Bioinformatics and variability in drug response: a protein structural perspective

Bioinformatics for personal genome interpretation

(2012) E. Capriotti et al.   BRIEFINGS IN BIOINFORMATICS

Protein Flexibility and Ligand Recognition: Challenges for Molecular Modeling

(2012) Francesca Spyrakis et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

A novel mutation of the PTCH1 gene activates the Shh/Gli signaling pathway in a Chinese family with nevoid basal cell carcinoma syndrome

(2011) Tingting Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Bioinformatics challenges for personalized medicine

(2011) Guy Haskin Fernald et al.   BIOINFORMATICS

sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins

(2011) J. Meslamani et al.   BIOINFORMATICS

Optimized Torsion-Angle Normal Modes Reproduce Conformational Changes More Accurately Than Cartesian Modes

(2011) Jenelle K. Bray et al.   BIOPHYSICAL JOURNAL

Old friends in new guise: repositioning of known drugs with structural bioinformatics

(2011) V. J. Haupt et al.   BRIEFINGS IN BIOINFORMATICS

Identify drug repurposing candidates by mining the Protein Data Bank

(2011) F. Moriaud et al.   BRIEFINGS IN BIOINFORMATICS

Conformational Control Inhibition of the BCR-ABL1 Tyrosine Kinase, Including the Gatekeeper T315I Mutant, by the Switch-Control Inhibitor DCC-2036

(2011) Wayne W. Chan et al.   CANCER CELL

An Allosteric Inhibitor of the Human Cdc34 Ubiquitin-Conjugating Enzyme

(2011) Derek F. Ceccarelli et al.   CELL

Drug Safety Sciences and the Bottleneck in Drug Development

(2011) P B Watkins   CLINICAL PHARMACOLOGY & THERAPEUTICS

Comparative Modeling: The State of the Art and Protein Drug Target Structure Prediction

(2011) Tianyun Liu et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Overcoming the Drug Resistance Problem with Second-Generation Tyrosine Kinase Inhibitors: From Enzymology to Structural Models

(2011) E. Crespan et al.   CURRENT MEDICINAL CHEMISTRY

Clinical Drugs Undergoing Polymorphic Metabolism by Human Cytochrome P450 2C9 and the Implication in Drug Development

(2011) S.-M. He et al.   CURRENT MEDICINAL CHEMISTRY

Structure-based druggability assessment—identifying suitable targets for small molecule therapeutics

(2011) Eric B Fauman et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Targeting FKBP isoforms with small-molecule ligands

(2011) Elizabeth A Blackburn et al.   CURRENT OPINION IN PHARMACOLOGY

Challenges for the prediction of macromolecular interactions

(2011) Mark N Wass et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Recent Advances in the Therapeutic Perspectives of Nutlin-3

(2011) Paola Secchiero et al.   CURRENT PHARMACEUTICAL DESIGN

Selectivity Filters to Edit Out Deleterious Side Effects in Kinase Inhibitors

(2011) Sean Sessel et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Structure-based drug design to augment hit discovery

(2011) Subha Kalyaanamoorthy et al.   DRUG DISCOVERY TODAY

In silico repositioning of approved drugs for rare and neglected diseases

(2011) Sean Ekins et al.   DRUG DISCOVERY TODAY

Investigation by site-directed mutagenesis of the role of cytochrome P450 2B4 non-active-site residues in protein-ligand interactions based on crystal structures of the ligand-bound enzyme

(2011) P. Ross Wilderman et al.   FEBS Journal

A new disease-specific machine learning approach for the prediction of cancer-causing missense variants

(2011) Emidio Capriotti et al.   GENOMICS

A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®)

(2011) Joanna Amberger et al.   HUMAN MUTATION

Genetics and Variable Drug Response

(2011) Russell A. Wilke et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Long-Range Effects of a Peripheral Mutation on the Enzymatic Activity of Cytochrome P450 1A2

(2011) Tao Zhang et al.   Journal of Chemical Information and Modeling

Let’s get honest about sampling

(2011) David L. Mobley   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Unexpected Active-Site Flexibility in the Structure of Human Neutrophil Elastase in Complex with a New Dihydropyrimidone Inhibitor

(2011) Guido Hansen et al.   JOURNAL OF MOLECULAR BIOLOGY

How Does a Drug Molecule Find Its Target Binding Site?

