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Items: 1 to 20 of 102


An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings.

Maffucci I, Hu X, Fumagalli V, Contini A.

Front Chem. 2018 Mar 5;6:43. doi: 10.3389/fchem.2018.00043. eCollection 2018.


Theoretical models of inhibitory activity for inhibitors of protein-protein interactions: targeting menin-mixed lineage leukemia with small molecules.

Jedwabny W, Kłossowski S, Purohit T, Cierpicki T, Grembecka J, Dyguda-Kazimierowicz E.

Medchemcomm. 2017 Dec 1;8(12):2216-2227. doi: 10.1039/c7md00170c. Epub 2017 Sep 12.


Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC).

Molano EPL, Cabrera OG, Jose J, do Nascimento LC, Carazzolle MF, Teixeira PJPL, Alvarez JC, Tiburcio RA, Tokimatu Filho PM, de Lima GMA, Guido RVC, Corrêa TLR, Leme AFP, Mieczkowski P, Pereira GAG.

BMC Genomics. 2018 Jan 17;19(1):58. doi: 10.1186/s12864-018-4440-4.


Systematic Testing of Belief-Propagation Estimates for Absolute Free Energies in Atomistic Peptides and Proteins.

Donovan-Maiye RM, Langmead CJ, Zuckerman DM.

J Chem Theory Comput. 2018 Jan 9;14(1):426-443. doi: 10.1021/acs.jctc.7b00775. Epub 2017 Dec 22.


Quantum mechanics implementation in drug-design workflows: does it really help?

Arodola OA, Soliman ME.

Drug Des Devel Ther. 2017 Aug 31;11:2551-2564. doi: 10.2147/DDDT.S126344. eCollection 2017. Review. Erratum in: Drug Des Devel Ther. 2017 Nov 08;11:3205.


Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints.

Liu J, Su M, Liu Z, Li J, Li Y, Wang R.

BMC Bioinformatics. 2017 Jul 18;18(1):343. doi: 10.1186/s12859-017-1750-5.


Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition.

Jedwabny W, Panecka-Hofman J, Dyguda-Kazimierowicz E, Wade RC, Sokalski WA.

J Comput Aided Mol Des. 2017 Aug;31(8):715-728. doi: 10.1007/s10822-017-0035-4. Epub 2017 Jul 7.


Micro-Environmental Signature of The Interactions between Druggable Target Protein, Dipeptidyl Peptidase-IV, and Anti-Diabetic Drugs.

Chakraborty C, Mallick B, Sharma AR, Sharma G, Jagga S, Doss CG, Nam JS, Lee SS.

Cell J. 2017 Apr-Jun;19(1):65-83. Epub 2016 Dec 21.


Prediction of kinase-inhibitor binding affinity using energetic parameters.

Usha S, Selvaraj S.

Bioinformation. 2016 Jun 15;12(3):172-181. doi: 10.6026/97320630012172. eCollection 2016.


Determination of locked interfaces in biomolecular complexes using Haptimol_RD.

Iakovou G, Laycock S, Hayward S.

Biophys Physicobiol. 2016 Jul 14;13:97-103. eCollection 2016.


Computational Methods Applied to Rational Drug Design.

Ramírez D.

Open Med Chem J. 2016 Apr 26;10:7-20. eCollection 2016.


Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.

Yilmazer ND, Korth M.

Int J Mol Sci. 2016 May 16;17(5). pii: E742. doi: 10.3390/ijms17050742. Review.


Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening.

Ain QU, Aleksandrova A, Roessler FD, Ballester PJ.

Wiley Interdiscip Rev Comput Mol Sci. 2015 Nov-Dec;5(6):405-424. Epub 2015 Aug 28. Review.


A Novel Scoring Based Distributed Protein Docking Application to Improve Enrichment.

Pradeep P, Struble C, Neumann T, Sem DS, Merrill SJ.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Nov-Dec;12(6):1464-9. doi: 10.1109/TCBB.2015.2401020.


Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs.

Lin CY, Wang CH, Hung CL, Lin YS.

Int J Genomics. 2015;2015:950905. doi: 10.1155/2015/950905. Epub 2015 Oct 13.


Energy Minimization on Manifolds for Docking Flexible Molecules.

Mirzaei H, Zarbafian S, Villar E, Mottarella S, Beglov D, Vajda S, Paschalidis ICh, Vakili P, Kozakov D.

J Chem Theory Comput. 2015 Mar 10;11(3):1063-76.


Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization.

Ibrahim TM, Bauer MR, Boeckler FM.

J Cheminform. 2015 May 20;7:21. doi: 10.1186/s13321-015-0074-6. eCollection 2015.


Structural dynamics and inhibitor searching for Wnt-4 protein using comparative computational studies.

Hammad MA, Azam SS.

Drug Des Devel Ther. 2015 Apr 29;9:2449-61. doi: 10.2147/DDDT.S79784. eCollection 2015.


Antiplasmodial activity of chloroquine analogs against chloroquine-resistant parasites, docking studies and mechanisms of drug action.

de Souza NB, Carmo AM, da Silva AD, França TC, Krettli AU.

Malar J. 2014 Dec 2;13:469. doi: 10.1186/1475-2875-13-469.


Using quantum mechanical approaches to study biological systems.

Merz KM Jr.

Acc Chem Res. 2014 Sep 16;47(9):2804-11. doi: 10.1021/ar5001023. Epub 2014 Jun 6.

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