 2014 Oct 22.

36.

A time-independent free energy estimator for metadynamics.

Tiwary P, Parrinello M.

J Phys Chem B. 2015 Jan 22;119(3):736-42. doi: 10.1021/jp504920s. Epub 2014 Jul 21.

PMID:
25046020
37.

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics.

Salvalaglio M, Tiwary P, Parrinello M.

J Chem Theory Comput. 2014 Apr 8;10(4):1420-5. doi: 10.1021/ct500040r. Epub 2014 Mar 10.

PMID:
26580360
38.

From metadynamics to dynamics.

Tiwary P, Parrinello M.

Phys Rev Lett. 2013 Dec 6;111(23):230602. Epub 2013 Dec 3.

PMID:
24476246
39.

Comparative evaluation of blood and serum samples in rapid immunochromatographic tests for visceral leishmaniasis.

Kumar D, Khanal B, Tiwary P, Mudavath SL, Tiwary NK, Singh R, Koirala K, Boelaert M, Rijal S, Sundar S.

J Clin Microbiol. 2013 Dec;51(12):3955-9. doi: 10.1128/JCM.01232-13. Epub 2013 Sep 18.

40.

Epidemiology of diabetes mellitus in young population in rural districts of northern Bihar.

Tewary K, Singh VK, Singh SK, Tiwary P, Garg A, Joshi KK.

J Indian Med Assoc. 2013 Feb;111(2):103-6.

PMID:
24003567
41.

Seasonal variation in the prevalence of sand flies infected with Leishmania donovani.

Tiwary P, Kumar D, Mishra M, Singh RP, Rai M, Sundar S.

PLoS One. 2013 Apr 9;8(4):e61370. doi: 10.1371/journal.pone.0061370. Print 2013.

42.

Molecular and serological markers of Leishmania donovani infection in healthy individuals from endemic areas of Bihar, India.

Srivastava P, Gidwani K, Picado A, Van der Auwera G, Tiwary P, Ostyn B, Dujardin JC, Boelaert M, Sundar S.

Trop Med Int Health. 2013 May;18(5):548-54. doi: 10.1111/tmi.12085. Epub 2013 Mar 7.

43.

Cloning, Expression and Purification of L. Donovani Specific Antigen for Serodiagnosis of Visceral Leishmaniasis.

Kumar D, Tiwary P, Dube A, Chakravarty J, Rai M, Sundar S.

J Mol Biomark Diagn. 2013 Jan 31;4(1):1000141.

45.

Epidemiological trends of leprosy in an urban leprosy centre of Delhi: a retrospective study of 16 years.

Tiwary PK, Kar HK, Sharma PK, Gautam RK, Arora TC, Naik H, Dhir V.

Indian J Lepr. 2011 Oct-Dec;83(4):201-8.

PMID:
22783754
46.

Genetic and functional evaluation of the role of DLL1 in susceptibility to visceral leishmaniasis in India.

Mehrotra S, Fakiola M, Mishra A, Sudarshan M, Tiwary P, Rani DS, Thangaraj K, Rai M, Sundar S, Blackwell JM.

Infect Genet Evol. 2012 Aug;12(6):1195-201. doi: 10.1016/j.meegid.2012.04.017. Epub 2012 Apr 24.

47.

Prevalence of sand flies and Leishmania donovani infection in a natural population of female Phlebotomus argentipes in Bihar State, India.

Tiwary P, Kumar D, Singh RP, Rai M, Sundar S.

Vector Borne Zoonotic Dis. 2012 Jun;12(6):467-72. doi: 10.1089/vbz.2011.0808. Epub 2012 Jan 4.

48.

Genetic and functional evaluation of the role of CXCR1 and CXCR2 in susceptibility to visceral leishmaniasis in north-east India.

Mehrotra S, Fakiola M, Oommen J, Jamieson SE, Mishra A, Sudarshan M, Tiwary P, Rani DS, Thangaraj K, Rai M, Sundar S, Blackwell JM.

BMC Med Genet. 2011 Dec 15;12:162. doi: 10.1186/1471-2350-12-162.

49.

No evidence for association between SLC11A1 and visceral leishmaniasis in India.

Mehrotra S, Oommen J, Mishra A, Sudharshan M, Tiwary P, Jamieson SE, Fakiola M, Rani DS, Thangaraj K, Rai M, Sundar S, Blackwell JM.

BMC Med Genet. 2011 May 20;12:71. doi: 10.1186/1471-2350-12-71.

50.

Diagnosis of Indian visceral leishmaniasis by nucleic acid detection using PCR.

Srivastava P, Mehrotra S, Tiwary P, Chakravarty J, Sundar S.

PLoS One. 2011 Apr 29;6(4):e19304. doi: 10.1371/journal.pone.0019304.

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