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List of works by Peter W. Rose

Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm

Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm

scientific article published on 22 April 2019

Automated derivation of reaction rules for the EROS 6.0 system for reaction prediction

BioJava 5: A community driven open-source bioinformatics library

scientific article published on 08 February 2019

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.

scientific article

BioJava: an open-source framework for bioinformatics in 2012

scientific article

Citing a Data Repository: A Case Study of the Protein Data Bank

scientific article

Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective

scientific article

Computational detection of the binding-site hot spot at the remodeled human growth hormone-receptor interface.

scientific article published in November 2003

Deciphering common failures in molecular docking of ligand-protein complexes.

scientific article

Design, synthesis, and biological evaluation of novel human 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) substrates

scientific article published in June 2005

Developing a Best Practices Training Program in Cyberinfrastructure-Enabled Machine Learning Research

scientific article published on 10 September 2023

Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains.

scientific article published in December 2001

Hierarchy of simulation models in predicting structure and energetics of the Src SH2 domain binding to tyrosyl phosphopeptides

scientific article published in January 2002

Impact of genetic variation on three dimensional structure and function of proteins

scientific article

Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank

scientific article

Integration of open access literature into the RCSB Protein Data Bank using BioLit

scientific article

Investigation of protein quaternary structure via stoichiometry and symmetry ınformation.

scientific article published on 4 June 2018

MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures

scientific article

Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface

scientific article published in August 2002

Multidimensional explorations into chemical reactivity: the reactivity space

NGL viewer: web-based molecular graphics for large complexes

scholarly article by Alexander S Rose published in May 2018

Navigating ligand–protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

Pre-calculated protein structure alignments at the RCSB PDB website

scientific article published in December 2010

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank

scientific article

Quaternary structure evaluation tool for protein assemblies

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank

scientific article

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

article

Recon3D enables a three-dimensional view of gene variation in human metabolism.

scientific article published on 19 February 2018

Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding

scholarly article

Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 8. Pharmacological optimization of orally bioavailable 2-pyridone-containing peptidomimetics.

scientific article published in October 2003

Systematic detection of internal symmetry in proteins using CE-Symm

scientific article

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

scientific article published on 25 July 2019

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

scientific article published on 19 November 2019

The Pfizer Crystal Structure Database: An essential tool for structure‐based design at Pfizer

scientific article published on 08 April 2022

The Protein Data Bank: Overview and Tools for Drug Discovery

The RCSB Protein Data Bank: new resources for research and education

scientific article (publication date: 2013)

The RCSB Protein Data Bank: redesigned web site and web services

scientific article

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

scientific article

The RCSB protein data bank: integrative view of protein, gene and 3D structural information

scientific article

The evolution of the RCSB Protein Data Bank website

The need for scientific software engineering in the pharmaceutical industry

scientific article published on 19 December 2016

Thermodynamics and kinetics of ligand-protein binding studied with the weighted histogram analysis method and simulated annealing

scientific article published on 01 January 1999

Towards an efficient compression of 3D coordinates of macromolecular structures

scientific article

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions

scientific article

Trendspotting in the Protein Data Bank

scientific article

Web-based molecular graphics for large complexes

Will widgets and semantic tagging change computational biology? ⬇️

scientific article

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