Research graph
References from Protein Binding Pocket Optimization for Virtual High-Throughput Screening (vHTS) Drug Discovery. Local targets link to admitted publications; unresolved targets remain external evidence.
EinfluSS der Konfiguration auf die Wirkung der Enzyme
10.1002/cber.18940270364 · 1894 · External reference
A geometric approach to macromolecule-ligand interactions
10.1016/0022-2836(82)90153-x · 1982 · External reference
Enzyme flexibility and enzyme action
10.1002/jcp.1030540420 · 1959 · External reference
Automated docking of substrates to proteins by simulated annealing
10.1002/prot.340080302 · 1990 · External reference
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
10.1371/journal.pcbi.1004586 · 2015 · External reference
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
10.1021/jm0306430 · 2004 · External reference
Improved protein-ligand docking using GOLD
10.1002/prot.10465 · 2003 · External reference
ICM-A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
10.1002/jcc.540150503 · 1994 · External reference
Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description
10.1016/j.abb.2015.08.002 · 2015 · External reference
Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions
10.1039/c0cp00151a · 2010 · External reference
“Soft docking”: matching of molecular surface cubes
10.1016/0022-2836(91)90859-5 · 1991 · External reference
Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis
10.1110/ps.041153605 · 2005 · External reference
Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins
10.1073/pnas.95.13.7406 · 1998 · External reference
ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility
10.1002/prot.21086 · 2006 · External reference
GlamDock: development and validation of a new docking tool on several thousand protein-ligand complexes
10.1021/ci7001236 · 2007 · External reference
LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
10.1016/s1093-3263(02)00164-x · 2003 · External reference
Predicting protein druggability
10.1016/s1359-6446(05)03624-x · 2005 · External reference
Docking and scoring with alternative side-chain conformations
10.1002/prot.22189 · 2009 · External reference
PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins
10.1093/nar/gkv462 · 2015 · External reference
FLIPDock: docking flexible ligands into flexible receptors
10.1002/prot.21423 · 2007 · External reference
Incorporation of side chain flexibility into protein binding pockets using MTflex
10.1016/j.bmc.2016.08.030 · 2016 · External reference
Ligand docking to proteins with discrete side-chain flexibility
10.1016/s0022-2836(05)80038-5 · 1994 · External reference
Applying Side-chain Flexibility in Motifs for Protein Docking
10.4137/gei.s29821 · 2015 · External reference
Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking
10.1021/jm800071v · 2008 · External reference
Side-chain flexibility in proteins upon ligand binding
10.1002/(sici)1097-0134(20000515)39:3<261::aid-prot90>3.0.co;2-4 · 2000 · External reference
Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation
10.1002/prot.1038 · 2001 · External reference
Ensemble Docking in Drug Discovery
10.1016/j.bpj.2018.02.038 · 2018 · External reference
Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs
10.1021/ci8004176 · 2009 · External reference
Docking ligands into flexible and solvated macromolecules. 7. Impact of protein flexibility and water molecules on docking-based virtual screening accuracy
10.1021/ci500299h · 2014 · External reference
Potential and limitations of ensemble docking
10.1021/ci2005934 · 2012 · External reference
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
10.1021/ct500381c · 2014 · External reference
Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding
10.1093/bioinformatics/bts395 · 2012 · External reference
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking
10.1021/jm300687e · 2012 · External reference
Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces
10.1021/acs.jcim.5b00182 · 2015 · External reference
Key Topics in Molecular Docking for Drug Design
10.3390/ijms20184574 · 2019 · External reference
Unveiling the full potential of flexible receptor docking using multiple crystallographic structures
10.1021/jm048972v · 2005 · External reference
Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations are Needed To Reproduce Known Ligand Binding?
10.1021/acs.jpcb.8b11491 · 2019 · External reference
Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23
10.1111/cbdd.13110 · 2018 · External reference
Virtual Screening Based on Ensemble Docking Targeting Wild-Type p53 for Anticancer Drug Discovery
10.1002/cbdv.201900170 · 2019 · External reference
Protein Binding Pocket Dynamics
10.1021/acs.accounts.5b00516 · 2016 · External reference
mkgridXf: Consistent Identification of Plausible Binding Sites Despite the Elusive Nature of Cavities and Grooves in Protein Dynamics
10.1021/acs.jcim.9b00103 · 2019 · External reference
Computer Simulation Study of Liquid CH2F2 with a New Effective Pair Potential Model
10.1063/1.477894 · 1999 · External reference
Grand-Canonical Ensemble Monte Carlo Simulation of Dense Fluids: Lennard-Jones, Soft Spheres and Water
10.1080/00268978700101321 · 1987 · External reference
Equation of State Calculations by Fast Computing Machines
10.1063/1.1699114 · 1953 · External reference
On the force bias Monte Carlo simulation of water: Methodology, optimization and comparison with molecular dynamics
10.1080/00268977900101321 · 1979 · External reference
The Anisotropic Virial-Biased Sampling for Monte Carlo Simulations in the Isobaric-Isothermal Ensemble
10.1080/00268979909482962 · 1999 · External reference
All-atom empirical potential for molecular modeling and dynamics studies of proteins
10.1021/jp973084f · 1998 · External reference
A new method for mapping macromolecular topography
10.1016/s1093-3263(02)00203-6 · 2003 · External reference
