pypi: Tcl | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0029018

Python as a Federation Tool for GENESIS 3.0
Cited by: 26
Author(s): Hugo Cornelis, Antony Rodríguez, Allan D Coop, James M. Bower
Software Mentions: 10
Published: almost 13 years ago

Circadian and Brain State Modulation of Network Hyperexcitability in Alzheimer’s Disease
Cited by: 31
Author(s): Rosalind Brown, Alice Lam, Alfredo Gonzalez-Sulser, Andrew Ying, Mary Jones, Robert Chang-Chih Chou, Makis Tzioras, Crispin Y. Jordan, Izabela Jedrasiak‐Cape, Anne-Laure Hemonnot-Girard, Maurice Abou Jaoude, Andrew J. Cole, Sydney S. Cash, Takashi Saito, Takaomi C. Saido, Richard R. Ribchester, K. Hashemi, Iris Oren
Software Mentions: 8
Published: over 6 years ago

10.1186/s13321-019-0338-7

Software solutions for evaluation and visualization of laser ablation inductively coupled plasma mass spectrometry imaging (LA-ICP-MSI) data: a short overview
Cited by: 30
Author(s): Ralf Weiskirchen, Sabine Weiskirchen, Philipp Kim, Robert Winkler
Software Mentions: 7
Published: almost 6 years ago

10.1186/1471-2105-9-86

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Cited by: 75
Author(s): Frédéric Chalmel, Michael Primig
Software Mentions: 6
Published: almost 17 years ago

10.1186/s13321-020-0415-y

The C++ programming language in cheminformatics and computational chemistry
Cited by: 13
Author(s): Dmitrii N. Rassokhin
Software Mentions: 6
Published: almost 5 years ago

10.1186/1471-2105-9-219

ConStruct: Improved construction of RNA consensus structures
Cited by: 36
Author(s): Andreas Wilm, Kornelia Linnenbrink, Gerhard Steger
Software Mentions: 5
Published: over 16 years ago

10.1371/journal.pcbi.1004867

An Introduction to Programming for Bioscientists: A Python-Based Primer
Cited by: 46
Author(s): Berk Ekmekci, Charles E. McAnany, Cameron Mura
Software Mentions: 5
Published: over 8 years ago

10.1074/jbc.RA118.004767

Two distinct conformations of factor H regulate discrete complement-binding functions in the fluid phase and at cell surfaces
Cited by: 9
Author(s): Amy J. Osborne, Ruodan Nan, Arthur I. Miller, Jayesh S. Bhatt, Jayesh Gor, Stephen J. Perkins
Software Mentions: 4
Published: about 6 years ago

10.3389/fnbeh.2020.599374

The Antarium: A Reconstructed Visual Reality Device for Ant Navigation Research
Cited by: 12
Author(s): Zoltán Kócsi, Trevor G. Murray, Hansjürgen Dahmen, Ajay Narendra, Jochen Zeil
Software Mentions: 4
Published: about 4 years ago

10.1002/humu.23277

MiSynPat: An integrated knowledge base linking clinical, genetic, and structural data for disease-causing mutations in human mitochondrial aminoacyl-tRNA synthetases
Cited by: 34
Author(s): Luc Moulinier, Raymond Ripp, Gaston Castillo, Olivier Poch, Marie Sissler
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-018-2510-x

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow
Cited by: 54
Author(s): Jonathan Ozik, Nicholson Collier, Justin M. Wozniak, Charles M. Macal, Chase Cockrell, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Randy Heiland, Gary An, Paul Macklin
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1002708

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
Cited by: 908
Author(s): Eva Chovancová, Antonín Pavelka, Petr Beneš, Ondřej Strnad, Jan Brezovský, Barbora Kozlíková, Artur Góra, Vilém Šustr, Martin Klvaňa, Petr Medek, Lada Biedermannová, Jiří Sochor, Jiřı́ Damborský
Software Mentions: 3
Published: about 12 years ago

10.1186/1758-2946-3-44

CML: Evolution and design
Cited by: 36
Author(s): Peter Murray‐Rust, Rzepa Henry S.
Software Mentions: 3
Published: about 13 years ago