(2011) Yibing Shan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The structural basis of agonist-induced activation in constitutively active rhodopsin

(2011) Jörg Standfuss et al.   NATURE

The structural basis for agonist and partial agonist action on a β1-adrenergic receptor

(2011) Tony Warne et al.   NATURE

How were new medicines discovered?

(2011) David C. Swinney et al.   NATURE REVIEWS DRUG DISCOVERY

Trends in the exploitation of novel drug targets

(2011) Mathias Rask-Andersen et al.   NATURE REVIEWS DRUG DISCOVERY

The productivity crisis in pharmaceutical R&D

(2011) Fabio Pammolli et al.   NATURE REVIEWS DRUG DISCOVERY

Probing the links between in vitro potency, ADMET and physicochemical parameters

(2011) M. Paul Gleeson et al.   NATURE REVIEWS DRUG DISCOVERY

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Allosteric Modulation of Family C G-Protein-Coupled Receptors: from Molecular Insights to Therapeutic Perspectives

(2011) S. Urwyler   PHARMACOLOGICAL REVIEWS

Drug discovery and the human kinome: Recent trends

(2011) Richard Eglen et al.   PHARMACOLOGY & THERAPEUTICS

Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase

(2011) P. W. Snyder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Turning a protein kinase on or off from a single allosteric site via disulfide trapping

(2011) J. D. Sadowsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

(2011) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP9 results compared to those of previous casp experiments

(2011) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP9 assessment of free modeling target predictions

(2011) Lisa Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template based protein structure predictions in CASP9

(2011) Valerio Mariani et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Definition of the hydrogen bond (IUPAC Recommendations 2011)

(2011) Elangannan Arunan et al.   PURE AND APPLIED CHEMISTRY

Biomolecular modeling and simulation: a field coming of age

(2011) Tamar Schlick et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Improving Protein Structure Prediction Using Multiple Sequence-Based Contact Predictions

(2011) Sitao Wu et al.   STRUCTURE

Remote Thioredoxin Recognition Using Evolutionary Conservation and Structural Dynamics

(2011) Grace W. Tang et al.   STRUCTURE

Analysis of in vitro bioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds

(2011) Christopher Southan et al.   Journal of Cheminformatics

In Silico Elucidation of the Recognition Dynamics of Ubiquitin

(2011) Dong Long et al.   PLoS Computational Biology

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

(2011) Daniel-Adriano Silva et al.   PLoS Computational Biology

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding

(2011) Tianyun Liu et al.   PLoS Computational Biology

Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence

(2011) Frederick E. Dewey et al.   PLoS Genetics

Exploring the cause of drug resistance by the detrimental missense mutations in KIT receptor: computational approach

(2010) R. Rajasekaran et al.   AMINO ACIDS

Pharmacogenetics and human genetic polymorphisms

(2010) Ann K. Daly   BIOCHEMICAL JOURNAL

Structures of Human Carbonic Anhydrase II/Inhibitor Complexes Reveal a Second Binding Site for Steroidal and Nonsteroidal Inhibitors,

(2010) Gyles E. Cozier et al.   BIOCHEMISTRY

Computational approaches for protein function prediction: A combined strategy from multiple sequence alignment to molecular docking-based virtual screening

(2010) Ciro Leonardo Pierri et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Flexibility of human cytochrome P450 enzymes: Molecular dynamics and spectroscopy reveal important function-related variations

(2010) Tereza Hendrychová et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar

(2010) Anaïs Mottaz et al.   BIOINFORMATICS

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

MK-2461, a Novel Multitargeted Kinase Inhibitor, Preferentially Inhibits the Activated c-Met Receptor

(2010) B.-S. Pan et al.   CANCER RESEARCH

Structural Determinants of PERK Inhibitor Potency and Selectivity

(2010) Hong Wang et al.   Chemical Biology & Drug Design

Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance

(2010) Tianjun Zhou et al.   Chemical Biology & Drug Design

Toward the Rational Design of p53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant

(2010) Nicolas Basse et al.   CHEMISTRY & BIOLOGY

Nutlin-3a Is a Potential Therapeutic for Ewing Sarcoma

(2010) K. I. Pishas et al.   CLINICAL CANCER RESEARCH

Dissecting Variability in Responses to Cancer Chemotherapy Through Systems Pharmacology

(2010) R Yang et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Reactivation of p53 by Novel MDM2 Inhibitors: Implications for Pancreatic Cancer Therapy

