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Computational methods in drug discovery
Computer-aided drug discovery/design methods have played a major role in the
development of therapeutically important small molecules for over three decades. These …
development of therapeutically important small molecules for over three decades. These …
De novo protein design, a retrospective
Proteins are molecular machines whose function depends on their ability to achieve
complex folds with precisely defined structural and dynamic properties. The rational design …
complex folds with precisely defined structural and dynamic properties. The rational design …
ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB
Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force
field is required. The Amber ff99SB force field improved protein secondary structure balance …
field is required. The Amber ff99SB force field improved protein secondary structure balance …
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
Automated docking of drug-like molecules into receptors is an essential tool in structure-
based drug design. While modeling receptor flexibility is important for correctly predicting …
based drug design. While modeling receptor flexibility is important for correctly predicting …
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks
Abstract A new program, TALOS-N, is introduced for predicting protein backbone torsion
angles from NMR chemical shifts. The program relies far more extensively on the use of …
angles from NMR chemical shifts. The program relies far more extensively on the use of …
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
New protein parameters are reported for the all-atom empirical energy function in the
CHARMM program. The parameter evaluation was based on a self-consistent approach …
CHARMM program. The parameter evaluation was based on a self-consistent approach …
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
The parametrization and testing of the OPLS all-atom force field for organic molecules and
peptides are described. Parameters for both torsional and nonbonded energetics have been …
peptides are described. Parameters for both torsional and nonbonded energetics have been …
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions
Rotamer libraries are used in protein structure determination, prediction, and design. The
backbone-dependent rotamer library consists of rotamer frequencies, mean dihedral angles …
backbone-dependent rotamer library consists of rotamer frequencies, mean dihedral angles …
Improved prediction of protein side‐chain conformations with SCWRL4
GG Krivov, MV Shapovalov… - … Structure, Function, and …, 2009 - Wiley Online Library
Determination of side-chain conformations is an important step in protein structure prediction
and protein design. Many such methods have been presented, although only a small …
and protein design. Many such methods have been presented, although only a small …
The penultimate rotamer library
All published rotamer libraries contain some rotamers that exhibit impossible internal atomic
overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues …
overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues …