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1.
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method.
J Chem Inf Model
; 63(21): 6655-6666, 2023 11 13.
Artículo
en Inglés
| MEDLINE | ID: mdl-37847557
2.
Improved Protein-Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference.
J Chem Inf Model
; 61(4): 1583-1592, 2021 04 26.
Artículo
en Inglés
| MEDLINE | ID: mdl-33754707
3.
A method to predict blood-brain barrier permeability of drug-like compounds using molecular dynamics simulations.
Biophys J
; 107(3): 630-641, 2014 Aug 05.
Artículo
en Inglés
| MEDLINE | ID: mdl-25099802
4.
Toward fully automated high performance computing drug discovery: a massively parallel virtual screening pipeline for docking and molecular mechanics/generalized Born surface area rescoring to improve enrichment.
J Chem Inf Model
; 54(1): 324-37, 2014 Jan 27.
Artículo
en Inglés
| MEDLINE | ID: mdl-24358939
5.
Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines.
J Comput Chem
; 34(11): 915-27, 2013 Apr 30.
Artículo
en Inglés
| MEDLINE | ID: mdl-23345155
6.
Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity.
Bioorg Med Chem Lett
; 23(5): 1529-36, 2013 Mar 01.
Artículo
en Inglés
| MEDLINE | ID: mdl-23352267
7.
Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE), Part II: development of inhibitors with broad spectrum, Gram-negative antibacterial activity.
Bioorg Med Chem Lett
; 23(5): 1537-43, 2013 Mar 01.
Artículo
en Inglés
| MEDLINE | ID: mdl-23294697
8.
Molecular recognition of aromatic rings by flavin: electrostatics and dispersion determine ring positioning above isoalloxazine.
J Phys Chem A
; 117(48): 12946-52, 2013 Dec 05.
Artículo
en Inglés
| MEDLINE | ID: mdl-24229368
9.
Toward a small molecule, biomimetic carbonic anhydrase model: theoretical and experimental investigations of a panel of zinc(II) aza-macrocyclic catalysts.
Inorg Chem
; 51(12): 6803-12, 2012 Jun 18.
Artículo
en Inglés
| MEDLINE | ID: mdl-22671132
10.
Effects of somatic mutations on CDR loop flexibility during affinity maturation.
Proteins
; 79(3): 821-9, 2011 Mar.
Artículo
en Inglés
| MEDLINE | ID: mdl-21287614
11.
E9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study.
J Phys Chem B
; 112(51): 16802-14, 2008 Dec 25.
Artículo
en Inglés
| MEDLINE | ID: mdl-19053689
12.
Efficient Computational Modeling of Human Ventricular Activation and Its Electrocardiographic Representation: A Sensitivity Study.
Cardiovasc Eng Technol
; 9(3): 447-467, 2018 09.
Artículo
en Inglés
| MEDLINE | ID: mdl-29549620
13.
Competition between intramolecular hydrogen bonds and solvation in phosphorylated peptides: simulations with explicit and implicit solvent.
J Phys Chem B
; 109(11): 5249-58, 2005 Mar 24.
Artículo
en Inglés
| MEDLINE | ID: mdl-16863191
14.
Understanding a substrate's product regioselectivity in a family of enzymes: a case study of acetaminophen binding in cytochrome P450s.
PLoS One
; 9(2): e87058, 2014.
Artículo
en Inglés
| MEDLINE | ID: mdl-24498291
15.
Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines.
PLoS One
; 9(9): e106298, 2014.
Artículo
en Inglés
| MEDLINE | ID: mdl-25191698
16.
Developing an approach for first-principles catalyst design: application to carbon-capture catalysis.
Acta Crystallogr C Struct Chem
; 70(Pt 2): 123-31, 2014 Feb.
Artículo
en Inglés
| MEDLINE | ID: mdl-24508957
17.
Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap.
Expert Opin Drug Discov
; 8(3): 277-87, 2013 Mar.
Artículo
en Inglés
| MEDLINE | ID: mdl-23286874
18.
Rapid catalytic template searching as an enzyme function prediction procedure.
PLoS One
; 8(5): e62535, 2013.
Artículo
en Inglés
| MEDLINE | ID: mdl-23675414
19.
Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics.
J Chem Theory Comput
; 9(3): 1320-7, 2013 Mar 12.
Artículo
en Inglés
| MEDLINE | ID: mdl-26587594
20.
Comparison and analysis of zinc and cobalt-based systems as catalytic entities for the hydration of carbon dioxide.
PLoS One
; 8(6): e66187, 2013.
Artículo
en Inglés
| MEDLINE | ID: mdl-23840420