相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Current Status of the AMOEBA Polarizable Force Field
Jay W. Ponder et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Do salt bridges stabilize proteins? A continuum electrostatic analysis
Zachary S. Hendsch et al.
PROTEIN SCIENCE (2010)
Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein-Ligand Docking Results
Tim ten Brink et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions
Robert S. Paton et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
The AGBNP2 Implicit Solvation Model
Emilio Gallicchio et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Effects of the biological backbone on DNA-protein stacking interactions
Cassandra D. M. Churchill et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2009)
Prediction of protein loop conformations using the AGBNP implicit solvent model and torsion angle sampling
Anthony K. Felts et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Self-contacts in Asx and Glx residues of high-resolution protein structures: Role of local environment and tertiary interactions
Tuhin Kumar Pal et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2008)
Recognition of a flipped base in a hairpinloop DNA by a small peptide
Junji Kawakami et al.
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS (2008)
Toward better refinement of comparative models: Predicting loops in inexact environments
Benjamin D. Sellers et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)
Improved methods for side chain and loop predictions via the protein local optimization program: Variable dielectric model for implicitly improving the treatment of polarization effects
Kai Zhu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling
Xin Li et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
Histidine/tryptophan π-stacking interaction stabilizes the heme-independent folding core of microsomal apocytochrome b5 relative to that of mitochondrial apocytochrome b5
Lijun Wang et al.
BIOCHEMISTRY (2006)
Long loop prediction using the protein local optimization program
Kai Zhu et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Protein-ligand docking: Current status and future challenges
Sergio Filipe Sousa et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Structure selection for protein kinase docking and virtual screening: Homology models or crystal structures?
William M. Rockey et al.
CURRENT PROTEIN & PEPTIDE SCIENCE (2006)
Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
Jason A. Wagoner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling in decalysine
M Machuqueiro et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
What role do surfaces play in GB models? A new-generation of surface-generalized Born model based on a novel Gaussian surface for biomolecules
ZY Yu et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
P Jurecka et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2006)
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
P Yakovchuk et al.
NUCLEIC ACIDS RESEARCH (2006)
Investigation of salt bridge stability in a generalized born solvent model
R Geney et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Comparative study of generalized Born models: Protein dynamics
H Fan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Structure-based drug discovery using GPCR homology modeling: Successful virtual screening for antagonists of the Alpha1A adrenergic receptor
A Evers et al.
JOURNAL OF MEDICINAL CHEMISTRY (2005)
A hierarchical approach to all-atom protein loop prediction
MP Jacobson et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
Virtual screening for kinase targets
I Muegge et al.
CURRENT MEDICINAL CHEMISTRY (2004)
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
E Gallicchio et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
M Feig et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Highly accurate coupled cluster potential energy curves for the benzene dimer: Sandwich, T-shaped, and parallel-displaced configurations
MO Sinnokrot et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2004)
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
AV Morozov et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Generalized born model with a simple smoothing function
WP Im et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Improved protein-ligand docking using GOLD
ML Verdonk et al.
PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)
SWISS-MODEL: an automated protein homology-modeling server
T Schwede et al.
NUCLEIC ACIDS RESEARCH (2003)
Free energy landscape of protein folding in water: Explicit vs. implicit solvent
RH Zhou
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
Force field validation using protein side chain prediction
MP Jacobson et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2002)
On the role of the crystal environment in determining protein side-chain conformations
MP Jacobson et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
Stacking and T-shape competition in aromatic-aromatic amino acid interactions
R Chelli et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)
A possible role for pi-stacking in the self-assembly of amyloid fibrils
E Gazit
FASEB JOURNAL (2002)
Extending the accuracy limits of prediction for side-chain conformations
ZX Xiang et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Solvent models for protein-ligand binding: Comparison of implicit solvent Poisson and surface generalized born models with explicit solvent simulations
LY Zhang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2001)
Modeling of loops in protein structures
A Fiser et al.
PROTEIN SCIENCE (2000)