10.1186/s13321-016-0157-z

Ligand-based virtual screening interface between PyMOL and LiSiCA
Cited by: 9
Author(s): Athira Athira, Samo Lešnik, Tanja Štular, Dušanka Janežič, Janez Konc
Software Mentions: 3
Published: about 8 years ago

10.1186/1471-2105-7-544

The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy
Cited by: 46
Author(s): Arnim Jenett, Johannes Schindelin, Martin Heisenberg
Software Mentions: 3
Published: almost 18 years ago

10.1186/1471-2105-7-439

TreeDyn: towards dynamic graphics and annotations for analyses of trees
Cited by: 908
Author(s): François Chevenet, Catherine Brun, Anne‐Laure Bañuls, Bernard Jacq, Richard Christen
Software Mentions: 3
Published: about 18 years ago

10.1371/journal.pcbi.1008249

PyOIF: Computational tool for modelling of multi-cell flows in complex geometries
Cited by: 14
Author(s): Iveta Jančigová, Kristína Kovalčíková, Rudolf Weeber, Ivan Cimrák
Software Mentions: 3
Published: about 4 years ago

10.6028/jres.114.005

Implementation of Two-Dimensional Polycrystalline Grains in Object Oriented Micromagnetic Framework
Cited by: 21
Author(s): Lau Jw, McMichael Rd, Donahue Mj
Software Mentions: 2
Published: almost 16 years ago

10.3389/fmicb.2020.560667

Non-adaptive Evolution of Trimeric Autotransporters in Brucellaceae
Cited by: 3
Author(s): Mohammad Reza Rahbar, Mahboubeh Zarei, Abolfazl Jahangiri, Saeed Khalili, Navid Nezafat, Manica Negahdaripour, Yaser Fattahian, Amir Savardashtaki, Younes Ghasemi
Software Mentions: 2
Published: about 4 years ago

10.3389/fnbot.2018.00079

CABots and Other Neural Agents
Cited by: 4
Author(s): Christian R. Huyck, Ian Mitchell
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1000918

An Introduction to Biomolecular Graphics
Cited by: 40
Author(s): Cameron Mura, Colin M. McCrimmon, Jason Vertrees, M.R. Sawaya
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2105-7-468

SNP-PHAGE – High throughput SNP discovery pipeline
Cited by: 31
Author(s): Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik‐Young Choi, Perry B. Cregan, Curtis P. Van Tassell
Software Mentions: 2
Published: about 18 years ago

10.3389/fmolb.2020.576689

Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes
Cited by: 7
Author(s): Jakob Schneider, Rui P. P. L. Ribeiro, Mercedes Alfonso‐Prieto, Paolo Carloni, Alejandro Giorgetti
Software Mentions: 2
Published: about 4 years ago

10.1038/srep26536

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts
Cited by: 141
Author(s): João V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, J. C. Phillips, Peter L. Freddolino, Klaus Schulten
Software Mentions: 2
Published: over 8 years ago

10.1038/srep31983

Rational improvement of gp41-targeting HIV-1 fusion inhibitors: an innovatively designed Ile-Asp-Leu tail with alternative conformations
Cited by: 12
Author(s): Yun Zhu, Shan Su, Lili Qin, Qian Wang, Lei Shi, Zhenxuan Ma, Jianchao Tang, Shibo Jiang, Lu Lu, Sheng Ye, Rongguang Zhang
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2466-7-15

Software for interpreting cardiopulmonary exercise tests
Cited by: 7
Author(s): Robert Ross, David B. Corry
Software Mentions: 2
Published: about 17 years ago

10.1038/s41598-018-31234-7

Phosphorylation promotes binding affinity of Rap-Raf complex by allosteric modulation of switch loop dynamics
Cited by: 8
Author(s): T Devanand, Prasanna Venkatraman, Satyavani Vemparala
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-70680-0

Antibody-protein binding and conformational changes: identifying allosteric signalling pathways to engineer a better effector response
Cited by: 25
Author(s): Mohammed M. Al Qaraghuli, Karina Kubiak-Ossowska, Valerie A. Ferro, Paul A. Mulheran
Software Mentions: 2
Published: over 4 years ago

