articles
- Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4 2019
- D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU 2019
- Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison. 33:307-330. 2019
- Enabling drug discovery project decisions with integrated computational chemistry and informatics. 31:287-291. 2017
- A probabilistic method to report predictions from a human liver microsomes stability QSAR model: a practical tool for drug discovery. 29:327-338. 2015
- An integrated suite of modeling tools that empower scientists in structure- and property-based drug design. 29:511-523. 2015
- In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. 29:79-87. 2015
- Blind prediction of HIV integrase binding from the SAMPL4 challenge. 28:327-345. 2014
- Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. 28:475-490. 2014
- Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge. 28:429-441. 2014
- NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41. 27:569-582. 2013
- Modeling the evolution of drug resistance in malaria. 26:1343-1353. 2012
- Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for gpcr modulators. 23:273-288. 2009
- Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives. 22:29-38. 2008
- Protein-ligand docking with multiple flexible side chains. 22:673-679. 2008
- Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase i7l using homology modeling and covalent docking approaches. 21:549-558. 2007
- A very large diversity space of synthetically accessible compounds for use with drug design programs. 19:47-63. 2005
- Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. 17:525-536. 2003
- Do active site conformations of small ligands correspond to low free-energy solution structures?. 12:563-572. 1998
- Design of stapled DNA-minor-groove-binding molecules with a mutable atom simulated annealing method. 11:539-546. 1997
- Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. 10:293-304. 1996
- Geom - a new tool for molecular modeling based on distance geometry calculations with NMR data. 3:195-210. 1989