(Q51777326)

12 April 2018

title

The basic concepts of molecular modeling. (English)

1 reference

12 April 2018

author

David Sept

4

1 reference

12 April 2018

author name string

Akansha Saxena

1

1 reference

12 April 2018

Diana Wong

2

1 reference

12 April 2018

Karthikeyan Diraviyam

3

1 reference

12 April 2018

language of work or name

English

0 references

publication date

1 January 2009

1 reference

12 April 2018

published in

Methods in Enzymology

1 reference

12 April 2018

volume

467

1 reference

12 April 2018

page(s)

307-334

1 reference

12 April 2018

Studies in Molecular Dynamics. I. General Method

cites work

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Basic local alignment search tool

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

PRINTS and its automatic supplement, prePRINTS.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Swiss-Prot: juggling between evolution and stability

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

1 reference

7 January 2021

The missing term in effective pair potentials

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Flexible protein-protein docking

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

CHARMM: the biomolecular simulation program

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Protein structure prediction servers at University College London

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

SCRATCH: a protein structure and structural feature prediction server

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

The Jpred 3 secondary structure prediction server

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Comparison of automated docking programs as virtual screening tools

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

A folding space odyssey

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Computer Modeling of the Membrane Interaction of FYVE Domains

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Profile hidden Markov models

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

ExPASy: The proteomics server for in-depth protein knowledge and analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Automated docking of substrates to proteins by simulated annealing

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Ab initio protein structure prediction.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Benchmarking sets for molecular docking

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

InterPro: the integrative protein signature database

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Assessing the role of polarization in docking.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Community benchmarks for virtual screening

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Scoring functions for protein-ligand docking

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

A genetic algorithm for flexible molecular overlay and pharmacophore elucidation.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Comparison of simple potential functions for simulating liquid water

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Enhanced genome annotation using structural profiles in the program 3D-PSSM

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Docking and scoring in virtual screening for drug discovery: methods and applications

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Theoretical and practical considerations in virtual screening: a beaten field?

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Prediction of protein structure

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Clustal W and Clustal X version 2.0

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

PROCHECK: a program to check the stereochemical quality of protein structures

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Docking and scoring protein complexes: CAPRI 3rd Edition

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

SMART 6: recent updates and new developments

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Assessment of protein models with three-dimensional profiles

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Comparative protein structure modeling of genes and genomes

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

The hinge-bending mode in lysozyme

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Dynamics of folded proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

BLAST: at the core of a powerful and diverse set of sequence analysis tools

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

T-Coffee: A novel method for fast and accurate multiple sequence alignment

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Rapid and sensitive sequence comparison with FASTP and FASTA

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Multiple protein sequence alignment

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

UCSF Chimera--a visualization system for exploratory research and analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Force fields for protein simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Membrane protein prediction methods

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Correlations in the Motion of Atoms in Liquid Argon

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Recent Progress and Future Directions in Protein-Protein Docking

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Protein structure prediction using Rosetta

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Prediction of protein secondary structure at better than 70% accuracy

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

The PredictProtein server

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Progress in modeling of protein structures and interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Binding site characteristics in structure-based virtual screening: evaluation of current docking tools

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

SWISS-MODEL: An automated protein homology-modeling server

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Virtual screening of chemical libraries

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Clustering of low-energy conformations near the native structures of small proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Protein-ligand docking: current status and future challenges

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Carborane clusters in computational drug design: a comparative docking evaluation using AutoDock, FlexX, Glide, and Surflex

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Convergence and combination of methods in protein-protein docking

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Comparison of the NCI open database with seven large chemical structural databases.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

WHAT IF: a molecular modeling and drug design program

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

A critical assessment of docking programs and scoring functions

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

InterProScan--an integration platform for the signature-recognition methods in InterPro

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

I-TASSER server for protein 3D structure prediction

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Protein sequence similarity searches using patterns as seeds

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

Docking, virtual high throughput screening and in silico fragment-based drug design

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2967012-9

7 January 2021

10.1016/S0076-6879(09)67012-9

Identifiers

DOI

1 reference

12 April 2018

1 reference

12 April 2018