(2010) A.S. Azmi et al.   CURRENT CANCER DRUG TARGETS

Applications of Current Proteomics Techniques in Modern Drug Design

(2010) Cheng-Cheng Zhang et al.   Current Computer-Aided Drug Design

Expanding the range of ‘druggable’ targets with natural product-based libraries: an academic perspective

(2010) Renato A Bauer et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Molecular dynamics simulations of protein dynamics and their relevance to drug discovery

(2010) Freddie R Salsbury Jr   CURRENT OPINION IN PHARMACOLOGY

Molecular Shape Technologies in Drug Discovery: Methods and Applications

(2010) Jerry O. Ebalunode et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Template-Based Protein Modeling: Recent Methodological Advances

(2010) Pankaj Daga et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Successful Applications of Computer Aided Drug Discovery: Moving Drugs from Concept to the Clinic

(2010) Tanaji Talele et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

(2010) Stéphanie Pérot et al.   DRUG DISCOVERY TODAY

Structural genomics—Impact on biomedicine and drug discovery

(2010) Johan Weigelt   EXPERIMENTAL CELL RESEARCH

Electrostatics in proteins and protein–ligand complexes

(2010) Predrag Kukić et al.   Future Medicinal Chemistry

Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases

(2010) Alexey Aleksandrov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Docking Studies on Isoform-Specific Inhibition of Phosphoinositide-3-Kinases

(2010) Dima A. Sabbah et al.   Journal of Chemical Information and Modeling

Large-Scale Comparison of Four Binding Site Detection Algorithms

(2010) Peter Schmidtke et al.   Journal of Chemical Information and Modeling

Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets

(2010) Andrea Volkamer et al.   Journal of Chemical Information and Modeling

Mechanism of the decrease in catalytic activity of human cytochrome P450 2C9 polymorphic variants investigated by computational analysis

(2010) Eri Sano et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites

(2010) Peter Schmidtke et al.   JOURNAL OF MEDICINAL CHEMISTRY

Validation and Comparison of Pharmacogenetics-Based Warfarin Dosing Algorithms for Application of Pharmacogenetic Testing

(2010) Nitin Roper et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Effects of the V82A and I54V mutations on the dynamics and ligand binding properties of HIV-1 protease

(2010) Pia Dirauf et al.   JOURNAL OF MOLECULAR MODELING

In silico point mutation and evolutionary trace analysis applied to nicotinic acetylcholine receptors in deciphering ligand-binding surfaces

(2010) Marimuthu Parthiban et al.   JOURNAL OF MOLECULAR MODELING

Challenges and advances in computational docking: 2009 in review

(2010) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Antitumour activity of MDV3100 in castration-resistant prostate cancer: a phase 1–2 study

(2010) Howard I Scher et al.   LANCET

Clinical assessment incorporating a personal genome

(2010) Euan A Ashley et al.   LANCET

MDM2 Inhibitors for Pancreatic Cancer Therapy

(2010) A.S. Azmi et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

Activity of the Aurora Kinase Inhibitor VX-680 against Bcr/Abl-Positive Acute Lymphoblastic Leukemias

(2010) F. Fei et al.   MOLECULAR CANCER THERAPEUTICS

Crystal Structure of a Cytochrome P450 2B6 Genetic Variant in Complex with the Inhibitor 4-(4-Chlorophenyl)imidazole at 2.0-A Resolution

(2010) S. C. Gay et al.   MOLECULAR PHARMACOLOGY

Targeting Bcr–Abl by combining allosteric with ATP-binding-site inhibitors

(2010) Jianming Zhang et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

The HADDOCK web server for data-driven biomolecular docking

(2010) Sjoerd J de Vries et al.   Nature Protocols

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Structure-based drug discovery and protein targets in the CNS

(2010) Roderick E. Hubbard   NEUROPHARMACOLOGY

ModBase, a database of annotated comparative protein structure models, and associated resources

(2010) U. Pieper et al.   NUCLEIC ACIDS RESEARCH

VnD: a structure-centric database of disease-related SNPs and drugs

(2010) Jin Ok Yang et al.   NUCLEIC ACIDS RESEARCH

3DLigandSite: predicting ligand-binding sites using similar structures

(2010) Mark N. Wass et al.   NUCLEIC ACIDS RESEARCH

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

Pharmacological reactivation of mutant p53: from protein structure to the cancer patient

