Ligand binding: functional site location, similarity and docking

An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families

1996 • 1,214 citations

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

2002 • 1,097 citations

Evolution of function in protein superfamilies, from a structural perspective 1 1Edited by A. R. Fersht

2001 • 665 citations

A review of protein-small molecule docking methods.

2002 • 633 citations

One Fold with Many Functions: The Evolutionary Relationships between TIM Barrel Families Based on their Sequences, Structures and Functions

2002 • 612 citations

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

2002 • 607 citations

Analysis of Catalytic Residues in Enzyme Active Sites

2002 • 575 citations

Detailed Analysis of Scoring Functions for Virtual Screening

2001 • 491 citations

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

2001 • 481 citations

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

2001 • 460 citations

FlexE: efficient molecular docking considering protein structure variations

2001 • 430 citations

A new test set for validating predictions of protein–ligand interaction

2002 • 429 citations

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

2002 • 423 citations

A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology

2002 • 419 citations

A method to predict functional residues in proteins

1995 • 418 citations

Protein clefts in molecular recognition and function.

1996 • 412 citations

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

2002 • 404 citations

Practical limits of function prediction

2000 • 342 citations

High-throughput docking for lead generation

2001 • 337 citations

Protein-protein interfaces: Analysis of amino acid conservation in homodimers

2000 • 323 citations

Evolutionary predictions of binding surfaces and interactions

2002 • 260 citations

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

2000 • 254 citations

THEMATICS: A simple computational predictor of enzyme function from structure

2001 • 237 citations

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins11Edited by J. Thornton

2001 • 231 citations

Prediction of functionally important residues based solely on the computed energetics of protein structure 1 1Edited by B. Honig

2001 • 190 citations

Co-evolutionary Analysis Reveals Insights into Protein–Protein Interactions

2002 • 184 citations

Statistical potentials and scoring functions applied to protein–ligand binding

2001 • 182 citations

Flexible docking under pharmacophore type constraints.

2002 • 173 citations

Adenine recognition: A motif present in ATP‐, CoA‐, NAD‐, NADP‐, and FAD‐dependent proteins

2001 • 133 citations

Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data

2001 • 131 citations

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

2002 • 127 citations

DrugScore Meets CoMFA: Adaptation of Fields for Molecular Comparison (AFMoC) or How to Tailor Knowledge-Based Pair-Potentials to a Particular Protein

2002 • 121 citations

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

2002 • 115 citations

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

2002 • 115 citations

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

2001 • 105 citations

Docking into Knowledge-Based Potential Fields: A Comparative Evaluation of DrugScore

2002 • 101 citations

Studying Enzyme Binding Specificity in Acetylcholinesterase Using a Combined Molecular Dynamics and Multiple Docking Approach

2002 • 94 citations

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

2001 • 90 citations

When fold is not important: A common structural framework for adenine and AMP binding in 12 unrelated protein families

2000 • 80 citations

Evaluation of Docking Functions for Protein−Ligand Docking

2001 • 71 citations

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

2002 • 68 citations

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

2002 • 66 citations

Enhanced Functional Annotation of Protein Sequences via the Use of Structural Descriptors

2001 • 53 citations

Enhanced docking with the mining minima optimizer: Acceleration and side‐chain flexibility

2002 • 53 citations

Ligand-induced changes in the binding sites of proteins

2002 • 48 citations

Finding important sites in protein sequences

2002 • 41 citations

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

2002 • 39 citations

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

2003 • 38 citations

Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs11Edited by B. Holland

2001 • 35 citations

Diversity in the SH2 domain family phosphotyrosyl peptide binding site

2003 • 33 citations

A fragment library based on gaussian mixtures predicting favorable molecular interactions 1 aEdited by G. von Heijne

2001 • 28 citations

Docking of Flexible Molecules Using Multiscale Ligand Representations

2002 • 25 citations

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

2002 • 22 citations

Recognition templates for predicting adenylate-binding sites in proteins

2001 • 15 citations