(Q27702220)

2 July 2019

title

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge (English)

1 reference

2 July 2019

main subject

protein design

0 references

computational biology

1 reference

inferred from title

computational benchmark

1 reference

David Baker

13

0 references

author name string

Richard D Smith

1

1 reference

2 July 2019

Kelly L Damm-Ganamet

2

1 reference

2 July 2019

James B Dunbar

3

1 reference

2 July 2019

Aqeel Ahmed

4

1 reference

2 July 2019

Krishnapriya Chinnaswamy

5

1 reference

2 July 2019

James E Delproposto

6

1 reference

2 July 2019

Ginger M Kubish

7

1 reference

2 July 2019

Christine E Tinberg

8

1 reference

2 July 2019

Sagar D Khare

9

1 reference

2 July 2019

Jiayi Dou

10

1 reference

2 July 2019

Lindsey Doyle

11

1 reference

2 July 2019

Jeanne A Stuckey

12

1 reference

2 July 2019

Heather A Carlson

14

1 reference

2 July 2019

publication date

9 October 2015

1 reference

2 July 2019

Journal of Chemical Information and Modeling

published in

1 reference

2 July 2019

volume

56

1 reference

2 July 2019

issue

6

1 reference

2 July 2019

page(s)

1022-1031

1 reference

2 July 2019

Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking

cites work

1 reference

12 December 2020

The Protein Data Bank

1 reference

12 December 2020

High-density miniaturized thermal shift assays as a general strategy for drug discovery

1 reference

12 December 2020

Molecular Recognition of Protein−Ligand Complexes: Applications to Drug Design

1 reference

12 December 2020

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

1 reference

12 December 2020

Gaussian docking functions

1 reference

12 December 2020

Comparative evaluation of 11 scoring functions for molecular docking

1 reference

12 December 2020

Improved protein-ligand docking using GOLD

1 reference

12 December 2020

Modeller: generation and refinement of homology-based protein structure models

1 reference

12 December 2020

Evaluation of docking performance: comparative data on docking algorithms

1 reference

12 December 2020

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

1 reference

12 December 2020

A hierarchical approach to all-atom protein loop prediction

1 reference

12 December 2020

Comparative evaluation of eight docking tools for docking and virtual screening accuracy

1 reference

12 December 2020

Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures

1 reference

12 December 2020

Emergence of protein fold families through rational design

1 reference

12 December 2020

An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function

1 reference

12 December 2020

Critical assessment of the automated AutoDock as a new docking tool for virtual screening.

1 reference

12 December 2020

Prediction of protein-ligand interactions. Docking and scoring: successes and gaps

1 reference

12 December 2020

A critical assessment of docking programs and scoring functions

1 reference

12 December 2020

Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes

1 reference

12 December 2020

Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.

1 reference

12 December 2020

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

1 reference

12 December 2020

M4T: a comparative protein structure modeling server.

1 reference

12 December 2020

Progress in computational protein design

1 reference

12 December 2020

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information

1 reference

12 December 2020

MedusaScore: an accurate force field-based scoring function for virtual drug screening

1 reference

12 December 2020

DOCK 6: combining techniques to model RNA-small molecule complexes

1 reference

12 December 2020

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

1 reference

12 December 2020

Computational design of ligand binding is not a solved problem

1 reference

12 December 2020

Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes.

1 reference

12 December 2020

Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database

1 reference

12 December 2020

I-TASSER: a unified platform for automated protein structure and function prediction

1 reference

12 December 2020

Rapid flexible docking using a stochastic rotamer library of ligands

1 reference

12 December 2020

Docking and scoring protein interactions: CAPRI 2009

1 reference

12 December 2020

Theoretical and computational protein design

1 reference

12 December 2020

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

1 reference

12 December 2020

CSAR benchmark exercise of 2010: selection of the protein-ligand complexes.

1 reference

12 December 2020

CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.

1 reference

12 December 2020

Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction

1 reference

12 December 2020

Surflex-Dock: Docking benchmarks and real-world application

1 reference

12 December 2020

Evaluation of DOCK 6 as a pose generation and database enrichment tool

1 reference

12 December 2020

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions

1 reference

12 December 2020

Teach-Discover-Treat (TDT): collaborative computational drug discovery for neglected diseases

1 reference

12 December 2020

GalaxyDock: protein-ligand docking with flexible protein side-chains

1 reference

12 December 2020

Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise

1 reference

12 December 2020

Protein-ligand docking in the new millennium--a retrospective of 10 years in the field

1 reference

12 December 2020

CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series

1 reference

12 December 2020

CSAR data set release 2012: ligands, affinities, complexes, and docking decoys

1 reference

12 December 2020

Computational design of ligand-binding proteins with high affinity and selectivity

1 reference

12 December 2020

Critical assessment of methods of protein structure prediction (CASP)--round x

1 reference

12 December 2020

SAMPL4, a blind challenge for computational solvation free energies: the compounds considered

1 reference

12 December 2020

PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions

1 reference

12 December 2020

Improvements, trends, and new ideas in molecular docking: 2012-2013 in review.

1 reference

12 December 2020

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model

1 reference

12 December 2020

Identifiers

DOI

10.1021/ACS.JCIM.5B00387

1 reference

2 July 2019

journals/jcisd/SmithDDACDKTKDD16

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 July 2019

PubMed publication ID

26419257

1 reference

2 July 2019