10.3390/molecules23040969

Self-Assembly Behavior of Amphiphilic Janus Dendrimers in Water: A Combined Experimental and Coarse-Grained Molecular Dynamics Simulation Approach
Cited by: 8
Author(s): Mariana E Elizondo-García, Valeria Márquez-Miranda, Ingrid Araya-Durán, Jesús A. Valencia-Gallegos, Fernando D. González-Nilo
Software Mentions: 2
Published: over 6 years ago

10.3390/molecules25112651

Cryptococcus neoformans Capsular GXM Conformation and Epitope Presentation: A Molecular Modelling Study
Cited by: 14
Author(s): Michelle M. Kuttel, Arturo Casadevall, Stefan Oscarson
Software Mentions: 2
Published: over 4 years ago

10.3390/antibiotics8040225

A New Look at the Structures of Old Sepsis Actors by Exploratory Data Analysis Tools
Cited by: 8
Author(s): Antonio Gnoni, Emanuele De Nitto, Salvatore Scacco, Luigì Santacroce, Luigi Leonardo Palese
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2105-10-354

Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB
Cited by: 41
Author(s): Aristotelis Chatziioannou, Panagiotis Moulos, Fragiskos N. Kolisis
Software Mentions: 2
Published: about 15 years ago

10.1155/2014/701357

Bflinks: Reliable Bugfix Links via Bidirectional References and Tuned Heuristics
Cited by: 2
Author(s): Lutz Prechelt, Alexander Pepper
Software Mentions: 2
Published: about 10 years ago

10.3390/s151229819

An On-Demand Emergency Packet Transmission Scheme for Wireless Body Area Networks
Cited by: 13
Author(s): Moshaddique Al Ameen, Choong Seon Hong
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13063-018-2960-5

A double-blind, randomized, placebo-controlled trial of a computer-based Interpretation Bias Training for youth with severe irritability: a study protocol
Cited by: 7
Author(s): Simone P. Haller, Joel Stoddard, Caroline MacGillivray, Kelsey Stiles, Gretchen Perhamus, Ian S. Penton-Voak, Yair Bar‐Haim, Marcus R. Munafò, Melissa A. Brotman
Software Mentions: 1
Published: about 6 years ago

10.1107/S0909049510028566

Software for the high-throughput collection of SAXS data using an enhanced<i>Blu-Ice</i>/<i>DCS</i>control system
Cited by: 37
Author(s): Scott Classen, Ivan Rodic, James M. Holton, Greg L. Hura, Michal Hammel, John A. Tainer
Software Mentions: 1
Published: about 14 years ago

10.1186/s12967-019-1772-z

Translational control mechanisms in cutaneous malignant melanoma: the role of eIF2α
Cited by: 7
Author(s): Isabel Maida, Paola Zanna, Stefania Guida, Anna Ferretta, Tiziana Cocco, Luigi Leonardo Palese, Paola Londei, Dario Benelli, Amalia Azzariti, Stefania Tommasi, Michele Guida, Giovanni Pellacani, Gabriella Guida
Software Mentions: 1
Published: almost 6 years ago

10.3390/s140508633

Implementation of WirelessHART in the NS-2 Simulator and Validation of Its Correctness
Cited by: 36
Author(s): Pouria Zand, Emi Mathews, Paul J.M. Havinga, Spase Stojanovski, Emiliano Sisinni, Paolo Ferrari
Software Mentions: 1
Published: over 10 years ago

10.3390/antibiotics9070381

Synthesis and Evaluation of the Antibacterial Activities of 13-Substituted Berberine Derivatives
Cited by: 15
Author(s): Hamza Olleik, Taher Yacoub, Laurent Hoffer, Senankpon Martial Gnansounou, Kehna Benhaiem-Henry, Cendrine Nicoletti, Malika Mekhalfi, Valérie Pique, Josette Perrier, Akram Hijazi, Elias Baydoun, Josette Raymond, Philippe Piccerelle, Marc Maresca, Maxime Robin
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2105-5-198

Cited by: 79
Author(s): Rohit Ghai, Torsten Hain, Trinad Chakraborty
Software Mentions: 1
Published: almost 21 years ago

