A Python Package for the Localization of Protein Modifications in Mass Spectrometry Data by Anthony S. Barente (14035175)

Subjects:

Average quality scores of the models of the analysis set as a function of the <i>w</i>_<i>SP</i> with which the DOPE potential has been included in the objective function... by Giacomo Janson (8138517)

Adaptive H-REMD simulation algorithm. by Danial Pourjafar-Dehkordi (7165523)

3D modeling qualities of the AS single-template models built by including DOPE in the objective function of MODELLER. by Giacomo Janson (8138517)

3D modeling qualities of the AM multiple-template models built by including DOPE in the objective function of MODELLER. by Giacomo Janson (8138517)

Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics by Paolo Cifani (1575613)

“…Termed SAMPEI for spectral alignment-based modified peptide identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. …”

Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics by Paolo Cifani (1575613)

“…Termed SAMPEI for spectral alignment-based modified peptide identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. …”

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling by Giacomo Janson (8138517)

“…<div><p>The most frequently used approach for protein structure prediction is currently homology modeling. …”

Modeling with uniform <i>σ</i> values. by Giacomo Janson (8138517)

Effect of <i>|Δd</i>_<i>n</i><i>|</i> perturbation on 3D modeling. by Giacomo Janson (8138517)

gmxapi usage examples. by M. Eric Irrgang (4487278)

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses by Dominykas Lukauskis (14143149)

“…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …”

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses by Dominykas Lukauskis (14143149)

“…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …”

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses by Dominykas Lukauskis (14143149)

“…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …”

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data by Jean-Christophe Lachance (6619307)

“…GEM-guided predictions of growth phenotypes rely on the accurate definition of a biomass objective function (BOF) that is designed to include key cellular biomass components such as the major macromolecules (DNA, RNA, proteins), lipids, coenzymes, inorganic ions and species-specific components. …”

PyPEFAn Integrated Framework for Data-Driven Protein Engineering by Niklas E. Siedhoff (11133851)

“…Data-driven strategies are gaining increased attention in protein engineering due to recent advances in access to large experimental databanks of proteins, next-generation sequencing (NGS), high-throughput screening (HTS) methods, and the development of artificial intelligence algorithms. …”

Integration of Morphoscanner with MDAnalysis, NGLview and Networkx. by Federico Fontana (533670)

datasheet1_ThermoScan: Semi-automatic Identification of Protein Stability Data From PubMed.xlsx by Paola Turina (10431428)

“…The collection of such data has been essential for the development and assessment of tools predicting the impact of protein variants at functional and structural levels. …”

presentation1_ThermoScan: Semi-automatic Identification of Protein Stability Data From PubMed.pdf by Paola Turina (10431428)

“…The collection of such data has been essential for the development and assessment of tools predicting the impact of protein variants at functional and structural levels. …”

VinaLigGen: a method to generate LigPlots and retrieval of hydrogen and hydrophobic interactions from protein-ligand complexes by Raghvendra Agrawal (17135479)

“…This paper describes an implementation of an automation technique on the executable programs like ligplot.exe, hbplus.exe and hbadd.exe to obtain the 2D interaction map (LigPlots) of the protein and ligand complex (*.ps) and hydrogen bonds and hydrophobic interactions in *.csv format for molecules to be considered for virtual screening by using some sorting & searching algorithms and python’s file handling functions, and it also mentions the program’s limitations and availability of the program. …”