Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4

P3DOCK: a protein–RNA docking webserver based on template-based and template-free docking

(2019) Jinfang Zheng et al.   BIOINFORMATICS

Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking

(2019) Kathryn A. Porter et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

(2018) José Jiménez et al.   Journal of Chemical Information and Modeling

Convolutional neural network scoring and minimization in the D3R 2017 community challenge

(2018) Jocelyn Sunseri et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges

(2018) Duc Duy Nguyen et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Monte Carlo on the manifold and MD refinement for binding pose prediction of protein–ligand complexes: 2017 D3R Grand Challenge

(2018) Mikhail Ignatov et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor

(2017) Rui Duan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2

(2017) Priscila da Silva Figueiredo Celestino Gomes et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016

(2017) Xavier Fradera et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2017) Maria Kadukova et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protein–ligand docking using FFT based sampling: D3R case study

(2017) Dzmitry Padhorny et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions

(2017) Lenna X. Peterson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function

(2017) Petras J. Kundrotas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics

(2016) Evangelos A. Coutsias et al.   Journal of Chemical Theory and Computation

Focused grid-based resampling for protein docking and mapping

(2016) Artem B. Mamonov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Template-Based Modeling of Protein-RNA Interactions

(2016) Jinfang Zheng et al.   PLoS Computational Biology

The Impact of Side-Chain Packing on Protein Docking Refinement

(2015) Mohammad Moghadasi et al.   Journal of Chemical Information and Modeling

Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation

(2015) Sereina Riniker et al.   Journal of Chemical Information and Modeling

Energy Minimization on Manifolds for Docking Flexible Molecules

(2015) Hanieh Mirzaei et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Accelerating molecular simulations of proteins using Bayesian inference on weak information

(2015) Alberto Perez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference

(2015) Justin L. MacCallum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bringing the MMFF force field to the RDKit: implementation and validation

(2014) Paolo Tosco et al.   Journal of Cheminformatics

Rigid Body Energy Minimization on Manifolds for Molecular Docking

(2012) Hanieh Mirzaei et al.   Journal of Chemical Theory and Computation

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B