(2010) K G Wiman   ONCOGENE

In-Silico Approaches to Multi-target Drug Discovery

(2010) Xiao Hua Ma et al.   PHARMACEUTICAL RESEARCH

PharmGKB summary: very important pharmacogene information for CYP2B6

(2010) Caroline F. Thorn et al.   Pharmacogenetics and Genomics

PharmGKB summary

(2010) Dorit S. Berlin et al.   Pharmacogenetics and Genomics

Pharmacogenomics and bioinformatics: PharmGKB

(2010) Caroline F Thorn et al.   PHARMACOGENOMICS

Role of warfarin pharmacogenetic testing in clinical practice

(2010) Guang-Ming Tan et al.   PHARMACOGENOMICS

Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library

(2010) Yoshifumi Fukunishi et al.   PROTEIN SCIENCE

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

A regression model to predict warfarin dose from clinical variables and polymorphisms in CYP2C9, CYP4F2, and VKORC1: Derivation in a sample with predominantly a history of venous thromboembolism

(2010) P.S. Wells et al.   THROMBOSIS RESEARCH

p53-based Cancer Therapy

(2010) D. P. Lane et al.   Cold Spring Harbor Perspectives in Biology

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures

(2009) Michael Ryan et al.   BIOINFORMATICS

Properties and identification of human protein drug targets

(2009) Tala M. Bakheet et al.   BIOINFORMATICS

SCAN: SNP and copy number annotation

(2009) Eric R. Gamazon et al.   BIOINFORMATICS

Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques

(2009) Ryan Brenke et al.   BIOINFORMATICS

EasyMIFs and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures

(2009) Dario Ghersi et al.   BIOINFORMATICS

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

(2009) Yves Dehouck et al.   BIOINFORMATICS

Force Field Bias in Protein Folding Simulations

(2009) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Structure-Based Virtual Ligand Screening: Recent Success Stories

(2009) Bruno Villoutreix et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Docking and chemoinformatic screens for new ligands and targets

(2009) Peter Kolb et al.   CURRENT OPINION IN BIOTECHNOLOGY

Convergence and combination of methods in protein–protein docking

(2009) Sandor Vajda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Guide to Template Based Structure Prediction

(2009) Xiaotao Qu et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Quality Assessment of Protein Structure Models

(2009) Daisuke Kihara et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Structure-Based Drug Design Strategies in Medicinal Chemistry

(2009) Adriano Andricopulo et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Homology modeling in drug discovery: current trends and applications

(2009) Claudio N. Cavasotto et al.   DRUG DISCOVERY TODAY

Managing protein flexibility in docking and its applications

(2009) Chandrika B-Rao et al.   DRUG DISCOVERY TODAY

Protein structure prediction and model quality assessment

(2009) Andriy Kryshtafovych et al.   DRUG DISCOVERY TODAY

Rational drug design

(2009) Soma Mandal et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Functional annotations improve the predictive score of human disease-related mutations in proteins

(2009) Remo Calabrese et al.   HUMAN MUTATION

Systematic Structure-Function Analysis of Androgen Receptor Leu701Mutants Explains the Properties of the Prostate Cancer Mutant L701H

(2009) Dennis J. van de Wijngaart et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs

(2009) Christopher R. Corbeil et al.   Journal of Chemical Information and Modeling

Effect of Input Differences on the Results of Docking Calculations

(2009) Miklos Feher et al.   Journal of Chemical Information and Modeling

Molecular Docking Screens Using Comparative Models of Proteins

(2009) Hao Fan et al.   Journal of Chemical Information and Modeling

Identifying and Characterizing Binding Sites and Assessing Druggability

(2009) Thomas A. Halgren   Journal of Chemical Information and Modeling

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural basis for decreased affinity of Emodin binding to Val66-mutated human CK2α as determined by molecular dynamics

(2009) Na Zhang et al.   JOURNAL OF MOLECULAR MODELING

Prospective virtual screening with Ultrafast Shape Recognition: the identification of novel inhibitors of arylamine N-acetyltransferases

(2009) P. J. Ballester et al.   Journal of the Royal Society Interface

The topology of drug–target interaction networks: implicit dependence on drug properties and target families

(2009) Jordi Mestres et al.   Molecular BioSystems

Novel mutant-selective EGFR kinase inhibitors against EGFR T790M

(2009) Wenjun Zhou et al.   NATURE

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Update of TTD: Therapeutic Target Database

(2009) Feng Zhu et al.   NUCLEIC ACIDS RESEARCH

SITEHOUND-web: a server for ligand binding site identification in protein structures