10.1186/1471-2105-12-190

Stereochemical errors and their implications for molecular dynamics simulations
Cited by: 50
Author(s): Eduard Schreiner, Leonardo G. Trabuco, Peter L. Freddolino, Klaus Schulten
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-8-204

Genomorama: genome visualization and analysis
Cited by: 10
Author(s): Jason Gans, Murray Wolinsky
Software Mentions: 1
Published: over 17 years ago

10.1186/s12859-019-2671-2

CirGO: an alternative circular way of visualising gene ontology terms
Cited by: 75
Author(s): Irina Kuznetsova, Artur Lugmayr, Stefan J. Siira, Oliver Rackham, Aleksandra Filipovska
Software Mentions: 1
Published: almost 6 years ago

10.1186/2046-1682-6-5

Time-resolved force distribution analysis
Cited by: 51
Author(s): Bogdan I. Costescu, Frauke Gräter
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2148-11-266

Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco
Cited by: 28
Author(s): Mingcong Wang, Maxim V. Kapralov, Maria Anisimova
Software Mentions: 1
Published: about 13 years ago

10.15252/msb.20145704

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci
Cited by: 92
Author(s): Siddharth S. Dey, Jason Foley, Prajit Limsirichai, David V. Schaffer, Adam P. Arkin
Software Mentions: 1
Published: over 9 years ago

10.3390/vaccines8040643

Molecular Modeling of the Shigella flexneri Serogroup 3 and 5 O-Antigens and Conformational Relationships for a Vaccine Containing Serotypes 2a and 3a
Cited by: 6
Author(s): Jason Hlozek, Sara Owen, Neil Ravenscroft, Michelle M. Kuttel
Software Mentions: 1
Published: about 4 years ago

10.3390/ph12010028

Conformation and Cross-Protection in Group B Streptococcus Serotype III and Streptococcus pneumoniae Serotype 14: A Molecular Modeling Study
Cited by: 12
Author(s): Michelle M. Kuttel, Neil Ravenscroft
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pbio.2002255

Teaching genetics prior to teaching evolution improves evolution understanding but not acceptance
Cited by: 36
Author(s): Rebecca Mead, Momna Hejmadi, Laurence D. Hurst
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1008024

Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli
Cited by: 19
Author(s): Tomasz Pieńko, Joanna Trylska
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1002283

Atypical AT Skew in Firmicute Genomes Results from Selection and Not from Mutation
Cited by: 34
Author(s): Catherine A. Charneski, Frank Honti, Josephine M. Bryant, Laurence D. Hurst, Edward J. Feil
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0025375

Substrate Binding Process and Mechanistic Functioning of Type 1 11β-Hydroxysteroid Dehydrogenase from Enhanced Sampling Methods
Cited by: 23
Author(s): Angelo D. Favia, Matteo Masetti, Maurizio Recanatini, Andrea Cavalli
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0047745

Mechanisms of Peptide-Induced Pore Formation in Lipid Bilayers Investigated by Oriented 31P Solid-State NMR Spectroscopy
Cited by: 39
Author(s): Kresten Bertelsen, Jerzy Dorosz, Sara K. Hansen, Niels Chr. Nielsen, Thomas Vosegaard
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0094986

Protein Dynamics of the HIF-2α PAS-B Domain upon Heterodimerization and Ligand Binding
Cited by: 10
Author(s): Matteo Masetti, Federico Falchi, Maurizio Recanatini
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0048212

Protein Dynamics Governed by Interfaces of High Polarity and Low Packing Density
Cited by: 11
Author(s): Vladimir Espinosa Angarica, Javier Sancho
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0209376

Shared and differential default-mode related patterns of activity in an autobiographical, a self-referential and an attentional task
Cited by: 15
Author(s): Paola Fuentes‐Claramonte, Marta Martín-Subero, Pilar Salgado‐Pineda, Silvia Alonso‐Lana, Ana Moreno‐Alcázar, Isabel Argila-Plaza, Aniol Santo-Angles, Anton Albajes‐Eizagirre, Maria Anguera-Camós, Antoni Capdevila, Salvador Sarró, Peter McKenna, Edith Pomarol‐Clotet, Raymond Salvador
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0133011

A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation
Cited by: 11
Author(s): Letizia Chiodo, Thérèse E. Malliavin, Luca Maragliano, Grazia Cottone, Giovanni Ciccotti
Software Mentions: 1
Published: over 9 years ago

10.1016/j.dib.2017.09.076

Analysis of the conformations of the HIV-1 protease from a large crystallographic data set
Cited by: 8
Author(s): Luigi Leonardo Palese
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmolb.2021.658312

Conformational Characterization of the Co-Activator Binding Site Revealed the Mechanism to Achieve the Bioactive State of FXR
Cited by: 6
Author(s): Anita Kumari, Lovika Mittal, Mitul Srivastava, Dharam Pal Pathak, Shailendra Asthana
Software Mentions: 1
Published: about 3 years ago

10.3389/fmolb.2021.721955

SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction
Cited by: 3
Author(s): Yuanzhe Zhou, Jun Li, Travis Hurst, Shijie Chen
Software Mentions: 1
Published: over 3 years ago

10.3389/fnins.2018.00107

Analysis of Vestibular Labyrinthine Geometry and Variation in the Human Temporal Bone
Cited by: 17
Author(s): Lejo Johnson Chacko, Dominik Schmidbauer, Stephan Handschuh, Alen Reka, Karl D. Fritscher, Patrik Raudaschl, Rami Saba, Michael Handler, Peter Schier, Daniel Baumgarten, Natalie Fischer, Elisabeth Pechriggl, Erich Brenner, Romed Hörmann, Rudolf Glueckert, Anneliese Schrott‐Fischer
Software Mentions: 1
Published: over 6 years ago

10.1107/S0021889812048698

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source
Cited by: 198
Author(s): Scott Classen, Greg L. Hura, James M. Holton, Robert P. Rambo, Ivan Rodic, Patrick J. McGuire, Kevin Dyer, Michal Hammel, G. Meigs, Kenneth A. Frankel, John A. Tainer
Software Mentions: 1
Published: almost 12 years ago

10.1007/s10858-012-9683-9

Database proton NMR chemical shifts for RNA signal assignment and validation
Cited by: 51
Author(s): Shawn Barton, Xiao Heng, B. V. Johnson, Michael F. Summers
Software Mentions: 1
Published: almost 12 years ago

10.1021/acs.jcim.0c00549

Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor
Cited by: 12
Author(s): Grazia Cottone, Letizia Chiodo, Luca Maragliano
Software Mentions: 1
Published: over 4 years ago

10.1186/1758-2946-6-S1-P34

Ushering the Cactvs Toolkit into the Python Age (without breaking the legacy)
Cited by: 2
Author(s): Wolf‐Dietrich Ihlenfeldt
Software Mentions: 1
Published: over 10 years ago

10.1186/s13321-019-0333-z

Implementing cheminformatics
Cited by: 0
Author(s): Rajarshi Guha
Software Mentions: 1
Published: almost 6 years ago

10.1007/s10822-014-9783-6

AFAL: a web service for profiling amino acids surrounding ligands in proteins
Cited by: 8
Author(s): Mauricio Arenas-Salinas, Samuel Ortega-Salazar, Fernando Gonzales-Nilo, Ehmke Pohl, David S. Holmes, Raquel Quatrini
Software Mentions: 1
Published: over 10 years ago

10.1038/srep41087

Comparative molecular dynamics studies of heterozygous open reading frames of DNA polymerase eta (η) in pathogenic yeast Candida albicans
Cited by: 7
Author(s): Suresh Satpati, Kodavati Manohar, Narottam Acharya, Anshuman Dixit
Software Mentions: 1
Published: almost 8 years ago

10.1155/2014/267403

Visual Quality Assessment after Network Transmission Incorporating NS2 and Evalvid
Cited by: 7
Author(s): Zhengyou Wang, Wan Wang, Yanhui Xia, Zheng Wan, Jin Wang, Liying Li, Cong Cai
Software Mentions: 1
Published: almost 11 years ago

10.3390/s121114442

Framework for End-User Programming of Cross-Smart Space Applications
Cited by: 6
Author(s): Marko Palviainen, Jarkko Kuusijärvi, Eila Ovaska
Software Mentions: 1
Published: about 12 years ago

Projects: pypi: Tcl

Papers Mentioning Tcl 70