Ligand binding: functional site location, similarity and docking (Q35165255)

6 August 2017

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title

Ligand binding: functional site location, similarity and docking (English)

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6 August 2017

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4

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6 August 2017

Stephen J Campbell

1

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PubMed ID

12831892

6 August 2017

Nicola D Gold

series ordinal

2

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PubMed ID

12831892

6 August 2017

Richard M Jackson

series ordinal

3

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6 August 2017

1 June 2003

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Current Opinion in Structural Biology

6 August 2017

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6 August 2017

13

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6 August 2017

3

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6 August 2017

389-395

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Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design

6 August 2017

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

A method to predict functional residues in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Analysis and prediction of functional sub-types from protein sequence alignments.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Evolutionary predictions of binding surfaces and interactions.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

An evolutionary trace method defines binding surfaces common to protein families

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Diversity in the SH2 domain family phosphotyrosyl peptide binding site

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Co-evolutionary analysis reveals insights into protein-protein interactions.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Finding important sites in protein sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

THEMATICS: a simple computational predictor of enzyme function from structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Prediction of functionally important residues based solely on the computed energetics of protein structure.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Analysis of catalytic residues in enzyme active sites

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Evolution of function in protein superfamilies, from a structural perspective.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Practical limits of function prediction

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Enhanced functional annotation of protein sequences via the use of structural descriptors

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

A fragment library based on Gaussian mixtures predicting favorable molecular interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Recognition templates for predicting adenylate-binding sites in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

A new method to detect related function among proteins independent of sequence and fold homology.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Identification of protein functions from a molecular surface database, eF-site.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

A review of protein-small molecule docking methods

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

High-throughput docking for lead generation

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Efficient docking of peptides to proteins without prior knowledge of the binding site

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Docking of flexible molecules using multiscale ligand representations

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Ligand-induced changes in the binding sites of proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

FlexE: efficient molecular docking considering protein structure variations.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Docking ligands onto binding site representations derived from proteins built by homology modelling.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Flexible docking under pharmacophore type constraints

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Statistical potentials and scoring functions applied to protein-ligand binding

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Detailed analysis of scoring functions for virtual screening

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Evaluation of docking functions for protein-ligand docking

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Docking into knowledge-based potential fields: a comparative evaluation of DrugScore

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

ConsDock: A new program for the consensus analysis of protein-ligand interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

A new test set for validating predictions of protein-ligand interaction.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

Ligand-protein database: linking protein-ligand complex structures to binding data

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2803%2900075-7

7 January 2021

10.1016/S0959-440X(03)00075-7

Identifiers

DOI

1 reference

6 August 2017

1 reference

PubMed ID

12831892