(2009) M. Hernandez et al.   NUCLEIC ACIDS RESEARCH

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions

(2009) Saskia Preissner et al.   NUCLEIC ACIDS RESEARCH

KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients

(2009) K. S. Gajiwala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

L2′ loop is critical for caspase-7 active site formation

(2009) Witold A. Witkowski et al.   PROTEIN SCIENCE

Predicting structurally conserved contacts for homologous proteins using sequence conservation filters

(2009) Mayako Michino et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure of P-Glycoprotein Reveals a Molecular Basis for Poly-Specific Drug Binding

(2009) S. G. Aller et al.   SCIENCE

Development of a Second-Generation Antiandrogen for Treatment of Advanced Prostate Cancer

(2009) C. Tran et al.   SCIENCE

Improving Structure-Based Function Prediction Using Molecular Dynamics

(2009) Dariya S. Glazer et al.   STRUCTURE

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

Outcome of a Workshop on Applications of Protein Models in Biomedical Research

(2009) Torsten Schwede et al.   STRUCTURE

The importance of discerning shape in molecular pharmacology

(2009) Sandhya Kortagere et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

The Human Gene Mutation Database: 2008 update

(2009) Peter D Stenson et al.   Genome Medicine

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites

(2008) R. Najmanovich et al.   BIOINFORMATICS

How to Measure the Similarity Between Protein Ligand-Binding Sites?

(2008) Esther Kellenberger et al.   Current Computer-Aided Drug Design

Allosteric modulation of kinases and GPCRs: design principles and structural diversity

(2008) Jana A Lewis et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Approaches and Resources for Prediction of the Effects of Non-Synonymous Single Nucleotide Polymorphism on Protein Function and Interactions

(2008) S. Teng et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Predicting druggable binding sites at the protein–protein interface

(2008) Jonathan C. Fuller et al.   DRUG DISCOVERY TODAY

Drugs and their molecular targets: an updated overview

(2008) Yves Landry et al.   FUNDAMENTAL & CLINICAL PHARMACOLOGY

Primary and Secondary Kinase Genotypes Correlate With the Biological and Clinical Activity of Sunitinib in Imatinib-Resistant Gastrointestinal Stromal Tumor

(2008) Michael C. Heinrich et al.   JOURNAL OF CLINICAL ONCOLOGY

Discovery of an Orally Bioavailable Small Molecule Inhibitor of Prosurvival B-Cell Lymphoma 2 Proteins

(2008) Cheol-Min Park et al.   JOURNAL OF MEDICINAL CHEMISTRY

Crystal Structures of Human 108V and 108M Catechol O-Methyltransferase

(2008) K. Rutherford et al.   JOURNAL OF MOLECULAR BIOLOGY

Meta-basic estimates the size of druggable human genome

(2008) Dariusz Plewczynski et al.   JOURNAL OF MOLECULAR MODELING

Flexibility of Human Cytochromes P450: Molecular Dynamics Reveals Differences between CYPs 3A4, 2C9, and 2A6, which Correlate with Their Substrate Preferences

(2008) Josef Skopalík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure of a β1-adrenergic G-protein-coupled receptor

(2008) Tony Warne et al.   NATURE

A quantitative analysis of kinase inhibitor selectivity

(2008) Mazen W Karaman et al.   NATURE BIOTECHNOLOGY

Protein crystallization: from purified protein to diffraction-quality crystal

(2008) Naomi E Chayen et al.   NATURE METHODS

Pharmacogenetics in drug discovery and development: a translational perspective

(2008) Allen D. Roses   NATURE REVIEWS DRUG DISCOVERY

The SWISS-MODEL Repository and associated resources

(2008) F. Kiefer et al.   NUCLEIC ACIDS RESEARCH

A conserved protonation-dependent switch controls drug binding in the Abl kinase

(2008) Y. Shan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity

(2008) J. Tsai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

(2008) K.-i. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP

(2008) C.-H. Yun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted rescue of a destabilized mutant of p53 by an in silico screened drug

(2008) F. M. Boeckler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using multiple templates to improve quality of homology models in automated homology modeling

(2008) Per Larsson et al.   PROTEIN SCIENCE

Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions

(2008) Ryoichi Minai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural determinants of species-selective substrate recognition in human andDrosophilaserotonin transporters revealed through computational docking studies

(2008) Kristian W. Kaufmann et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE

HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures

(2008) Bosco K Ho et al.   BMC STRUCTURAL BIOLOGY

Characterization of local geometry of protein surfaces with the visibility criterion

(2007) Bin Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS