Protein-Ligand Interactions: Knowledge-Based Methods

DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

Journal of Cheminformatics ◽

10.1186/s13321-019-0373-4 ◽

2019 ◽

Vol 11 (1) ◽

Cited By ~ 13

Author(s):

Pin Chen ◽

Yaobin Ke ◽

Yutong Lu ◽

Yunfei Du ◽

Jiahui Li ◽

...

Keyword(s):

Energy Function ◽

Ideal Gas ◽

Reference State ◽

Knowledge Based ◽

SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions

Journal of Medicinal Chemistry ◽

10.1021/jm0105833 ◽

2002 ◽

Vol 45 (13) ◽

pp. 2770-2780 ◽

Cited By ~ 86

Author(s):

Alexey V. Ishchenko ◽

Eugene I. Shakhnovich

Keyword(s):

Small Molecule ◽

Scoring Function ◽

Knowledge Based ◽

An iterative knowledge-based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials

Journal of Computational Chemistry ◽

10.1002/jcc.20504 ◽

2006 ◽

Vol 27 (15) ◽

pp. 1866-1875 ◽

Cited By ~ 106

Author(s):

Sheng-You Huang ◽

Xiaoqin Zou

Keyword(s):

Scoring Function ◽

Interaction Potentials ◽

Knowledge Based ◽

Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein–Ligand Interactions

Journal of Chemical Information and Modeling ◽

10.1021/ci2003939 ◽

2011 ◽

Vol 51 (11) ◽

pp. 2994-3004 ◽

Cited By ~ 12

Author(s):

Mingyue Zheng ◽

Bing Xiong ◽

Cheng Luo ◽

Shanshan Li ◽

Xian Liu ◽

...

Keyword(s):

Hydrogen Bonding ◽

Drug Design ◽

Scoring Functions ◽

Two Dimensional ◽

Knowledge Based ◽

Ligand Interactions ◽

Hydrogen Bonding Potential

Improving the Accuracy of Knowledge-Based Scoring Functions for Protein-Ligand Interactions by Accounting for Sparse Data in the Training Set

Biophysical Journal ◽

10.1016/j.bpj.2011.11.2238 ◽

2012 ◽

Vol 102 (3) ◽

pp. 409a

Author(s):

Sam Z. Grinter ◽

Xiaoqin Zou

Keyword(s):

Sparse Data ◽

Scoring Functions ◽

Training Set ◽

Knowledge Based ◽

Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions

Journal of Chemical Information and Modeling ◽

10.1021/ci9002987 ◽

2010 ◽

Vol 50 (2) ◽

pp. 262-273 ◽

Cited By ~ 76

Author(s):

Sheng-You Huang ◽

Xiaoqin Zou

Keyword(s):

Scoring Function ◽

Knowledge Based ◽

Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-017-0068-8 ◽

2017 ◽

Vol 31 (10) ◽

pp. 943-958 ◽

Cited By ~ 13

Author(s):

Maria Kadukova ◽

Sergei Grudinin

Keyword(s):

Convex Optimization ◽

Knowledge Based ◽

Ligand Interactions ◽

Structural Databases

A knowledge-based scoring function for protein-ligand interactions: Probing the reference state

Virtual Screening: An Alternative or Complement to High Throughput Screening? ◽

10.1007/0-306-46883-2_7 ◽

2005 ◽

pp. 99-114 ◽

Cited By ~ 7

Author(s):

Ingo Muegge

Keyword(s):

Scoring Function ◽

Reference State ◽

Knowledge Based ◽

DrugScoreFP: profiling protein-ligand interactions using fingerprint simplicity paired with knowledge-based potential fields

Chemistry Central Journal ◽

10.1186/1752-153x-2-s1-s16 ◽

2008 ◽

Vol 2 (S1) ◽

Cited By ~ 6

Author(s):

Patrick Pfeffer ◽

Gerd Neudert ◽

Gerhard Klebe

Keyword(s):

Potential Fields ◽

Knowledge Based ◽